NSS Spectral Imaging System Handbook Version 3.0

Transcription

1 NSS Spectral Imaging System Handbook Version 3.0

2 The information in this publication is provided for reference only. All information contained in this publication is believed to be correct and complete. Thermo Fisher Scientific shall not be liable for errors contained herein nor for incidental or consequential damages in connection with the furnishing, performance or use of this material. All product specifications, as well as the information contained in this publication, are subject to change without notice. This publication may contain or reference information and products protected by copyrights or patents and does not convey any license under our patent rights, nor the rights of others. We do not assume any liability arising out of any infringements of patents or other rights of third parties. We make no warranty of any kind with regard to this material, including but not limited to the implied warranties of merchantability and fitness for a particular purpose. Customers are ultimately responsible for validation of their systems Thermo Fisher Scientific Inc. All rights reserved. No part of this publication may be stored in a retrieval system, transmitted, or reproduced in any way, including but not limited to photocopy, photograph, magnetic or other record, without our prior written permission. For Technical Support, please contact: Thermo Fisher Scientific 5225 Verona Road Madison WI U.S.A. Telephone: us.techsupport.analyze@thermofisher.com World Wide Web: For International Support, please contact: Thermo Fisher Scientific Telephone: support.madison@thermofisher.com World Wide Web: Microsoft, Windows, Excel, and PowerPoint are either trademarks or registered trademarks of Microsoft Corporation in the United States and/or other countries. All other trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries , Rev A

3 Contents Introduction... 1 Manual conventions... 1 Questions or concerns... 2 Applications... 2 Capabilities... 2 Software... 3 Optional modules... 3 Additional software... 4 Hardware... 4 Microscope and x-ray detectors... 4 Ethernet support... 5 Acquisition chassis... 5 Getting Started... 6 Before you use the system... 6 Starting the software... 6 The NSS window... 7 Window panes... 7 Navigation pane... 8 File name and file list panes... 8 Image panes... 9 Analysis controls pane Spectrum pane Working from the toolbars NSS toolbar Acquisition toolbar Extract toolbar Spectrum toolbar Ident toolbar Elements toolbar Point & Shoot toolbar Detector Selector toolbar Defining a project Acquisition properties Microscope parameters Acquiring and Managing Data Acquiring images and spectra Viewing the spectrum Expanding the spectrum Compressing a spectrum NSS Spectral Imaging System Handbook i

4 Scrolling through a spectrum Zooming in on a peak Displaying the full spectrum Applying a log scale Managing files Project Explorer Opening and saving files Labeling a data set Renaming a file Adding note text Compressing Spectral Imaging files Extracting data Selecting areas for analysis Selecting areas of similar intensity for analysis Spectrum Mode Setting spectral acquisition properties Comparing spectra SpectraCheck Performing math operations on spectra with Spectrum Math software Naming the result file Selection of files to process Selection of the math operation to perform The operand type Processing the selected spectra Resetting the dialog The right click menu Ending the dialog Performing math operations on regions of interest Point & Shoot Mode Performing a Point & Shoot acquisition Immediate acquisitions Selecting areas for analysis Batch acquisitions Specifying points and areas to display Spectral Imaging Mode Setting acquisition properties Acquiring an image Extracting spectral data About maximal spectra Image intensity cursor Measuring features with the image ruler Extracting multiple spectra Extracting linescans ii NSS Spectral Imaging System Handbook

5 Adjusting linescan appearance Analyzing linescans Overlaying extracted linescans on the image Quantitative linescans X-ray mapping Creating x-ray maps Analyzing x-ray maps Image intensity cursor Overlaying an element map on the x-ray image Map intensity and color Extracting quantitative maps Using Compass Setting properties Spectrally simple maps Spatially simple maps Managing Compass data Direct-to-Phase analysis D Visualization Mode Setting 3-D image display parameters Selecting a data presentation type Specifying a color scheme and color range Clipping the data outside the color range Selecting a cursor style for the 3-D image Smoothing the 3-D image Setting the opacity of the 3-D image Displaying an outline box X-ray Linescans Mode Setting linescan acquisition properties Setting up the linescan elements Acquiring a linescan Analyzing a linescan Overlaying acquired linescans on the image Adjusting linescan appearance Quantitative linescans Electron Imaging Mode Setting imaging acquisition properties Acquiring an electron image Preparing for an Analysis Selecting elements for analysis Highlighting elements for analysis Automatic selection Manual selection NSS Spectral Imaging System Handbook iii

6 Setting advanced element parameters Specifying lines for quantification and display Excluding elements from quantitative results only Excluding elements from peak identification analysis Clearing identification results Viewing the history periodic table Specifying identification sensitivity Setting processing parameters Identifying Peaks Manually Locating possible elements Viewing KLM lines Scrolling KLM lines with keyboard arrow keys Scrolling for KLM lines on the spectrum Finding possible elements at a peak Customizing x-ray line energies and intensities Labeling peaks Labeling all peaks Editing the label for a specific peak Adding peak ID labels for a specific element Removing peak labels Searching for KLM lines and adding labels Changing the appearance of peak labels Energy cursor (kev) Spectral Match Using the Database Manager Setting up a search Quantifying Spectra Preparing the quantitative settings Quant fit method Matrix correction Initial quantitative analysis Automatic quantification Automatic quantification for a series of spectra Manual quantification Specifying quantitative output Rerunning quantitative analysis Ratioed elements Calculating weight percentage Developing quantitative analysis standards Getting ready to create a standard Selecting properties for a standard Creating a standard Using standards for quantification iv NSS Spectral Imaging System Handbook

7 Standardless references Batch processing quantitative analyses Using a MagnaRay Spectrometer Manual spectrometer control and status Starting the spectrometer Controlling the spectrometer and checking its status Inserting the spectrometer Aligning the spectrometer Changing or positioning the sample Ending your MagnaRay microanalysis session Working with WDS Setup Setting up peak-to-background measurements Element-line-crystal rules Setting up x-ray detection Setting up peak search Setting up and acquiring standards Setting up quantification of unknown samples Confirming elements using WDS Confirming elements with manual scans Confirming elements automatically Quantitative analysis using combined WDS and EDS acquisitions Setting up WDS standards Acquiring standards data Setting up the unknown sample Acquiring unknown sample data Combining Point & Shoot analysis with WDS Performing linescan and spectral image acquisitions with WDS Finding Phases With XPhase Analysis Automation Analysis Automation and Drift Compensation Analysis Automation with Point & Shoot operation and linescans Setting Analysis Automation parameters Using Selected Areas Using Grid and Circular Using the grid list to index rectangular or circular samples Creating a new rectangular grid Creating a new circular grid Working with existing grids Working with grid lists Using Linescan Acquiring a large linescan Performing an Analysis Automation acquisition Creating an image montage NSS Spectral Imaging System Handbook v

8 Saving a montage Minimizing mismatch Drift Compensation Drift Compensation properties Simple Drift Compensation Advanced Drift Compensation Drift diagnostics Drift Compensation for JEOL STEM microscopes Electron Backscatter Diffraction Getting started with EBSD Sample preparation Sample positioning EBSD navigation pane File list name pane Acquisition Properties for EBSD EBSD display sizing Equal Dominant Exclusive EBSD Setup mode Calibration Sample Geometry tab Camera tab Background Correction tab Immersion Lens Correction tab (optional) Pattern Center tab Editing found lines Analysis Camera tab Background Correction tab Find Crystals tab EBSD Views tab Selecting views Common view types Pattern Orientation Cell Pattern Quality Map Index Quality Map Strain Map Orientation Phase Map Orientation Phase Boundary Map Overlay Map Phase view types Orientation Maps vi NSS Spectral Imaging System Handbook

9 Texture Histograms Grain Boundary Maps Histograms/Plots EBSD Point & Shoot mode Performing a Point & Shoot acquisition EBSD Point & Shoot toolbar Immediate acquisitions Batch acquisitions EBSD views available in Point & Shoot mode EBSD Point & Shoot Analysis Pane Orientation/Phase ID Toolbar Find Crystals tab Misorientation Summary Tab Spectrum Tab Phase ID tab Selecting crystals Editing your Crystal Phase ID database EBSD Mapping Mode EBSD Views available in the Mapping Mode EBSD Mapping Analysis Pane Xray Maps tab Spectrum tab EBSD Mapping Extractions and Filtering Spatial extraction Angular filtering Stacking EBSD Pixel Enhancement How pixel enhancement works Performing pixel enhancement Advanced details Examples of pixel enhancement EBSD Attributes Microscope tab EBSD tab Map tab Feature Sizing Morphology overview Helpful tips Feature Sizing Setup mode Defining particles to size Selecting guard regions Selecting filters Defining processing parameters and setting acquisition criteria Feature Sizing Analysis mode Managing Feature Sizing results Viewing Feature Sizing graphics NSS Spectral Imaging System Handbook vii

10 Sorting results Filter the display of results Examining particles Moving the stage to a particle Saving Feature Sizing results Feature Sizing Chem Lib mode Creating a chemical library Creating chemical types Manually creating chemical types Creating chemical types from spectra Creating chemical types from unknowns Working with chemical libraries Reclassifying chemical type libraries Merging chemical types Using the Feature Sizing periodic table Removing carbon from chemical typing Feature Sizing with Analysis Automation Feature Sizing parameters Reports and Printing Printer reports Generating Microsoft Word reports Generating Microsoft PowerPoint reports Copying objects to third-party programs Generating JPEG files Directly generating Microsoft Excel data Using Feature Sizing data in Microsoft Excel Using quantitative results in Microsoft Excel Software Reference Material Operating system support Supported file formats More about projects and templates Project folders Creating a new project Opening a project Importing a file Creating a new project template Project and system security Resetting a project to the original template settings Searching for project keywords Menu commands File menu Edit menu View menu Spectrum menu viii NSS Spectral Imaging System Handbook

11 . Image menu Batch Processing menu Image menu Linescan menu Help menu Installing the software Enabling roaming user accounts for Spectral Imaging Screen appearance Changing the size of window panes Rearranging, removing and restoring toolbars Saving your rearranged screen Screen resolution and color Detector status Advanced detector status Acquisition Parameters/Values Diagnostic message history Status LEDs Connectivity and control EDS Calibration Fine Gain calibration procedure NSS Spectral Imaging System Handbook ix

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13 Introduction This manual explains how to use Thermo Scientific NSS spectral imaging systems. Except where noted, all the described software functions are available, either as standard features or as options, on all systems. For specific information about the MagnaRay spectrometer, see Using a MagnaRay Spectrometer. Warning The site and safety information manual that came with your system contains important safety information. This guide is available in several languages. Contact your local sales office for information about the languages that are available. Before you use the system, read the entire guide. To prevent personal injury and damage to equipment, follow the safety precautions contained in the guide whenever you use the system. Manual conventions Note Notice The following conventions are used in this manual to draw your attention to important information: Notes contain helpful supplementary information. Follow instructions labeled Notice to avoid damaging the system hardware or losing data. NSS Spectral Imaging System Handbook 1

14 Caution Warning Danger Indicates a hazardous situation which, if not avoided, may result in minor or moderate injury. Indicates a hazardous situation which, if not avoided, could result in death or serious injury. Indicates a hazardous situation which, if not avoided, will result in death or serious injury. Questions or concerns In case of emergency, follow the procedures established by your facility. If you have questions or concerns about safety or need assistance with operation, repairs or replacement parts, you can contact our sales or service representative in your area or use the information at the beginning of this document to contact us. Applications NSS is used with electron microscopes and x-ray detectors for a variety of applications, including the study of: General materials Metallurgical and geological samples Semiconductors Biological specimens Other electron microscope-based samples that can be analyzed with energy-dispersive spectrometry Capabilities NSS is a combination of high-performance x-ray microanalysis acquisition electronics connected to an energy-dispersive spectrometry (EDS) x-ray detector and microanalysis software installed on a dedicated x-ray microanalysis computer. The system can be connected to a variety of SEMs (scanning electron microscopes), TEMs (transmission electron microscopes) and STEMs (scanning transmission electron microscopes). In this manual, NSS refers to both hardware and software components. 2 NSS Spectral Imaging System Handbook

15 Software NSS software is compatible with the U.S., German and Japanese versions of Windows XP operating system. It offers a single user interface program accessing Spectrum, Point & Shoot, Spectral Imaging, 3-D Visualization, ray Linescans and Electron Imaging modes. Project Explorer ensures that your acquisitions and analyses are saved and organized in convenient project directories. In this manual, the English version of software is used for illustration and to describe operations and functions. Optional modules NSS supports the following optional software modules: Analysis Automation Using the electron microscope automated stage, Analysis Automation enables you to setup an analysis and then automatically perform repetitive acquisitions on large scale analyses without the need for user intervention. Compass Using Compass, you can automatically extract pure component spectra and images from a Spectral Imaging data set. Direct-to-Phase Using advanced algorithms, Direct-to-Phase extracts and displays known phases from a spectral imaging database while data is being collected, producing an information rich picture of your samples composition. Drift Compensation With Drift Compensation software you can correct for sample and image drift during acquisitions. Electron Backscatter Diffraction (EBSD) Using EBSD, you can characterize the crystallographic structure of crystalline materials. Feature Sizing and Chemical Typing These options measure morphological parameters for particles on your sample as well as determining their chemical makeup. Spectral Match Spectral Match software lets you search a spectrum against a database of spectra. XPhase XPhase software lets you find phases using any map and extract the underlying spectra for each phase. NSS Spectral Imaging System Handbook 3

16 Additional software The following additional software is available: Electron Microscope Column Communication This software integrates the reading and writing of selected column control parameters with NSS applications. This option is required for Analysis Automation. Integrated third-party software Microsoft Word is included for reports. Additional Microsoft Office programs, such as Excel for data analysis and PowerPoint for creating presentations, are available for purchase. Hardware NSS includes the following hardware components: Acquisition chassis that holds NSS electronics. NSS computer, video monitor, mouse and keyboard. Dedicated Ethernet connection between the acquisition chassis and the NSS computer. Ethernet, parallel, serial and USB interfaces for use with networks and peripheral devices. These interfaces are standard with the host computer. Optional components for serial or Ethernet connections to a microscope column, automated stage, beam current monitor, WDS spectrometer or parallel beam spectrometer. Microscope and x-ray detectors NSS can be installed on almost any microscope with EDS interface capabilities. We offer several models of detectors with various atmospheric thin windows, resolutions and cooling options: NanoTrace Liquid-nitrogen cooled lithium drifted silicon (Si(Li)) x-ray detector UltraDry silicon drift detector (SDD) Peltier cooled Cryocooled dewar Si(Li) x-ray detector SuperDry II electrically cooled Si(Li) x-ray detector QuasOr electron backscatter detector Norvar ultra-thin window options 4 NSS Spectral Imaging System Handbook

17 Ethernet support Connections from the acquisition chassis to the computer are accomplished using a direct crossover Ethernet connection. Our support of Ethernet connections is limited to the support of NSS component connections. Contact your network administrator for other Ethernet issues. Acquisition chassis The acquisition chassis contains the electronic components needed to accept data from the EDS detector, electron microscope and WDS spectrometer and convert it to useful data for display by the computer. Before you can collect and analyze data, power on the acquisition chassis. Use the power switch on the front panel. Active LED The system is on and working. When you turn on the system, the green light does not turn on until the system has finished startup. LED is on solid until communications starts with the host PC. Double flashes indicate normal operation. Continuous fast flashes indicate an error condition. The chassis is protected by two 250 V, 2 A, T-type (time lag) 5 mm x 20 mm fuses located in a fuse drawer on the rear panel. To access the fuses, use a small flat-blade screwdriver to pry the drawer out of the chassis. Danger Avoid shock hazard. Always use an exact replacement for the fuses. NSS Spectral Imaging System Handbook 5

18 Getting Started This chapter explains how to start NSS and use its basic features. Before you use the system Before you use NSS, you should be familiar with: Operating procedures for the electron microscope used with your spectral analysis system. Basic Windows procedures such as logging in to the computer, running programs and managing files. Terms and abbreviations used commonly in electron microscopy, including atomic symbols and energy lines (for example, O, Cu and L) as well as x-ray detector types (for example, EDS and WDS). Matrix correction methods; for example, ZAF and φ(ρz). Starting the software To start NSS software: 1. Double-click the NSS shortcut on the desktop. If there is no shortcut on the desktop, use the Start menu: Click Start > Programs > Thermo Scientific > NSS. 2. When the Project Explorer opens, select an existing project or create a new one. NSS starts in Spectrum mode by default but, if possible, returns to the mode used when the program was last closed. Notice When you are finished working, be sure to shut down the computer properly before turning it off. Turning off a computer while programs are running can result in data loss, require software reinstallation or cause configuration changes. 6 NSS Spectral Imaging System Handbook

19 The NSS window After you start the software and select or create a project, you are ready to use the NSS window to acquire, view, process and store data: NSS window The window is highly customizable. You can arrange the window panes (containing analytical views) and move toolbars for your convenience. Note Work in a maximized window with a screen resolution of 1280 x 1024 for the best viewing. Window panes The NSS window is arranged with main panes for analysis and controls, plus panes on the left for navigating between analysis modes and files. The contents of the main panes change as you switch analytical modes. NSS Spectral Imaging System Handbook 7

20 Navigation pane The navigation pane contains icons for the acquisition modes available on your system. These may include Spectrum, Spectral Imaging, Electron Imaging, Point & Shoot, and ay Linescans. This pane may also contain an icon for the Feature Sizing option. Click a mode icon to switch to that mode. File name and file list panes The file name you wish to be used to store the next analysis is entered in the box in the file name pane. Each successive acquisition appends an increasing number in parentheses to provide a unique file name. All files associated with the current mode are listed below the base name, in the file list pane. In addition to managing your data in projects, you have the ability to assign a base file name for your data before acquisitions. In the file name pane, you can change the default base file name to something more specific to your application. 8 NSS Spectral Imaging System Handbook

21 Image panes Once an image has been acquired, you can view it in the image pane. If map, Compass, or phase data has been extracted, they also may be viewed in an image pane. NSS Spectral Imaging System Handbook 9

22 Analysis controls pane The analysis controls pane lets you set parameters for elements, processing and analysis along with quant results and comparison information. Other control panels contain other tabbed dialog boxes that report control information or let you set additional controls. Spectrum pane The current spectrum appears in the spectrum pane. The location of the pane in the window depends on the analysis mode. 10 NSS Spectral Imaging System Handbook

23 Working from the toolbars The toolbars that are available depend on the current mode. The next sections identify the buttons on each toolbar. To view a toolbar button s function, move the cursor over the button for one second. NSS toolbar The NSS toolbar contains buttons for general functions, including opening and saving files, copying, printing, exporting and viewing Help information. Acquisition toolbar The Acquisition toolbar contains buttons for acquisition operations, including starting, stopping, pausing and aborting. It also includes buttons for setting acquisition properties and microscope parameters. NSS Spectral Imaging System Handbook 11

24 Extract toolbar The Extract toolbar contains buttons for extracting spectral data and maps from a Spectral Imaging database. It also contains buttons for turning on and off the image intensity cursor and the image ruler. Spectrum toolbar The Spectrum toolbar contains buttons for adjusting the scale and range of displayed spectra. Ident toolbar The Ident toolbar contains buttons for identifying and quantifying a spectrum as well as a button for acquiring a WDS spectrum (if a WDS detector is attached to your microscope). 12 NSS Spectral Imaging System Handbook

25 Elements toolbar The Elements toolbar contains buttons for viewing KLM lines and labeling peaks. Point & Shoot toolbar The Point & Shoot toolbar appears when you are in Point & Shoot mode. It contains buttons for Point & Shoot extraction. Detector Selector toolbar The Detector Selector toolbar contains a button for selecting a detector or detectors for acquiring data. Click the button to toggle between the available selections. NSS Spectral Imaging System Handbook 13

26 Defining a project In order to acquire and analyze data, you must define a project to contain the data. When you first open the software, the Project Manager appears, allowing you to open an existing project or create a new one. Once a project is open, you can then set the acquisition properties and verify that the microscope properties are correct. Acquisition properties Before you can collect data, you must set the acquisition properties for your project. Click the Edit Acquisition Properties button on the Acquisition toolbar (or choose on Properties from the Edit menu) to display the Acquisition Properties dialog box: This dialog box lets you control how acquisitions occur. More information about the individual properties tabs is included later in this handbook. EDS tab (and EDS 2 tab, if available) Setting spectral acquisition properties in the Spectrum Mode chapter. Imaging tab Setting Imaging acquisition properties in the Imaging Mode chapter. Spectral Imaging tab Setting mapping acquisition properties in the Spectral Imaging mode chapter. 14 NSS Spectral Imaging System Handbook

27 Linescan tab Setting linescan acquisition properties in the ay Linescans Mode chapter. Drift Comp tab Drift Compensation properties in the Drift Compensation chapter. Microscope parameters You also will want to check and, if necessary, adjust the microscope parameters for your project. Generally, these parameters are reported values from your microscope and do not change. To check the parameters, select the detector(s) you plan to use for your project. Use the detector select button. Once the appropriate detector(s) is selected, click the Edit Microscope Parameters button (or choose Microscope Parameters from the Edit menu) on the Acquisition toolbar to display the Microscopic Properties And Status Bar Selection dialog box: NSS Spectral Imaging System Handbook 15

28 This dialog box lets you record column and stage settings. The available parameters vary according to the type of x-ray detector you have. If you have Column Automation, this dialog box reflects the microscope s settings, and you can use it to control some aspects of microscope operation. Also use this dialog box to specify which items to display in the status bar. Note The EDS Slide Position, Storage Count Rate, Time Constant, EDS Dead Time and Takeoff Angle are associated with the currently selected detector. These parameters change as you change detectors. If both detectors are selected, the parameters are associated with EDS1. 16 NSS Spectral Imaging System Handbook

29 Acquiring and Managing Data Acquiring images and spectra The data available to you following an acquisition depends on the mode you are in. In Spectrum mode, EDS or WDS spectra are acquired from the area of focus. In Point & Shoot mode, spectra are acquired from specified points in an existing image. (Use the Acquire Electron Image button to acquire the initial image.) You can do two different styles of Point & Shoot acquisitions, immediate and batch, using a mixture of five different shapes (point, rectangle, irregular, Fat Spot and polygon). An immediate acquisition begins when you click a new point or area with the acquire point shape button. In a batch acquisition you select a batch of point or areas and then acquire data. In Spectral Imaging mode, an image is acquired from the area of focus. Once an image is collected, spectral information is extracted from selected areas of interest. You may use electron intensity or a defined shape or line to define the area for extraction. You may also open and analyze x-ray map sets and Map Phase or Compass data. In 3-D Visualization mode, a three-dimensional representation of various types of map data is generated. First use the appropriate mode to display the desired type of data, and then switch to 3-D Visualization mode to view and manipulate a 3-D image. Use X-ray Linescans mode to acquire an electron image and linescan data. After the acquisition, analyze the linescan using the image intensity cursor. You can save and load standard linescans in this mode. Also, you can define the length, direction, and width of the line. Before a linescan acquisition, you must have prior knowledge of the sample s elements. You can acquire, load and save electron image files in Electron Imaging mode. NSS automatically names spectra and images as they are acquired they are acquired. Before you begin the first acquisition in a project, use the text box in the File Name window to set a base name for your data files. Note Before the acquisition, make sure all acquisition and processing properties are properly set. Information about those properties is included in the mode specific chapters that follow. 17 NSS Spectral Imaging System Handbook

30 To acquire a spectrum or image: 1. Choose the acquisition mode from the Navigation pane. 2. Click the Start Acquisition button on the Acquisition toolbar. The spectrum appears in the spectrum pane. To pause the acquisition, click the Pause Acquisition button resume, click the Pause Acquisition button again.. To To stop the acquisition and retain the data taken, click the Stop Acquisition button. To stop the acquisition without retaining the data, click the Abort Acquisition button. In Spectrum mode, you can view the analyzer status and Livetime and Deadtime information on the Detector Status tab in the bottom-right pane. Acquisition and microscope information is shown in the status bar at the bottom of the screen. The Status Bar options are specified using Microscope Parameters in the Edit menu. Note The microscope parameter settings affect all modes, not just Spectrum mode. You can view peak identification manually during the acquisition or have peak IDs automatically applied during the acquisition. The identification and analysis properties of the spectrum are specified on the Processing tab in the analysis controls pane. 18 NSS Spectral Imaging System Handbook

31 Viewing the spectrum You can change the size and range displayed for a spectrum by using the mouse, the Spectrum toolbar (shown below) or the number keypad (see the following table). Following an image extraction, the spectrum is displayed in its full range. Function Keypad Method Reset Spectrum Home (7) Move Spectrum Left Num Lock + left arrow (4) Expand Spectrum Compress Spectrum Page Up Page Down Move Spectrum Right Num Lock + right arrow (6) Increase Y Scale Num Lock + up arrow (8) Decrease Y Scale Num Lock + down arrow (2) Auto Scale To Highest Peak End (1) Expanding the spectrum You can expand a spectrum to look more closely at a specific part in any of three ways: Drag right to expand the spectrum from the 0 energy. Drag the spectrum left to expand the spectrum from the highest energy. NSS Spectral Imaging System Handbook 19

32 Click the Expand Spectrum button on the Spectrum toolbar to expand the spectrum from the center of the spectrum pane. Compressing a spectrum Note To reduce the magnification of the spectrum and show a greater energy range, click the Compress Spectrum button on the Spectrum toolbar. There is no mouse action to compress the spectrum. Double-click the spectrum to view the entire energy range. Scrolling through a spectrum You can scroll through a spectrum to look more closely at a specific part in two ways: After a spectrum is expanded, drag left or right to scroll through the spectrum horizontally, or up and down to scroll vertically. As the spectrum is expanded or scrolled, it scales vertically to fit the tallest visible peak. You can also click the Move Spectrum Left, Move Spectrum Right, Increase Y Scale and Decrease Y Scale buttons on the Spectrum toolbar. Zooming in on a peak To zoom in on a portion of the spectrum, hold down the Ctrl or Shift key and drag across the peak of interest. When you release the mouse button, the peak is enlarged. 20 NSS Spectral Imaging System Handbook

33 Displaying the full spectrum There are three ways to restore the spectrum to full view: Click the Reset Spectrum button on the Spectrum toolbar. Press Home on the keyboard. Double-click the spectrum pane, but not near a peak. Applying a log scale Use the Change To Log Mode button to display the spectrum with a logarithmic vertical scale for the intensity values. Managing files After you acquire spectral, electron image, x-ray map, linescan data, you can rename it, add notepad text to it, save it, automatically identify it, quantify it, or manually change its peak labels. You can also open an existing spectral file and compare the spectra. Project Explorer All data is stored within projects. Each project can consist of several subprojects. A project includes the elements list, identification configuration, base file name, and acquisition properties from the project s previous use. When you start NSS, Project Explorer appears allowing you to select an existing project or create a new one. Project Explorer allows you to visually manage your project folders. NSS Spectral Imaging System Handbook 21

34 Using the buttons in the upper left corner, you can: Create a new project Create a new folder Copy a project or folder Paste a project or folder Rename a project or folder Delete a project or folder Opening and saving files NSS or files from a third-party EDS system can be opened and saved from NSS acquisition and analysis modes. File names appear in the Files pane when you are in an acquisition or analysis mode that supports the file type. You can open many of the files by using a text editor like Notepad. When a project is open, you can open any files included in that project by clicking the file name in the file list pane. To open a file outside the current project: 1. Choose Open from the File menu. 2. When Open dialog box appears, navigate to the directory that contains the file you wish to open. 3. Double-click the file or click the file then choose Open. The file is imported into the project s temporary directory. When you close the project, a prompt asks whether to save the file in the project folder or delete it. The temporary directory is emptied when you close the project. You can save a file at any time by clicking the Save button on the NSS toolbar or choosing Save from the File menu. To change the file s name, double-click the label, type the desired name and then choose OK. You can also select a pane and use Copy To in the Edit menu to save the pane to a JPEG file. 22 NSS Spectral Imaging System Handbook

35 Most NSS files are stored in industry-standard formats, such as EMSA for spectra files, TIFF for image files, etc. Due to their unique nature, Spectral Imaging files are stored in a Thermo Scientific proprietary format. You can save data in an industry standard format by switching to a mode that supports the file format. For example, switch from Spectral Imaging to Spectrum mode to save an EMSA spectrum file. See the section entitled Supported file formats in the Software Reference Materials chapter later in this manual for complete information about supported file types. Labeling a data set Follow these steps to label the data set: 1. Double-click the image, map, or spectrum title at the top of the viewing pane. A box appears: 2. Enter the new label. 3. Choose OK. Note If you change the image label, the file name is automatically changed to match the new label. Renaming a file When you rename a spectrum, map, linescan or image, the new name is saved with the spectrum in a new file and is used for printing. The original name is determined by Base Name in the file name pane. You can rename the file by double-clicking the spectrum name at the top of the spectrum pane or by changing the name in the Details dialog of the Attributes tab. Adding note text To add additional notes regarding the spectrum, click the Notes tab in the bottom-right pane. Enter the text in the notepad area. Notepad text is saved with the spectrum. NSS Spectral Imaging System Handbook 23

36 Compressing Spectral Imaging files Note Follow these steps to reduce the size of a Spectral Imaging file: 1. Choose Compress SI File from the File menu. This menu item is disabled if a Spectral Imaging file is currently open or if an acquisition is in progress. No dialog box appears if all of the selected.si files have already been compressed. When the dialog box appears, select one or more SPECTRAL IMAGE files in the same directory to compress to a minimal size. 2. Choose OK. A progress dialog box appears during the compression. Compression might take several minutes per file. The selected files are significantly reduced in size. The ultimate size reduction depends on the complexity of the underlying data. Extracting data Once a spectral image is acquired, spectral data can be extracted. Features of interest can be defined by area or by intensity. 24 NSS Spectral Imaging System Handbook

37 Selecting areas for analysis You can draw multiple unique shapes on an image to select areas for data extraction and analysis. Note If the Intensity Cursor is on, click the Intensity Cursor button on the Extract toolbar to turn off the image intensity cursor before starting the extraction. To draw a shape on the image for extraction: 1. Click the appropriate cursor button on the Extract toolbar. Extract Polygon Extract Rectangle Extract Spot Extract Image Intensity Use the cursor to draw the desired shape on the image. To draw a closed shape, drag the polygon or rectangle tool. To draw straight lines, use the polygon tool to click the points where you want corners. Lines appear connecting the points. To change the size or shape of an area, drag a side or corner. For spot extractions, be sure to enter a spot size radius (in μm) on the Image Extract tab in the General Properties dialog box for the image. Here is an example of some shapes being drawn: Note If you want to isolate a particularly small area, drag the borders of the image pane down and right to increase the image size. NSS Spectral Imaging System Handbook 25

38 Also, you can click the small yellow maximize icon in the upper-right corner of a rectangle to expand it to fill the entire image. To restore the original rectangle, click anywhere inside the maximized rectangle. You can drag a side or corner of the maximized rectangle just as you would any other rectangle to make it smaller. 2. Right-click the shape to fill it. This begins the analysis and extraction of the spectrum. The identification and analysis of the spectrum depend on the Processing settings. See Setting processing parameters in the Preparing for an Analysis chapter. To use the image intensity cursor over the extracted area, click the Intensity Cursor button on the Extract toolbar. To remove an existing shape, draw a new shape. To draw multiple shapes, hold down the Ctrl key while starting a new drawing. Selecting areas of similar intensity for analysis In Spectral Imaging mode you can extract a spectrum from an image based on similar pixel intensity; that is, how close the intensities of points are to the average intensity of a specified point. To extract a spectrum from an adjacent area of similar intensity: 1. Open or acquire an image if the desired image is not already displayed. 26 NSS Spectral Imaging System Handbook

39 2. Click the Extract Shape Defined By Image Intensity button on the Extract toolbar. 3. Set the parameters described below to specify which points are included in the area data. Parameter Cursor Diameter Similarity Smoothing Brightness Spectrum Auto Extract Description The diameter of the cursor (the spot over which intensities are averaged), normally expressed as a percentage of the image width. If desired, you can select Diameter In Microns to use micrometers instead. How close to the clicked points average intensity that adjacent points must be to be included. The distance in pixels from a clicked point within which adjacent points are included. The desired pixel intensity of included points. Select this option if you want spectra to be extracted automatically when you click locations on the image. If this option is not selected, you can extract spectra by using the Extract Spectrum button after clicking locations. 4. Click the desired location on the image. Color is used to indicate the area from which the spectrum will be extracted. If Spectrum Auto Extract is not selected, skip to the next step. NSS Spectral Imaging System Handbook 27

40 If Spectrum Auto Extract is selected, the extracted spectrum from all contained pixels is created and appears in the bottom-right pane. The exact appearance of the spectrum and the identification depend on the Processing settings. You can modify the specified areas by changing the parameter settings. To abort an extraction and begin another, click a different location. To add another area, wait for the previous extraction to finish, and then click a new location. The software begins a new extraction in the new area using a different file name. When you are finished, skip to step Click the Extract Spectrum button to extract the spectrum. You can change the parameter settings or click a different location and then click the Extra Spectrum button again to extract a new spectrum. You can also click the Extract Map Images button on the Extract toolbar to extract maps and a spectrum. If desired, specify different elements on the periodic table on the Element Setup tab in the analysis controls pane before extracting the maps. 6. Choose Close to close the Image Intensity Selection dialog box. 28 NSS Spectral Imaging System Handbook

41 Spectrum Mode Use Spectrum mode to acquire and analyze EDS spectra. Spectrum mode You can control how acquisitions occur by using the Acquisition Properties dialog box, available through the Edit Acquisition Properties button on the Acquisition toolbar or Acquisition Properties in the Edit menu. See the next section for details. Note If you have our WDS detector installed on your microscope, the WDS Scan button on the Ident toolbar is active. Within Spectrum mode, you can acquire and compare both EDS and WDS spectra. 29 NSS Spectral Imaging System Handbook

42 Setting spectral acquisition properties To set the acquisition properties for acquiring a spectrum: 1. Click the Edit Acquisition Properties button on the Acquisition toolbar. You can also choose Acquisition Properties from the Edit menu. The Acquisition Properties dialog box appears. Here is an example: The EDS tab and EDS 2 tab (if available) let you set the detector parameters described below. Acquisition properties are stored in the.tnp file in the project folder. The following table describes the available properties. Use the Detector Selector toolbar to select the detector to use for acquisition. See Detector Selector toolbar in the Getting Started chapter. 30 NSS Spectral Imaging System Handbook

43 Field Termination Criteria Live Time Limit (s) Max Peak Counts Element and Line Max Counts User Define Low (ev) and High (ev) Low Energy Cutoff (ev) Max kev Acquire WDS Elements Simultaneously For Quantitative Analysis Description The acquisition ends whenever any of the settings in the Termination Criteria box are exceeded. The settings are explained below. The duration of the acquisition in livetime seconds. A general rule for spectral acquisitions that do not have a high count rate is to use at least 100 seconds of livetime for acquisition. Setting this value to Zero means the acquisition runs continuously and you must stop the acquisition using the Stop button on the Acquisition toolbar or via another termination method. The acquisition terminates when the counts (on the vertical scale) in any channel reach this number. Setting this value to Zero means the acquisition runs continuously and you must stop the acquisition using the Stop button on the Acquisition toolbar or via another termination method. Enter the atomic symbol for the element. Specify a KLM line for the element. Setting the symbol to Blank means that this option is ignored. The acquisition terminates when the intensity for the selected element or region reaches this value. If this is checked, you can redefine the low and high ev values for the region of interest. Low and high ev values corresponding to the userdefined region of interest energy range. X-ray counts below this energy are ignored during an EDS acquisition. The Auto setting changes the value according to the Pulse Processor Time Constant setting to remove the zero peak. X-ray counts up to this limit are included in the EDS acquisition. The Auto setting uses the setting of Accelerating Voltage in the Microscope Parameters And Status Bar Selection dialog box as the limit. If a WDS detector is available, this feature lets you acquire EDS and WDS elements simultaneously for comparative quantitative analysis. NSS Spectral Imaging System Handbook 31

44 Field Time Constant Measure Beam Current Before EDS Acquisition Description Select a time constant from the drop-down list box. The list box displays the approximate maximum throughput for each time constant. In general, the resolution of the detector reduces as the throughput increases. Auto automatically optimizes the DPP settings for the best throughput and resolution and keeps the dead time between 30% and 50%. (The range of rates depends on the detector type.) With the microscope set for best image and focus conditions, the software takes care of the rest. As the beam current changes, the software tracks it to maintain the optimum time constant setting. The Projected Maximum Throughput value is the sum of real x-ray events and noise events, per second. As the Time Constant value changes, the Projected Maximum Throughput value changes, indicating the maximum number of both noise and x-ray events that can be processed at this setting. If you have the optional software and hardware, you can select this option to have the microscope beam current measured and stored automatically each time you acquire data. This eliminates the need to type the beam current value in the Microscope Parameters And Status Bar Selection dialog box (see Microscope parameters in the Getting Started chapter). The measured value appears on the Attributes tab in the lower-right pane. If your system uses a manually positioned Faraday cup, you will be prompted to position the cup before a measurement is made. If Beam Current is selected in the Microscope Parameters And Status Bar Selection dialog box, you can measure the beam current at any time by clicking the BC button in the status bar near the lower-right corner of the NSS window: 2. Set the parameters for your acquisition. 3. Choose OK. 32 NSS Spectral Imaging System Handbook

45 Comparing spectra You can compare two or more spectra in the spectrum pane. If you acquire a WDS spectrum, you can compare it with an EDS spectrum using this procedure. To compare spectra: 1. Switch to Spectrum mode. 2. In the Spectrum list on the Compare Information tab in the analysis controls pane, check one or more overlapped spectra to compare against the base spectrum. You can also select a synthetic, background or residual spectrum if SpectraCheck is active. The following table describes how these spectra are compared. Spectrum Type Synthetic Background Residual Comparison Based on the elements identified in the periodic table, the software calculates how the spectrum should appear and generates this synthetic spectrum. Applies the background spectrum. The peaks of the elements defined in the periodic table are removed from the spectrum to create the residual spectrum. This spectrum shows what peaks were not accounted for in the original spectrum. NSS Spectral Imaging System Handbook 33

46 3. In the Method box, select Overlap. The spectra are applied to the spectrum pane. Note You can select Match instead to overlay and compare database spectra listed on the Match Results tab in the lower-right pane. See Setting up a search in the Spectral Match chapter for more information. 4. Select the desired Normalize To option. These options adjust the selected spectra to the factor you select; they do not affect the base spectrum. The following table describes the available options. Option None Livetime Element Multiplier Range Maximum Description No normalization is applied. Normalizes the overlapped spectra to simulate the same length of acquisition time as the base spectrum. Uses the selected element to adjust the overlapped spectra to the height of the base spectrum. The peak or line used is based on accelerating voltage and the energy range of the spectrum. Simple multiplier to scale all overlapped spectra by the multiplier value. Allows you to select an energy range to create multipliers with respect to the same region in the overlapped spectrum and the base spectrum. The overlapped spectrum is scaled by the entered multiplier value to normalize the overlapped spectra relative to the base spectra. Two range cursors appear in the spectrum pane, appearing as dashed vertical lines. Move each cursor to create the region. In the currently displayed range, scales the largest peak in each overlapped spectrum to match the largest displayed peak in the base spectrum. This method will scale a peak in an overlapped spectrum to match a base spectrum peak even if there is no energy overlap (that is, two WDS spectra). 34 NSS Spectral Imaging System Handbook

47 Option Maximum in Overlap Description Scales the largest peak of each overlapped spectrum to match the largest peak of the base spectrum in the region where both spectra have data. For example, if you display a copper K WDS spectrum on a copper EDS spectrum, the largest peak of the WDS spectrum is scaled to match the copper K peak of the EDS spectrum, not the more intense copper L peak. This is unlike the Maximum option, which may scale a peak in an overlapped spectrum to match a base spectrum peak with no overlap. SpectraCheck When SpectraCheck is active, a synthetic spectrum may be overlapped on the currently displayed spectrum. The synthetic spectra are based on the elements found in the identified spectrum. The SpectraCheck value represents the goodness of fit. A lower value indicates a better elemental fit. SpectraCheck is an easy method to verify automatic qualitative analysis or manual peak identification of EDS spectra. This feature gives you greater confidence that your data interpretation is correct. It is part qualitative analysis, part quantitative analysis, part spectrum background calculation, and part statistical analysis. The algorithm takes the spectrum, performs a qualitative analysis, performs a quantitative analysis, calculates a spectrum background specifically for your detector and sample, creates a synthetic spectrum, and then calculates the SpectraCheck value. This value is displayed on the periodic table in the analysis controls pane. NSS Spectral Imaging System Handbook 35

48 Performing math operations on spectra with Spectrum Math software One of the items in the Spectrum menu is Spectrum Math. Selecting the Spectrum Math menu item brings up a dialog box to allow you to add, subtract, multiply or divide any or all of the spectra in a project by a constant or by another spectrum. In addition, you have the option of getting the average or summed spectrum from any of the project spectrum files. Naming the result file You can type in a name for the result spectrum in the Result Name edit box. This is the spectrum that will be created when you click the Calc. Result button to perform the spectrum math operation. 36 NSS Spectral Imaging System Handbook

49 Selection of files to process You select which files in the project to use in the spectrum math calculation by clicking the Select button to bring up a file selection box shown below. The type of files displayed for selection depends upon the NSS mode currently in effect. NSS Mode Spectrum Point & Shoot Spectral Imaging Xray Linescans File Type.emsa.psmsa.fzs and.fzsa.lsmsa You can change the type of file display by changing the selection in the Files of Type combo box at the bottom of the dialog. If you are selecting one file to process, you can click on the file name and click the OK button. For more than one file, you can hold the Ctrl key on the keyboard down and click the desired files. If the files are in a sequence, you can click the first file then hold the Shift key down on the keyboard and click the last file. When you click the OK button all the selected files are transferred to the Spectrum Math file list for processing. NSS Spectral Imaging System Handbook 37

50 For convenience, you can double left-click on a file name to choose it as a single file. This is equivalent to clicking the file and then clicking OK. You can also double right-click on a file name to add a file to the file list that is already defined. Selection of the math operation to perform You can choose the type of math operation to perform from the choices in the Spectrum Math operator combo box. The choices are: Math Operator Result of the Operation + (Add) Add to each spectrum - (Subtract) Subtract from each spectrum X (Multiply) Multiply each spectrum (Divide) Divide each spectrum Average Sum Normalize Beam Current Normalize Livetime Normalize Beam Curr. and LT Normalize Vertical Full Scale Average several spectra Sum several spectra Normalize each spectrum by beam current Normalize Livetime Normalize by both beam current and livetime Normalize each spectrum by the maximum counts When you choose the Average or Sum operators, each of the selected files is read into memory and the average or sum spectrum is generated by averaging or summing the data on a channel-by-channel basis. Any of the other choices result in the math operation being performed on each of the selected files with a new result spectrum being created for each. A default name is used for each result spectrum after the first spectrum has been saved. This default name has the Result Name as a base name with a sequence number in parentheses appended to the base name. 38 NSS Spectral Imaging System Handbook

51 The operand type There are two ways that Spectrum Math can be performed on the selected files. One in which a constant is used in the math operation, and the second in which a spectrum is used. You can choose which type to use by clicking the choices in the Operand Type combo box. When you select Constant for the Operand Type, the constant that is present in the Operand combo box is used to perform the math operation. When you select Spectrum for the Operand Type, you must also select a spectrum from the file choices in the Operand combo box in order to conduct the math operation. Processing the selected spectra After you have made all the selections required by the program, the Calc. Result button at the bottom of the dialog is activated and the selected files can be processed. When you click this button a progress bar appears if several spectra are being processed along with an indication of which file in the set being analyzed. All math operations are performed on a channel by channel basis. The calculations are conducted with floating point arithmetic. Upon completion of the calculation for a given channel the floating point number is rounded to the nearest integer count value before the result is stored. If the calculation results in a negative number for the number of counts in a channel, the negative value is stored in the spectrum. All result spectra are stored in the ~temp directory for the project. When you normalize a selected spectrum to a constant beam current or livetime, the constant beam current or livetime is stored with the attributes of the result spectrum. The normalization of a constant beam current and livetime is the same as livetime normalization. The counts of the result spectrum will be normalized to what they would be if the constant beam current or livetime had been used for the spectrum acquisition. However, if you normalize a selected spectrum to another spectrum, the result spectrum will have counts that would have been present if the selected spectrum had been counted with the same beam current or livetime as the Operand spectrum. Upon completion the result spectrum will have attributes that reflect those of the Operand spectrum upon which the normalization is based. Each result spectrum generated by Spectrum Math has an entry in the Notes section that shows the math operation that was conducted to obtain the spectrum. If a result spectrum is from the Average or Sum operation, all NSS Spectral Imaging System Handbook 39

52 spectra used to calculate the average or sum are listed in the spectrum Notes section. When a result spectrum is created by Spectrum Math, the date and time of creation is stored with the spectrum attributes. Other attributes are based on the spectrum being processed or for Average and Sum on the first file processed. Resetting the dialog You can initialize the Spectrum Math dialog by clicking the Reset button. This clears the selected file list and resets the Result Name to a default based on the Base name for the project. It also resets the Operator to Add, the Operand Type to Constant and the Operand to 1.0. The right click menu If you click right when the cursor is within the dialog boundaries, a menu is displayed so that you can easily perform common actions. The menu items are: Clear the Selected Spectrum List Add Current to List Calculate the Result Spectrum The first permits you to remove all spectra from the selected file list without performing a complete reset of the dialog. The second gives you an easy way to add a currently displayed spectrum to the selected file list. And the third is an alternate way to start the Spectrum Math processing of the selected spectra. Ending the dialog When you have completed the Spectrum Math operations for your project, click the Cancel button, or click the X in the upper right corner to end the dialog. 40 NSS Spectral Imaging System Handbook

53 Performing math operations on regions of interest In Spectrum mode or Point & Shoot mode, the Region Tool tab in the bottom-right pane lets you add, subtract, multiply and divide two selected regions of interest in terms of net and gross counts. You can choose to work with either counts or rate data. You can also simply report the gross and net counts for a single region. This tab is useful for finding peak ratios or ratioing a peak to the background. The background for calculating net intensities for regions is determined by using the mean of five neighboring channels on either side of the region and fitting a linear curve between the two mean values. You can include the results of math operations in your printed output by selecting ROI Results on the Spectra tab of the Page Setup dialog box, available through Page Setup in the File menu. Region settings are stored in the.tnp file in the project folder. To perform math operations: 1. Specify the first region to use in the operation. To the left of Operator on the Region Tool tab, click the Element down arrow button to display a periodic table, and then click the desired element. Select the desired line for the element from the Line drop-down list box. NSS Spectral Imaging System Handbook 41

54 You can also specify up to five numbered regions that are not associated with an element and use them in operations instead of selecting an element. For example, you can specify a background region and divide an element region by it. Type user in the appropriate Element text box, and then enter the region limits in the User Region Range (ev) text boxes. You can also drag the vertical dashed lines in the spectrum pane to specify the limits. To specify a region's number, use Line to select or enter a number. 2. Select the desired math operation from the Operator drop-down list box. The operation will be performed in the order shown on the tab; for example, (first region) + (second region). 3. Specify the second region to use in the operation just as you did the first region, except use Element and Line to the right of Operator. 4. Click the button. The operation and the results appear in the list at the top of the tab. To delete an operation, click it and then click the button. 42 NSS Spectral Imaging System Handbook

55 Point & Shoot Mode In Point & Shoot mode you can acquire an image, specify numbered points and areas on the image, and then acquire spectra at those points and areas. Point & Shoot mode Note You must acquire a new image before adding new points or areas if you have switched modes, changed projects, or opened a Point & Shoot file containing areas that were previously acquired. If you switch to another mode or open a different project, acquired areas will be retained and areas that have not been acquired will be removed. NSS Spectral Imaging System Handbook 43

56 Note In Point & Shoot mode you can use the Region tool tab in the bottom-right pane to add, subtract, multiply and divide regions of interest and perform other math operations. See Performing math operations on regions of interest in the Spectrum Mode chapter for details. Performing a Point & Shoot acquisition You can either start with an existing image or acquire a new image. To acquire the new image, click the Acquire An Averaged Electron Image button. You can do two different styles of Point & Shoot acquisitions, immediate and batch, using a mixture of five different shapes (point, rectangle, irregular, Fat Spot and polygon). An immediate acquisition begins when you click a new point or area. In a batch acquisition you select a batch of point or areas and then acquire data. See Immediate acquisitions or Batch acquisitions for instructions. For best image registration, use an acquisition time that is at least 10 seconds. Spectral analysis works the same way in this mode as in other modes using the Processing tabbed dialog selections. Immediate acquisitions Notice An immediate acquisition begins right after you specify a new point or area. When the acquisition is finished, you can repeat the procedure to acquire additional data. Before performing an immediate acquisition, be sure to click the first button on the Point & Shoot toolbar so that it appears pressed in. To acquire data from a single point: 1. Click the Acquire Point Shape button on the Point & Shoot toolbar. 2. Click an image location where you want to acquire data. To abort this acquisition and begin another, click a new location. 44 NSS Spectral Imaging System Handbook

57 To add another point, wait for the previous analysis to complete, and then click a new location. The software begins a new acquisition in the new position using a different file name. Selecting areas for analysis You can draw multiple unique shapes on an image to select areas for data acquisition and analysis. To draw a shape on the image for acquisition: 1. Click the appropriate cursor button on the Point & Shoot toolbar. Acquire Polygon Acquire Rectangle Acquire Spot Use the cursor to draw the desired shape on the image. To draw a closed shape, drag the polygon or rectangle tool. To draw straight lines, use the polygon tool to click the points where you want corners. Lines appear connecting the points. To change the size or shape of an area, drag a side or corner. For spot extractions, be sure to enter a spot size radius (in μm) on the Image Extract tab in the General Properties dialog box for the image. Here is an example of some shapes being drawn: Note If you want to isolate a particularly small area, drag the borders of the image pane down and right to increase the image size. NSS Spectral Imaging System Handbook 45

58 Also, you can click the small yellow maximize icon in the upper-right corner of a rectangle to expand it to fill the entire image. To restore the original rectangle, click anywhere inside the maximized rectangle. You can drag a side or corner of the maximized rectangle just as you would any other rectangle to make it smaller. 2. Right-click the shape to fill it. This begins the analysis and extraction of the spectrum. The identification and analysis of the spectrum depend on the Processing settings. See Setting processing parameters in the Preparing for an Analysis chapter. To use the image intensity cursor over the extracted area, click the Intensity Cursor button on the Extract toolbar. To remove an existing shape, draw a new shape. To draw multiple shapes, hold down the Ctrl key while starting a new drawing. To acquire data from an irregularly shaped area based on image intensity: 1. Click the Acquire Shape Defined By Image Intensity button on the Point & Shoot toolbar. The Image Intensity Selection dialog box appears: 46 NSS Spectral Imaging System Handbook

59 2. Set the parameters described below to specify which points to include in the area data. Parameter Guard Ring Width Cursor Diameter Similarity Smoothing Brightness Description The width in micrometers of the area border that is not included when data is acquired. This width is applied after smoothing (described below). If the feature is less than 1 micrometer in size, no guard is used. The diameter of the cursor (the spot over which intensities are averaged), normally expressed as a percentage of the image width. If desired, you can select Diameter In Microns to use micrometers instead. How close to the clicked points average intensity that adjacent points must be to be included. The distance in pixels from a clicked point within which adjacent points are included. The desired pixel intensity of included points. 3. Click a location on the image where you want to acquire a spectrum. Color is used to indicate the area from which the spectrum will be acquired. You can modify the specified areas by changing the parameter settings. 4. To add another area, hold down the Ctrl key and click a new location. 5. When all of the areas have been defined, click the Start Acquisition button on the Acquisition toolbar. 6. Choose Close to close the Image Intensity Selection dialog box. NSS Spectral Imaging System Handbook 47

60 Batch acquisitions Notice With batch acquisitions you first specify a group of sequentially numbered points or areas, or a combination of both. You then acquire the data by clicking the Start Acquisition button on the Acquisition toolbar. A separate spectrum is acquired for each specified point or area. See the section entitled Selecting areas for analysis if you are unfamiliar with selecting areas for acquisition. When an acquisition is finished, you can repeat the procedure to acquire additional data. Before performing any of the following procedures (except the last one), be sure to click the first button on the Point & Shoot toolbar so that it does not appear pressed in. To acquire data from a group of points: 1. Click the Acquire Point Shape button on the Point & Shoot toolbar. 2. Click the image locations you want to acquire. 3. Click the Start Acquisition button on the Acquisition toolbar. To acquire data from a group of rectangular areas: 1. Click the Acquire Rectangle Shape button on the Point & Shoot toolbar. 2. Drag within the sample image to draw rectangles of the desired size and shape. 3. Click the Start Acquisition button on the Acquisition toolbar. 48 NSS Spectral Imaging System Handbook

61 Specifying points and areas to display In Point & Shoot mode you can use the P&S Select tab in the analysis controls pane to specify which points and areas to display on the image. You can also use the tab to select for deletion a point or area that has not yet been acquired. Each time you draw a point or area, it is listed on the tab. You can hide a listed point or area by checking its box in the Hide column. To hide all of the points and areas, click the Hide All button. To display all of the points and areas, click the Show All button. To delete a point or area that has not been acquired, select it in the list or select it using the button on the Point & Shoot toolbar, and then press the Delete key on the keyboard. To delete a point that is overlapped by an area, first hide the area as explained above. NSS Spectral Imaging System Handbook 49

62 Spectral Imaging Mode Use Spectral Imaging mode to acquire a data set of dead time-corrected spectra at every point (pixel) in a map. Once the information is acquired and stored, you can generate a spectrum for qualitative and quantitative analysis, create x-ray maps and linescans, and print reports. Compass uses data from Spectral Imaging mode to extract and present pure components. The Spectral Imaging view is a multipane view containing a gray scale image display, analysis control and results area, spectral display, and an x-ray map area that changes to an ay Linescan area for linescan extractions. Spectral Imaging mode 50 NSS Spectral Imaging System Handbook

63 Use the Acquisition toolbar to collect an image and Spectral Imaging data. Use the Extract toolbar to select a portion of the electron image to obtain data (spectrum, maps, linescans) of the extracted area. Peaks are identified in the spectrum pane, which includes tools for additional peak identification and analysis. You can create quantitative analysis results with the initial analysis and requantify the data with the Quantify Spectrum button. You can display maps or linescans to illustrate spatial distributions of elements. Spectral Imaging files are saved with an.si file extension. Specify the base file name in the file name pane. The files are stored in the project s temporary directory after acquisition. You can save the spectral image data for future use by telling the program to save the data when you close the project. Before the acquisition, make sure all acquisition properties and microscope parameters are properly set. A Spectral Imaging analysis uses settings on the EDS (or EDS 2), Imaging and Spectral Imaging tabs of the Acquisition Properties dialog box. If you have the Drift Compensation option, you can use it while acquiring data. See the Drift Compensation chapter. Setting acquisition properties Follow these steps to set Spectral Imaging acquisition properties: 1. Click the Edit Acquisition Properties button on the Acquisition toolbar. The Acquisition Properties dialog box appears. Spectral Imaging termination criteria are determined by image or mapping parameters only. NSS Spectral Imaging System Handbook 51

64 2. On the Imaging tab set the parameters for your averaged electron acquisition. The following table describes the available properties. Field Resolution Frame Time (s) Dwell Time (µs) Description The size of the image in pixels. A higher resolution produces greater image detail and increases acquisition time. A longer frame time increases the acquisition time and reduces image noise. A shorter frame time can result in blurred and streaked images. Optimum values depend on microscope and detector type. Select Fastest to automatically select the fastest frame time. The amount of time the beam is placed at each pixel location. A longer dwell time results in better statistics and longer acquisition times. A shorter dwell time might cause a blurred or streaked image. 52 NSS Spectral Imaging System Handbook

65 Field Number Of Frames Acquisition Time (s) Use Input 1 and Use Input 2 Description The number of frames to be acquired or summed. A frame is one complete scan from the upper-left corner to the lower-right corner of the map. For beam-sensitive samples, increase the number of frames and decrease the dwell time. If you type 0 in this field, you must stop acquisitions manually by clicking the Stop Acquisition button or Abort Acquisition button on the Acquisition toolbar. The estimated total acquisition time. Specify the channel (for example, SEI or BEI imaging detectors of your microscope) from which the image data is acquired. Most microscopes will only have Input 1 connected. 3. On the Spectral Imaging tab set the parameters for the spectrum-per-point acquisition. If individual elements of interest are selected in the periodic table (see step 1 in the next section), maps grow in intensity in the map pane as data is extracted. If no elements are selected, you can still generate maps during the extraction by enabling Auto ID on the Processing tab or pressing the peak ID button during the acquisition. As elements are identified, maps are generated. 4. Choose OK. Acquiring an image To acquire an image: 1. To observe x-ray mapping during the analysis, mark the elements to map as Identified on the periodic table on the Element Setup tab. You can select these elements from a Spectrum mode or Point & Shoot mode analysis, or you can select the elements manually. If Auto ID is enabled, elements will be added or removed automatically, based on the spectrum. NSS Spectral Imaging System Handbook 53

66 2. Switch to Spectral Imaging mode. If the Drift Compensation option is installed, click the Enable Drift Compensated Acquisitions button on the Acquisition toolbar before acquiring a new image. Click the Acquire An Averaged Electron Image button on the Acquisition toolbar when not using drift compensation. 3. Click the Start Acquisition button on the Acquisition toolbar to acquire x-ray data. Extracting spectral data Once the Spectral Imaging data set is created, you can extract rectangular, circular and other areas of the electron image for spectral analysis. The Extract toolbar contains buttons for specifying the area. Step-by-step instructions are provided later in this chapter. The Processing tab in the analysis controls pane contains the parameters that determine how the spectrum is handled after it is acquired. See Setting processing parameters in the Preparing for an Analysis chapter. Note If the Extract toolbar is not available, the image intensity cursor could be on. Click the Intensity Cursor button on the Extract toolbar to turn it off. 54 NSS Spectral Imaging System Handbook

67 You can perform two kinds of extractions. In a normal extraction all the spectra in the specified sample area are added. The count value for a given channel in the extracted spectrum is the sum of the count values for that channel in all the spectra (see the example below). This type of extraction will be performed if the button above the image is labeled Extract. A maximal extraction, on the other hand, uses the maximum count value for each channel from all the spectra in the specified sample area (see the example below and the discussion in the next section). This type of extraction will be performed if the button above the image is labeled Maximal. Notice that the count values are generally lower and that the relative size of small peaks is greater than in the normal extracted spectrum. NSS Spectral Imaging System Handbook 55

68 Click the Extract/Maximal button to toggle between the two types of extraction before performing the extraction. About maximal spectra Identifying the major peaks in a Spectral Imaging extracted spectrum is important. This can be done by analyzing a cumulative or summed spectrum of all of the pixel spectra in a selected region. In some cases, identifying low concentration elements or elements that occur only in a few pixels is more important. In the past, this kind of analysis was much more difficult due to the reduced statistics or number of these peaks. Maximal spectrum extraction was developed for just such investigations. It determines, on a channel-by-channel basis, the maximum counts that have occurred for any pixel within the selected region. This technique is powerful because an element that occurs in a single pixel will have as much weighting in the resulting spectrum as all of the other pixels, which are dominated by the majority matrix elements. Note that this kind of analysis is only for element (that is, peak) identification purposes for the selection of maps, not for phase analysis. The results are only as good as the underlying data set. The more counts that are acquired, the better the peak identification will be. If peak overlaps occur in the summed spectra, they may not be uniquely identified in the maximal spectrum if the statistics are low. Image intensity cursor NSS includes a coordinated image intensity cursor for analysis of the image. Click the Intensity Cursor button on the Extract toolbar to turn the cursor on or off. When you place the image intensity cursor on the electron image, the coordinated cursors move to the same point on each map. When you move the cursor to a new point, readouts for the cursor s X-Y position (in pixels) and intensity appear above the electron image and to the right of the x-ray maps (for example, x:177 y:76 i:94). Measuring features with the image ruler The image ruler lets you measure features of interest in the image pane in Spectral Imaging and Electron Imaging modes. Follow these steps: 1. Click the Image Ruler button on the Extract toolbar. 56 NSS Spectral Imaging System Handbook

69 The image ruler appears centered on the image pane in the default color with a measurement scale in micrometers. 2. Drag one end of the ruler to the start of a feature of interest. The measurement is updated automatically. 3. Drag the other end of the ruler to the end of the feature. Note You can move the pointer near the center of the ruler and drag the entire ruler to a new position. Extracting multiple spectra To compare spectra from multiple extraction regions, each file must be manually saved to the project folder. Spectral comparison is then performed in Spectrum mode. To gather additional spectra from one acquisition, perform another extraction. Switch to Spectrum mode and rename the spectrum. Extracting linescans Linescan extraction lets you investigate and analyze the elemental transitions from point to point on the sample. You can specify the direction and width of the extracted line. Note Click the Intensity Cursor button on the Extract toolbar to turn off the image intensity cursor before starting the extraction. To extract a linescan from the image: NSS Spectral Imaging System Handbook 57

70 1. Select the elements in the periodic table on the Element Setup tab. Note If you are unsure whether to display an element, include it in the initial linescan (mark it as Identified ). You can later turn off elements that are not of interest. 2. Right-click the image. The General Properties dialog box appears. 3. On the Image Extract tab, enter a Thickness value (as a percentage of the image size). 4. Set Number Of Points to the number of points to show in the linescan. 5. Choose OK. 58 NSS Spectral Imaging System Handbook

71 6. Click the Extract Line Cursor button on the Extract toolbar. A yellow arrow appears on the image. Here is an example: Linescan data appears in the top-right pane. For each measured element, the software displays a color-coded plot of the number of counts at each point along the line. Here is an example: Note Depending on whether you have used Spectral Imaging mode earlier in this work session, you may need to click the yellow arrow to generate the linescan data. You can overlay these plots on the image to better see the association between them and the sample surface. See Overlaying extracted linescans on the image later in this chapter for details. NSS Spectral Imaging System Handbook 59

72 7. Adjust the length, direction and position of the yellow arrow as desired by dragging. To change the length or direction of the arrow, drag either end of the line. To move the arrow, move the mouse pointer over its center and then drag the arrow. You can replace the current arrow by drawing a new one. To use the image intensity cursor over the extracted area, click the Intensity Cursor button on the Extract toolbar. Then click a location on the arrow in the image pane, or drag the vertical black cursor to the left or right across the linescan data. Adjusting linescan appearance You can modify the linescan display by several means: To remove an element from the analysis, right-click the element in the periodic table. Select Inactive. This removes the element from the display. To view the new linescan data, redraw the line on the screen. To increase the signal or avoid peak overlap problems, it might be advantageous to modify the default x-ray line for display in the Element Setup periodic table. 60 NSS Spectral Imaging System Handbook

73 To change the appearance of the linescan data, right-click the linescan pane. In the Graph Properties dialog box, you can change the background color, symbols, and title of the linescan. You can also apply a grid or cursor to the linescan. Log Scale and Thick Lines also affect overlaid linescans (see Overlaying extracted linescans on the image ). Note Toolbar buttons are active for vertical full scale. Analyzing linescans The electron image in the image pane and the linescan data in the linescan pane both use the image intensity cursor. To activate it, click the Intensity Cursor button on the Extract toolbar. As you move the cursor in one pane, the cursor in the other pane moves in a coordinated manner. The X-ray counts at the bottom of the linescan pane are updated when you move the image intensity cursor. NSS Spectral Imaging System Handbook 61

74 Overlaying extracted linescans on the image You can overlay one or more extracted linescans on the image to better see the association between the linescan data and the analyzed area of the sample surface. To overlay a linescan, click the button in the legend at the bottom of the linescan pane that is labeled with the desired element. Here is an example: To remove an overlaid linescan from the image, click the appropriate element button again. You can change the appearance of the overlaid linescans (and the linescans in the linescan pane) by right-clicking the linescan pane and setting Log Scale and Thick Lines in the Graph Properties dialog box (see Adjusting linescan appearance ). The other parameters in the dialog box do not affect the overlaid linescans. To display a legend in the image pane that shows the colors used for each element, use Legend On/Off in the Image menu. (Click the image pane if the Image menu is not present.) The legend will be included if you print a report of the overlaid linescans. Note You can use Export To Word or Export To PowerPoint in the File menu to place the image with its overlaid linescans, the data in the linescan pane, and the element buttons into Microsoft Word or Microsoft PowerPoint, respectively. 62 NSS Spectral Imaging System Handbook

75 You can specify how linescans are overlaid by setting parameters in the General Properties dialog box. Follow these steps: 1. Right-click the image pane. The General Properties dialog box appears. 2. Set the parameters on the Linescan Overlay tab. The options in the Line Profiles box determine where the selected linescans are placed in the image pane: Option On The Linescan Description Places the linescans on the drawn arrow: NSS Spectral Imaging System Handbook 63

76 Option On An Axis Using Smart Axis Description Places the linescans on the horizontal or vertical axis of the image pane, depending on the angle of the drawn arrow: The options in the Display Style box determine whether the selected linescans are overlaid on each other or stacked and how they are scaled: Option Overlaid Description Overlays the linescans on each other so that their peak heights are easier to compare: 64 NSS Spectral Imaging System Handbook

77 Option Stacked Description Offsets the linescans into a stack so that they are easier to see: Scaled Independently When the linescans are stacked, maximizes the Y-axis scale of each to make them easier to see: When this option is not selected, the linescans are displayed using the same Y-axis scale, as shown in the illustration for the Stacked option. To see the effects of your settings without closing the dialog box, choose Apply. NSS Spectral Imaging System Handbook 65

78 3. When you are finished, choose OK. You can also use the keyboard to manipulate the display of the overlaid linescans, as explained in the following table. Key(s) Up arrow Down arrow Shift + up arrow Shift + down arrow Home End Page Up Page Down Effect Expands the scale of the vertical axis of the linescans. Shrinks the scale of the vertical axis of the linescans. Moves the linescans upward (adds a positive offset). Moves the linescans downward (adds a negative offset). Displays the default view of the linescans (with their original scale and without any offset). When the linescans are stacked, toggles between independently scaled axes and all axes scaled to the same maximum value. Toggles between displaying the overlaid linescans on the drawn arrow and on an axis. Toggles between stacked mode and overlaid mode. Quantitative linescans Quantitative data types for identified elements may be selected for extraction. Follow these steps: 1. On the Processing tab in the analysis controls pane, select the quantitative data type in the Map/LS Data Type box. 2. Click the Extract Line Cursor button on the Extract toolbar. 3. Drag the start of the line to the end of the line to extract the image again. To abort, click the Cancel button in the dialog box. Note When any quantitative data type is selected for linescan, Auto Extract is automatically disabled (as Auto Extract is used only for maps). 66 NSS Spectral Imaging System Handbook

79 When Linescan Error Bars is activated on the Processing tab, error bars appear on the spectral graph (± 1 standard deviation). There are no error bars for counts. X-ray mapping New x-ray maps are created, analyzed and extracted maps in Spectral Imaging mode. Creating x-ray maps Note The appearance of a spectrum following extraction is determined by the Processing settings. On the Processing tab in the analysis controls pane, you can select to have the spectrum identified, quant data calculated, and maps extracted automatically following the acquisition. Both the image intensity cursor and the Spectral Imaging extraction cursor are toggled on and off. If both cursors are visible, the mouse controls the image cursor. To use the extraction cursor, turn the image intensity cursor off by clicking the Intensity Cursor button on the Extract toolbar. Follow these steps to create x-ray maps from a Spectral Imaging data set: 1. Open or acquire the Spectral Imaging file. NSS Spectral Imaging System Handbook 67

80 2. Perform an extraction. The spectrum appears. If Auto ID is active (on the Processing tab in the analysis controls pane), the spectrum s peaks are identified. 3. If the spectrum is not identified, click the Identify Spectrum button on the Ident toolbar to identify the elements in the spectrum and mark them in the periodic table on the Element Setup tab. 4. Click the Extract Map Images button on the Extract toolbar. The new map set is created in the top-right pane. To save the maps you extracted, go to Spectral Imaging mode and use Save map file in the File menu. You can remove or add elements from the maps: In the periodic table on the Element Setup tab, mark those elements you want removed as Inactive, and mark elements you want included as Identified. Then click the Extract Map Images button on the Extract toolbar. Analyzing x-ray maps As explained in the next sections, use the Intensity Cursor button, map overlays, and map intensity and colors to help you analyze x-ray maps. 68 NSS Spectral Imaging System Handbook

81 Image intensity cursor NSS includes a coordinated image intensity cursor for analyzing x-ray map sets. Click the Intensity Cursor button on the Extract Toolbar to turn the cursor on or off. When you place the cursor on the electron image or any of the x-ray maps, coordinated cursors move to the same point on the image and all maps. See Analyzing x-ray maps in the Spectral Imaging mode chapter. When you move the cursor to a new point, readouts for the cursor s X-Y position (in pixels) and intensity appear above the electron image and to the right of the x-ray maps (for example, x:177 y:76 i:94). Overlaying an element map on the x-ray image To overlay an element map on the x-ray image, click the element label above the map. See Analyzing x-ray maps in the Spectral Imaging Mode chapter. To adjust the SEM image visibility, right-click the image and modify the transparency in the General Properties dialog box. See Acquiring x-ray maps in the Spectral Imaging mode chapter. Map intensity and color The intensity range of the x-ray map elements appear to the right of the maps and above the image. The image s graylevel values are shown above the image. To adjust the brightness or contrast, right-click the image or map and adjust the brightness and contrast slider bars in the General Properties dialog box or Map Properties dialog box. NSS Spectral Imaging System Handbook 69

82 To change the color of an element, right-click the element s map and select a new color in the Map Properties dialog box. All color changes are stored per element for each user for consistency. Extracting quantitative maps Select counts and quantitative data types for identified elements for extraction. Follow these steps: 1. On the Processing tab in the analysis controls pane, select the count or quantitative data type from the Map/LS Data Type drop-down list box. See the descriptions below. Setting Counts Atomic % Weight % K-Ratio % Net Counts Description The counts in the peak. The atomic percentage of an element in the sample. The calculated weight concentration expressed as a percentage for an element in the sample. The measured net counts divided by the net counts from a pure element sample. The net counts in the peak. 2. Set Kernel Size to Auto. This ensures that there is ample data for quantitative analysis by automatically setting the kernel size based on the total number of counts within the kernel. You can also use manual settings from 1 x 1 to 19 x 19. These affect the accuracy of quantitative results: the larger the size, the less detail that occurs in the map resolution but in a shorter calculation time. 70 NSS Spectral Imaging System Handbook

83 3. Select a detail (speed) setting from the Quant Map Detail drop-down list box. Setting High (Slow) Medium (Medium) Low (Fast) Description Overlaps the kernel areas by one pixel and provides the highest detail (and takes a long calculation time). Overlaps the kernel areas by less than half a kernel width and provides medium detail (and takes a significant calculation time). Tiles the kernel areas with no overlap and provides the lowest level of detail (and takes the shortest calculation time). 4. Click the Extract Map Images button on the Extract toolbar. To abort the extraction, click the Cancel button in the dialog box. To save the map you extracted, switch to Spectral Imaging mode and use Save in the File menu. Note When any quantitative data type is selected for mapping, Auto Extract is automatically disabled. After you use the Extract toolbar buttons to select an area on the image, you must click the Extract Map Images button to extract the map. After you set Map/LS Data Type, you can enable Auto Extract to automatically extract maps. Using Compass Principal Component Analysis (PCA) is commonly used in factor analysis of complex samples. By changing between area and spectral component modes, Compass lets you find the locations of elements in these samples even when they are highly overlapped or entail small signals superimposed on large backgrounds. NSS Spectral Imaging System Handbook 71

84 Compass identifies image locations that have the same spectral fingerprint and extracts compositionally distinct components from a Spectral Imaging data set. You have a choice of advanced statistical analysis algorithms that produce spectrally or spatially simple component maps. Pressing the Compass selector on the Phase toolbar displays compass data. With Compass selected, when you use the Phases button, phases derived from compass data are displayed. Deselecting Compass displays maps and allows the display of phases associated with maps. During acquisitions of spectral image data, if you select the compass display you can see live compass results or live phases derived from the compass data depending on the stage of the Components/Phases button. Compass is an optional software module. It does not appear in the software unless it was purchased and installed. To obtain Compass, contact your sales representative. 72 NSS Spectral Imaging System Handbook

85 Setting properties The Properties command in the Edit menu lets you choose the method for extracting Compass data, change the way Compass calculates the background of the spectra, set a low energy cutoff value, and specify the number of principal components to obtain from a Spectral Imaging data set. NSS Spectral Imaging System Handbook 73

86 The following parameters are available. Parameter Spectral method Area method Calculate Background Using Data (default) Use Internal Model Low Energy Cutoff Number Of Components Description Find spectrally unique areas of the sample without concern for where the spectra come from. Suitable for finding very small areas of composition. Find spectrally unique areas of the sample where results are weighted for spectra close to each other. Uses only the data in the Spectral Imaging file to calculate the background of the spectra. This is the original Compass background calculation routine. It removes the peaks from the cumulative spectral data to get an empirical background. Uses an internal algorithm to calculate the background. This option uses an advanced method to calculate a more realistic low energy background shape, as well as incorporation of absorption edges. This results in an automated peak identification for each component with a more life-like, theoretical background shape than what is obtained using the Calculate Background Using Data option. Enter a spectral energy value (in ev) below which Compass will ignore values. This eliminates inclusion of a noise peak or carbon at the low end of the spectrum. Select the maximum number of significant components from the drop-down list box, or select 0 (Auto) to have the number of components determined automatically. Choose Reset to restore the factory default settings. Choose OK to save the settings and exit the dialog. Choose Cancel to exit without saving changes. Spectrally simple maps Spectrally simple maps are used for finding very small areas with unique composition. If you are interested in seeing how different areas of the same component correlate, use spatially simple maps. 74 NSS Spectral Imaging System Handbook

87 To produce spectrally simple component maps: 1. Acquire a Spectral Imaging data set. 2. Select Compass from the Phases toolbar. 3. Choose Properties from the Edit menu. 4. Set the parameters and then choose OK. 5. If the Area button appears on the Phase toolbar, click it so that the button name changes to Spectrum. 6. Click the Extract map images button on the Extract toolbar to start processing the data. The size and complexity of the data set affects the amount of time it takes Compass to run. Expect several seconds to several minutes of processing time depending on the size and complexity of your spectral imaging data cube. When processing is complete, component maps appear in the top-right pane. Each map represents a unique component in the sample. The first map contains the component that measured furthest away from the data average. The second map contains the component that measured second furthest from the average, and so forth. NSS Spectral Imaging System Handbook 75

88 Click a map to see its spectrum. You can also perform an identification if it was not performed with the processing. Spatially simple maps Spatially simple maps are used to see how different areas of the same component correlate. These maps may miss very small areas. If you are interested in finding very small areas, use spectrally simple maps. To produce spatially simple component maps: 1. Acquire a Spectral Imaging data set. 2. Select Compass on the Phases toolbar. 3. Choose Properties from the Edit menu, select the Compass tab, set the parameters and then choose OK. The Calculate Background Using Data option is more accurate than the Use Internal Model option. However, if the amount of Spectral Imaging data is small, the data background is not well defined and the Use Internal Model option may give better results. Set Number Of Components to 0 (Auto) unless you know how many components you want to find. 4. If the Spectrum button appears on the Phases toolbar, click it so that the button name changes to Area. 5. Click the Extract map image button on the Extract toolbar to start processing the data. When processing is complete, component maps appear in the top-right pane. Each map represents a unique component in the sample. The first map contains the component that measured furthest away from the data average. The second map contains the component that measured second furthest from the average, and so forth. Click a map to see its spectrum. You can also perform an identification if it was not performed with the processing. 76 NSS Spectral Imaging System Handbook

89 Managing Compass data Each map represents a unique component in the sample. The first map contains the component measured furthest from the data average. The second map contains the component measured second furthest from the average, and so forth. Click a map to see its spectrum. Compass processing adds a spectrum (.pcs or.pcsa) and component map (.pcm or.pcma) to the Spectral Imaging data set for each component found. Once created, Compass data files are associated with the Spectral Imaging file from which they were derived. If you reload the Spectral Imaging file, the Compass phase maps and spectra are also loaded. If you move the Spectral Imaging files (.csi,.si,.siref), also move the associated Compass files (.pcm or.pcma, and.pcs or.pcsa). All map editing and coloring options are available while Compass is enabled. Direct-to-Phase analysis If your system is equipped with optional Direct-to-Phase software, choose both Compass and Phases before you start the acquisition. Phase data is extracted and displayed while data is acquired. NSS Spectral Imaging System Handbook 77

90 3-D Visualization Mode 3-D Visualization mode lets you view a three-dimensional representation of various types of map data. First use the appropriate mode to display the desired type of data, and then switch to 3-D Visualization mode to view and manipulate a 3-D image. For example, if you have displayed x-ray map data using Spectral Imaging mode, you can view a 3-D image of the distribution of x-ray count values for an element over the measured sample surface: When you click the element symbol in the upper-left corner of the element s map display box, the 3-D image for the element is generated and displayed. See Selecting a data presentation type for information about the different ways you can display 3-D data. 78 NSS Spectral Imaging System Handbook

91 You can rotate the 3-D image in any direction to see the data from different angles. Simply drag the image in the direction you want to rotate it; the image rotates as you move the mouse. Release the mouse button when you have displayed the desired view of the data. If you release the mouse button while the mouse is moving (and the image is still rotating), the image will continue to rotate. This can help you study the shape of the data from all sides. To move the image to a new location within the pane, hold down the Shift key and drag the image. To enlarge or shrink the image, drag vertically across it with the right mouse button held down. Note Just as you can in Spectral Imaging and some other modes, you can right-click the image pane to set the brightness, contrast and other properties of the image. See Acquiring x-ray maps in the Spectral Imaging mode chapter for more information. The next sections explain how to set parameters that affect how the 3-D image is displayed. Setting 3-D image display parameters You can specify how to display the 3-D image by setting parameters on the 3-D Visualization tab of the Properties dialog box, available through Properties in the Edit menu. See the next sections for descriptions of the parameters. To set the parameters, follow these steps: 1. Choose Properties from the Edit menu. The Properties dialog box appears. NSS Spectral Imaging System Handbook 79

92 2. On the 3-D Visualization tab (shown below), set the parameters as desired. When you change a setting, the 3-D image is updated immediately. (An exception to this is the Combine Electron Image option. You must choose OK in the next step to apply a new setting of this option.) If you choose Apply, the current settings (except for Combine Electron Image) are placed in memory so that you can return to them easily in the next step if desired. 3. Choose OK or Cancel. If choose OK, the current settings are saved. If you choose Cancel, the parameters (except for Combine Electron Image) are returned to the settings they had when last you chose Apply, or to their original settings if you did not choose Apply. Selecting a data presentation type Use the options in the Data Presentation box to specify how to display the 3-D data. The following table describes the available options and shows examples. Option What the Option Displays 80 NSS Spectral Imaging System Handbook

93 Show Surface A warped, interpolated surface showing values at different locations on the sample. This is a conversion of the contour display (see the description of Contour below) to a three-dimensional form that makes it easier to see the values across the sample. NSS Spectral Imaging System Handbook 81

94 Option Wireframe What the Option Displays Black lines running along the intersecting edges of the imaginary planes of the surface plot (see the description of Show Surface above) but without the planes themselves displayed. Contour Contour lines representing constant values. If Show Surface is selected, the contour lines are black. If Show Surface is not selected, the values are indicated by colors defined in the color bar, as in the example below. These lines are similar to the contour lines of a geographical relief map that indicate constant elevation. 82 NSS Spectral Imaging System Handbook

95 Option Profile (Waterfall) What the Option Displays Profile lines representing constant Y-axis values. If Show Surface is selected, the profile lines are black. If Show Surface is not selected, the Z (vertical axis) values are indicated by colors defined in the color bar. Combine Electron Image A three-dimensional gray scale image in which the grays match those in the electron image. Values are indicated by peak heights (Z values) rather than by colors. See the discussion below for more information. NSS Spectral Imaging System Handbook 83

96 The example below shows a use of Combine Electron Image, with the 3-D image rotated to make its X-Y plane coplanar with the electron image. Notice that the use of the grays from the electron image in the 3-D image makes the two similar in appearance. Note You cannot select both Show Surface and Wireframe, or both Contour and Profile (Waterfall). 84 NSS Spectral Imaging System Handbook

97 Specifying a color scheme and color range Specify a color scheme for the 3-D image by selecting an option in the Color Scheme box. The following table describes how each option represents values. Color Scheme Gray Scale Rainbow Banded Blue To Red Description Uses shades of gray along a gradient to represent values. This option is useful for printing 3-D images on a black-and-white or gray-scale printer. Since the values change as the gray shades become darker, it is easy to identify areas of relative low and high value on the printed image. If you print a 3-D image on the same printer, however, the darkness of the resulting printed gray shades will not necessarily correlate with the values. A color that represents a high value, for example, may appear as a light gray on paper. This option is also useful for seeing contrast in the display of data. Uses a gradient of blended rainbow colors to represent values. Uses bands of colors, rather than a gradient of blended colors, to represent values. Uses blended colors from blue to red to represent values. The color bar below the Color Scheme box shows the colors used in the 3-D image. The scale below the color bar indicates the values of the colors. The vertical bars on the color bar indicate the limits of the value range currently used for the colors in the 3-D image. You can change this range by horizontally dragging the vertical bars. This in turn changes the distribution of the colors. If one or both of the vertical bars have been moved away from the ends of the color bar, you can drag the portion between the vertical bars to the left or right. To specify a different color scheme for the data, select the desired option in the Color Scheme box. NSS Spectral Imaging System Handbook 85

98 Clipping the data outside the color range Select Clip Data Outside Color Range if you want data outside the range specified by the color bar not to be displayed in the 3-D image. This results in the display of only the data in the range of interest. The illustrations below show a 3-D image before and after being clipped. Completely visible 3-D image Clipped 3-D image 86 NSS Spectral Imaging System Handbook

99 Selecting a cursor style for the 3-D image Specify a cursor style for the 3-D image by selecting an option in the Cursor Style box. The following table describes the available styles and shows examples (with the 3-D image displayed with reduced opacity to better reveal the cursor). Cursor Style Wireframe Planes Description Outlines of three imaginary orthogonal (perpendicular) planes intersect at the cursor location. Perpendicular lines that pass through that location appear as well. Extended Cross Hairs Perpendicular lines pass through the cursor location and extension lines that connect those lines to the axes. NSS Spectral Imaging System Handbook 87

100 Smoothing the 3-D image Select an option in the Smoothing box if you want the 3-D image to have smoother edges and more blended color transitions. The following illustrations show a 3-D image with no smoothing and with mesh smoothing and shading (Gouraud) smoothing applied. Note that mesh smoothing has a greater effect on peak heights than does shading (Gouraud) smoothing. Unsmoothed image Mesh smoothed image 88 NSS Spectral Imaging System Handbook

101 Shading (Gouraud) smoothed image Setting the opacity of the 3-D image If Show Surface is selected on the 3-D Visualization tab (see Selecting a data presentation type ), you can set the opacity of the 3-D image by dragging the small vertical bar below Opacity % to the left or right. Reducing the opacity lets you see peak shapes through other, closer peaks as though they were translucent. The illustrations below show the effects of changing the opacity from 100% to a lower value. 100% opacity NSS Spectral Imaging System Handbook 89

102 Reduced opacity Displaying an outline box Select Show Outline Box if you want the outer limits of the 3-D image to be indicated by lines that form a bounding box around the image. Here is an example: 90 NSS Spectral Imaging System Handbook

103 X- ay Linescans Mode Use - ay Linescans mode to acquire an electron image and linescan data. After the acquisition, analyze the linescan using the image intensity cursor. You can save and load standard linescans in this mode (with qualifications, as described in this chapter). Setting linescan acquisition properties Follow these steps to set up acquisition properties for the linescan: 1. Click the Edit Acquisition Properties button on the Acquisition toolbar. The Acquisition Properties dialog box appears. 2. On the Linescan tab set the parameters for your acquisition. NSS Spectral Imaging System Handbook 91

104 The following table describes the available properties. Field Number Of Points In Scan Number Of Scans Dwell Time Per Pixel (s) Acquisition Time(s) Total Line Time(s) Acquire Video Scan Stage Use Current Value Measure at First Point Measure at Every Point Description These appear as data points in the linescan. The general rule for a scanning electron microscope is to include at least one point per micrometer. The extract properties for linescan points apply only to Spectral Imaging linescans and do not affect the acquisition number of points in X-ray Linescans mode. The number of scans on the line for a linescan. A greater number of scans increases element intensities. For sensitive samples, increase the scan count and reduce the dwell time. The amount of time the beam is placed at each pixel location. A longer dwell time results in better statistics and longer acquisition times.. The estimated total acquisition time. The amount of time for each line. Acquires a gray scale intensity profile concurrently with the linescans. This profile can then be used as a reference intensity at each linescan point. Moves the stage (instead of the beam) to keep the linescan point in the center of the scan. This greatly increases acquisition time and is normally used in WDS acquisitions only to ensure that the WDS stays in focus throughout the linescan. Uses the last measured beam current. Automatically measures the beam current at the first point in the scan. Measures the beam current at each point. 92 NSS Spectral Imaging System Handbook

105 3. Choose OK. Setting up the linescan elements Before a linescan acquisition, you must have prior knowledge of the sample s elements. If you already know the elements, you can either specify the individual elements as Always Identified in the periodic table on the Element Setup tab in the analysis controls pane or select History on the tab to set the elements as Identified. If you don t already know the elements, you can determine them from a Point & Shoot data set or by acquiring a spectrum. After the acquisition, the elements are marked as Identified in the periodic table. Note Elements in the periodic table do not change when you switch analysis modes. This lets you analyze a spectrum in Point & Shoot mode or Spectrum mode and then switch to - ay Linescan mode using the current element list. Acquiring a linescan Before acquiring a linescan, you should have acquired and identified a spectrum in Spectral Imaging, Spectrum, or Point & Shoot mode. Make sure the elements and Acquisition Properties have been defined. To acquire a linescan: 1. Switch to - ay Linescans mode. 2. Acquire an image if the desired image is not already displayed. 3. Draw a line across the image. To change the length or direction of the line, drag either end of the line. To move the line, move the mouse pointer over its center and then drag the line. You can replace the current line by drawing a new one by dragging. NSS Spectral Imaging System Handbook 93

106 To adjust the contrast and brightness of the image, right-click it and use Contrast and Brightness on the Image View tab. 4. Start the acquisition using the Start Acquisition button. Analyzing a linescan As a linescan is acquired, the data appears in the top-right pane: To analyze the linescan, drag either the image cursor or the Linescan cursor. Both cursors are coordinated to move to the same point. The count values for each displayed element are shown below the linescan graph. Colored lines or symbols represent each element. The spectrum stored at the current cursor location appears in the spectrum pane. 94 NSS Spectral Imaging System Handbook

107 Overlaying acquired linescans on the image You can overlay the linescans on the image to better see the association between them and the sample surface just as you would overlay extracted linescans in Spectral Imaging mode. See Overlaying extracted linescans on the image in the Spectral Imaging Mode chapter for details. Adjusting linescan appearance You can modify the linescan display by several means: To remove an element from the analysis, right-click the element in the periodic table and choose Inactive. Reselect the line to extract, or redraw the line to refresh the graph. This element is removed from the display. To change the appearance of the linescan data, right-click the linescan. The Graph Properties dialog box appears: In this dialog box you can change the background color, symbols, and title of the linescan. You can also apply a grid or cursor to the linescan. To increase the signal or avoid peak overlap, it might be advantageous to modify the default x-ray line for display in the periodic table on the Element Setup tab in the analysis controls pane. A better way to do this is to use quantitative linescans. To view the new linescan data, redraw the line on the screen. Note Toolbar buttons are active for vertical full scale. NSS Spectral Imaging System Handbook 95

108 Quantitative linescans You can select quantitative data types for identified elements for acquisition. Follow these steps: 1. On the Processing tab in the analysis controls pane select the quantitative data type from the Map/LS Data Type drop-down list box. The following table describes the available types. Type Counts Atomic % Weight % K-Ratio % Net Counts Description The counts in the peak. The atomic percentage of an element in the sample. The calculated weight concentration expressed as a percentage for an element in the sample. The measured net counts divided by the net counts from a pure element sample. The net counts in the peak. 2. Click the Extract Line Cursor button on the Extract toolbar. 3. On the image drag from the start of the line to the end of the line to specify the location of acquisition. 4. Click the Start Acquisition button on the Acquisition toolbar. Note When any quantitative data type is selected for a linescan, Auto Extract is automatically disabled on the Processing tab. When Linescan Error Bars is selected, error bars appear on the spectral graph (± 1 standard deviation). Note There are no error bars for counts. 96 NSS Spectral Imaging System Handbook

109 Electron Imaging Mode You can acquire, load and save electron image files in Electron Imaging mode. These files are stored with a.tif file extension. You can also export these images to other programs, such as Microsoft PowerPoint. Electron Imaging mode Setting imaging acquisition properties Follow these steps to set the acquisition properties for electron imaging: 1. Click the Edit Acquisition Properties button on the Acquisition toolbar. The Acquisition Properties dialog box appears. NSS Spectral Imaging System Handbook 97

110 2. On the Imaging tab set the parameters for your acquisition. The following properties are available: Field Resolution Frame Time (s) Dwell Time (µs) Description The size of the image in pixels. A higher resolution produces greater image detail and increases acquisition time. Resolution values for X versus Y are determined by the aspect ratio of the scanned area setup in the Image Calibration. A longer frame time increases the acquisition time and reduces image noise. A shorter frame time can result in blurred and streaked images. Optimum values depend on microscope and detector type. Select Fastest to automatically select the fastest available frame time. The amount of time the beam is placed at each pixel location. A longer dwell time results in better statistics and longer acquisition times. A shorter dwell time might cause a blurred or streaked image. 98 NSS Spectral Imaging System Handbook

111 Field Number Of Frames Acquisition Time (s) Use Input 1 and Use Input 2 Description The number of frames to be acquired or averaged. A frame is one complete scan from the upper-left corner to the lower-right corner of the map. For beam-sensitive samples, increase the number of frames and decrease the dwell time. If you type 0 in this field, you must stop acquisitions manually by clicking the Stop Acquisition button or Abort Acquisition button on the Acquisition toolbar. The estimated the total acquisition time. Specify the channel (for example, SEI or BEI imaging detectors of your microscope) from which the image data is acquired. Availability of a second image input depends on the microscope. 3. Choose OK. Acquiring an electron image By default, NSS acquires an averaged electron image rather than a live image. Before acquisition, make sure the acquisition properties are properly set. To acquire an electron image: 1. Switch to Electron Imaging mode. 2. On the Acquisition toolbar, click the Acquire An Averaged Electron Image button to acquire an averaged electron image, or click the Start Acquisition button to acquire a live electron image. Either wait until the acquisition terminates according to the criteria set on the Imaging tab of the Acquisition Properties dialog box, or click the Stop Acquisition button on the Acquisition toolbar. The image acquisition will stop at the end of the current frame. To pause the acquisition, click the Pause Acquisition button. The image acquisition pauses at the completion of the current frame. To resume, click the Pause Acquisition button again. NSS Spectral Imaging System Handbook 99

112 To stop the acquisition at the end of the current line, click the Abort Acquisition button. The data will not be saved. To adjust the image s contrast and brightness, right-click the image. The General Properties dialog box appears: On the Image View tab, adjust the Contrast and Brightness slider bars. Choose OK when you are finished. 100 NSS Spectral Imaging System Handbook

113 Preparing for an Analysis When preparing for an analysis, you can select elements for it, adjust for oxides, specify the identification sensitivity, and set the processing parameters. Selecting elements for analysis Following a peak identification, the software creates a list of possible elements in the periodic table on the Element Setup tab. Here is an example: You can refine these results to search for or identify specific elements or exclude other elements. Elements marked as Identified are used in quantifications, x-ray maps and linescans. Note The periodic table does not change when you switch analysis modes. This lets you analyze a spectrum in one mode and then switch to another mode and use the same identification results. Any edits to the periodic table are stored in the project template. NSS Spectral Imaging System Handbook 101

114 Highlighting elements for analysis The next sections explain how to highlight elements in the periodic table for analysis. Automatic selection The software can automatically identify the peaks in spectra. It scans for all elements in the periodic table except for those marked Excluded. Hydrogen, helium, lithium, the noble gases and the actinide and lanthanide series elements are excluded by default. When analysis is complete, the results appear in the periodic table. To identify and label peaks, click the Identify Spectrum button Ident toolbar. on the Manual selection To edit an element s status, right-click the element in the periodic table and choose the desired status from the pop-up menu. You can also click the element repeatedly until it is the color that corresponds to the status you want to apply. The following labels and colors are available. Label Color Meaning Inactive (default) light gray The element was not identified. Identified bright green The element was identified in the sample. Excluded dark gray The element will not be included in any identification. Choose this label before analysis. Always Identified magenta The presence of the element will be determined. Choose this label before analysis. 102 NSS Spectral Imaging System Handbook

115 Label Color Meaning Possible orange The element could be in the sample but was not confirmed during automatic peak identification. Selected red outline The element is currently selected for operation. Near cyan outline The element s KLM lines are close to the energy cursor in the spectrum pane. This changes as you move the cursor. Setting advanced element parameters Using the Advanced Element dialog box, you can obtain information elements that are included in a compound. You can correct for elements that are chemically bound as oxides, nitrides, borides, carbides, or fluorides. This feature provides information about a compound, the individual element being analyzed, and the binding element. 1. In the periodic table on the Element Setup tab, click the bound element and then choose Advanced. 2. When the Advanced Element dialog box appears, choose how the quantification is to be applied to this element. Calculated To obtain a calculated concentration of an individual element or a compound including Weight % for the individual element, the binding element, and the compound as a whole, choose Calculated. By difference If you are using a quant method that employs full standards, you can choose By difference. With this application, the analyzed element weights are subtracted from the total sample weight, NSS Spectral Imaging System Handbook 103

116 and the difference is reported as the weight of the element you selected. This option can be used for individual elements only. Fixed In samples that have an element of known concentration, you can choose a fixed percentage of the total sample weight to be reported as the Weight % of the element. For this option, enter the fixed percentage in the text box. This option can be used for individual elements only. 3. To analyze a compound, choose Use Compound and then select the binding formula from the Compound Formula list box. 4. To analyze an element using a standards-based method, choose Use Derivative References. 5. Where overlapping peaks are expected in standards-based data, leave both Use Compound and Use Derivative References unchecked. 6. Identify the EDS detector or WDS spectrometer that is the data source for the spectrum and element you are analyzing. 7. If you chose a quantification method that uses Cliff-Lorimer, select Ratio Element if this element is the ratio element. 8. When you are finished, choose Close to save the element analysis information and return to the Element tab. Specifying lines for quantification and display NSS identifies which lines are used for spectral imaging, mapping linescans and quantitative analysis based on the element and the accelerating voltage. If you decide to use a different line, use the Lines Utilized drop-down list boxes on the Element Setup tab to select a line. Some elements might have only one selection. Usually the same line is used for quant and linescan mapping. However, if a line is too close to the accelerating voltage, set Overvoltage on the 104 NSS Spectral Imaging System Handbook

117 Analysis Setup tab in the analysis controls pane to a higher voltage for quant data. To exclude an element from quantitative results when it is identified as present in the sample (for example, elements for anti-charging coatings), set Quant in the Lines Utilized box on the Element Setup tab to Absent. If your system has the needed capability, you can create maps and linescans for multiple lines by setting Mapping to All. In Spectral Imaging mode you can also select line sums. For example, the available selections for copper, which has a K-line and L-line, are K, L, K+L and All. The K+L data will be summed during the extraction to generate the desired map or linescan. The All setting will display both the K and L line data. Mapping Energy Range in the periodic table identifies the range of energies that you want included in the element s map. If the default energy range is too wide or the range overlaps some other identified element s mapping range, enter an adjusted range that yields more specific maps. Clicking in either text box enables editing within both text boxes and dragging of the dashed vertical lines within the spectrum pane to set the range limits. Each selection in the Mapping drop-down list box has a separate associated energy range. To reset all regions to their default energy ranges, click the Reset ROIs button. Note Your changes are permanent and applied to future analyses in the current project until the history is cleared. Excluding elements from quantitative results only Follow these steps to exclude an element from quantitative results: 1. In the periodic table, click the element you want to exclude. 2. Set Quant in the Lines Utilized box to Absent. NSS Spectral Imaging System Handbook 105

118 Excluding elements from peak identification analysis To exclude an element from the analysis, in the periodic table right-click the element you want excluded and choose Excluded from the pop-up menu. You can also click the element repeatedly until it is set to Excluded (dark gray). The L, A and n boxes in the periodic table all work the same to toggle excluded lanthanide, actinide and noble gas elements, respectively. When you click one of the L, A or n boxes, the elements in that group are toggled according to these rules: If an element was excluded before, it changes to Inactive. If an element was anything other than Excluded, it becomes Excluded. Helium, hydrogen and lithium are always Excluded regardless of how you mark them, because those elements have no detectable x-ray lines. Clearing identification results The Clear button in the Element Setup tab has two functions: To clear the identification results from the one spectrum currently displayed, make sure History is not selected and then choose Clear. To clear the cumulative identification results from all previous analyses in the project and the current spectrum, select History and then choose Clear. Viewing the history periodic table The history periodic table displays the cumulative identification results from all previous spectra within the project. Select History on the Element Setup tab to view the cumulative identification results for the open project. Results from an identification are added to the history when you do any of the following: Acquire and identify peaks in a spectrum Run a quantitative analysis Acquire or extract a linescan Acquire or extract maps Close the project 106 NSS Spectral Imaging System Handbook

119 When History is selected, those elements in the history are used for analysis. When History is not selected, only the current spectrum elements are used. To clear the entire history for the project, select History and then choose Clear. Specifying identification sensitivity On the Analysis Setup tab in the analysis controls pane, set Ident Sensitivity to how large a peak must be before it is detected. A larger value reduces the number of element labels on the spectrum by making the peak detection algorithm less sensitive. The default value is 5. The peak-finding algorithm smoothes the spectrum and searches it for local peaks. If the ratio of the height of a peak to the error at the same point exceeds the Ident sensitivity factor, the peak is identified. Note The other parameters on the Analysis Setup tab deal with quantitative analysis or Spectral Match. See the Quantifying Spectra chapter or Identifying Spectra With Spectral Match chapter. NSS Spectral Imaging System Handbook 107

120 Setting processing parameters The parameters on the Processing tab in the analysis controls pane let you specify the types of identification and analysis that will automatically take place after data is acquired. Feature Auto ID Quant Match Instructions If Auto ID is active, the software identifies the spectrum peaks with each acquisition. If Auto ID is not active, you must click the Identify Spectrum button on the Ident toolbar to see identification results. When Quant is active, the software calculates the quant information and displays it on the Quant Results tab. If Quant is active, Auto ID must be active unless you are in History mode. If Quant is inactive, you can still do a quantification by identifying the elements to quantify and clicking the Quantify Spectrum button on the Ident toolbar. When Match is active, the software searches the specified databases after an acquisition or extraction. When Match is inactive, you can still perform a search by clicking the Spectral Match button on the Ident toolbar. See the Identifying Spectra With Spectral Match chapter for information about Spectral Match. 108 NSS Spectral Imaging System Handbook

121 Feature Auto Extract Map/LS Data Type Linescan Error Bars Kernel Size Quant Map Detail (Speed) Instructions When Auto Extract is active in Spectral Imaging mode, the maps of identified elements are created immediately following an extraction. Quantitative maps are active in Spectral Imaging mode. Linescans are active in Spectral Imaging mode and X-ray Linescans mode. Counts and quantitative data types for identified elements may be selected for extraction. When any quantitative data type is selected for a map or linescan, Auto Extract is automatically disabled. After you use the extraction tools to select an area on the image, you must click the Extract Map Images button to extract the map. You can enable Auto Extract to automatically extract maps after selecting Map/LS Data Type. When Linescan Error Bars is selected, error bars appear on the spectral graph (± 1 standard deviation). There are no error bars for counts. When Kernel Size is set to Auto, the system makes sure that there is ample data for quantitative analysis by automatically setting kernel size based on total number of counts within the kernel. You can also use manual settings from 1 x 1 to 19 x 19. These affect the accuracy of quantitative results: the larger the size, the less detail that occurs in the map resolution but in a shorter calculation time. Extraction speed settings are as follows: High (Slow) overlaps the extraction areas by one pixel and provides the highest detail. Medium (Medium) overlaps the extraction areas by less than one pixel and provides medium detail. Low (Fast) tiles the extraction areas with no overlap and provides the lowest level of detail. NSS Spectral Imaging System Handbook 109

122 Identifying Peaks Manually Although NSS automatically identifies peaks following or during an acquisition, several tools are included for manual peak identification: Peak ID lines following automatic identification or by clicking the Identify Spectrum button on the Ident toolbar. KLM marker scrolling using the left and right arrow keys. Element scrolling using the up and down arrow keys. Mouse- and keypad-driven spectrum shifting and scrolling. Standard, logarithm and outline spectral display. Note The identification sensitivity controls how strong a peak must be to be automatically identified. See Specifying identification sensitivity in the Preparing for an Analysis chapter. Locating possible elements NSS displays lines that locate each peak in the spectrum when KLM markers are hidden. The automatic peak identification function labels each identified peak. Use these markers as a starting point for manual peak identification. The Elements toolbar contains tools for labeling peaks and displaying KLM lines. Viewing KLM lines You can view the KLM lines in two ways. The first is on the Elements toolbar: Click the KLM Lines On/Off button. The KLM lines appear on the spectrum for the selected element. From here you can click other elements or scroll through the periodic table using the arrow keys. 110 NSS Spectral Imaging System Handbook

123 The second is in the Spectrum Properties dialog box and allows for more customization: 1. Right-click the spectrum pane. The Spectrum Properties dialog box appears. 2. On the KLM Page tab select Show KLMs. Here you can adjust the types and range of lines you want displayed. 3. Choose OK. 4. In the periodic table on the Element Setup tab, click the element. The KLM markers appear in the spectrum. The bottom-left corner of the spectrum pane shows the symbol of the current element that has its KLM markers displayed. Use the arrow keys to scroll through the periodic table and see the KLM lines for each element. Scrolling KLM lines with keyboard arrow keys You can scroll KLM markers by using the arrow keys on your keyboard. Here is an example showing KLM lines displayed for tungsten: NSS Spectral Imaging System Handbook 111

124 To display the KLM markers, click the KLM Lines On/Off button on the Elements toolbar. The atomic symbol for the element with its KLM lines displayed appears in the lower-left corner of the spectrum pane. The Next Element and Previous Element buttons scroll the KLM markers by atomic number. You can also use the left and right arrow keys on the keyboard: The Element Search Up and Element Search Down buttons use the energy reading at the energy cursor to search an NSS database of element lines and display candidate KLM lines for each element found. You can also use the up and down arrow keys. A low-pitched beep signals that you have reached the end or the beginning of the possible elements. Scrolling for KLM lines on the spectrum You can place the energy cursor at a point on the spectrum and then search for elements that have KLM lines higher or lower than that point. To search for KLM lines: 1. Click the spectrum to place the energy cursor at a point of interest. 2. Click the Element Search Down or Element Search Up button, or press the up or down arrow key on the keyboard. A high-pitched beep means the software found another element near the cursor. The element is outlined with a dotted red border in the periodic table and its KLM lines appear on the spectrum. The elements with KLM lines near the cursor are outlined in cyan on the periodic table. A low-pitched buzz means you have reached the end of the periodic table from that cursor point. 112 NSS Spectral Imaging System Handbook

125 Finding possible elements at a peak NSS provides several aids in locating an element at a peak, including peak ID lines, labels and KLM lines. To view a list of possible elements, place the energy cursor on the peak. Those elements with a K, L or M energy level near the cursor position are outlined with a cyan border in the periodic table. You can change any of them to Identified if they match the element you are seeking. Some knowledge of the sample and other element peaks is useful in determining which elements should be identified manually. Customizing x-ray line energies and intensities Use Element X-ray Lines in the Spectrum menu (whenever the spectrum pane is active) to add or adjust element x-ray line energies and relative intensity values. This can improve manual peak identification when lines are closely spaced. Also, since x-ray line energies and intensities are used to determine counts with the Gaussian method, better quantitative analysis results (element weight % concentrations) can be obtained with accurately adjusted values. Follow these steps: 1. Choose Element X-ray Lines from the Spectrum menu. The X-ray Lines dialog box appears: NSS Spectral Imaging System Handbook 113

126 2. Specify the element whose energies or intensities you want to adjust. You can type the element symbol in the Element text box. You can also click the down arrow button to the right and then click the desired element in the periodic table that appears. 3. Specify the lines series you want to work with. You can type the line letter (K, L or M) in the Line Series text box or select a letter from the drop-down list box. The lines in the specified series are listed along with their energies and intensities as currently stored in the database. 4. Select the line whose energy or intensity you want to adjust by clicking it in the list. The selected line s current values appear in the Selected Line box. 5. Type the desired values in the Energy and Intensity text boxes, and then click the button. For most elements the energies are well known; normally only the intensity is adjusted. However, you may find some differences in energies when comparing different published tables. The new information appears in the list. 6. If you want to add a line to the list (and to the database), select it from the Line drop-down list box, enter the desired energy and intensity values, and then click the button. 7. If you want to delete a line from the list (and from the database), select it and then click the button. 114 NSS Spectral Imaging System Handbook

127 8. If you want to restore the default values for the listed lines, click the Default Values button. 9. When you are finished customizing the x-ray line energies and intensities, choose OK to make your changes permanent. Choose Cancel if you don t want to change the database. Labeling peaks After you have manually identified a peak, you might want to label it on the spectrum for reference and reports. The Peak ID labeling options are in the Spectrum Properties dialog box. You can use Auto ID on the Processing tab in the analysis controls pane to specify whether to display peak labels during or after an acquisition automatically. See Setting processing parameters in the Preparing for an Analysis chapter. Labeling all peaks To label all peaks: Click the Identify Spectrum button on the Ident toolbar. Editing the label for a specific peak Follow these steps to edit the label for a specific peak: 1. Double-click a peak label. Here is an example: NSS Spectral Imaging System Handbook 115

128 A drop-down list box appears containing the possible elements for that peak: 2. Select an element. 3. Choose OK. Adding peak ID labels for a specific element To add peak ID labels for a specific element, click the element in the periodic table on the Element Setup tab until it is bright green. You can also right-click the element and choose Identified from the pop-up menu. If KLM lines are displayed, you can also click the element in the periodic table and then click the Label Peak button on the Elements toolbar. (You can turn the display of KLM lines on or off with the KLM Lines On/Off button on the Element toolbar or with Show KLMs on the KLM Page tab in the Spectrum Properties or Properties dialog box.) You can also right-click the element and choose Always Identified from the pop-up menu. Labels appear for all the element s KLM lines. Removing peak labels You can remove a single peak label or all the peak labels for one element. To remove a single peak label: 1. Click the label. 116 NSS Spectral Imaging System Handbook

129 2. Press the Delete key on the keyboard. To delete all the peak labels for one element: 1. Right-click the element in the periodic table. 2. Choose Inactive from the pop-up menu. Searching for KLM lines and adding labels Follow these steps to use the keyboard to search for KLM lines and add labels: 1. Click the peak of interest to place the cursor over it. The elements that have a line near the cursor location are labeled as Near (cyan) in the periodic table. The currently selected element is outlined in the table with both red and light blue. 2. Use the keyboard to move to another element. Press the up arrow key to move to the next Near element in order of increasing atomic number. Press the down arrow key to move to the next Near element in order of decreasing atomic number. Press the right arrow key to increase the atomic number by one. Press the left arrow key to decrease the atomic number by one. Note Excluded elements are skipped. The KLM lines appear in the spectrum pane as you move from element to element. 3. To add a label for the selected element, press the space bar on the keyboard. NSS Spectral Imaging System Handbook 117

130 Changing the appearance of peak labels Follow these steps to change the appearance of peak labels: 1. Right-click the spectrum. 2. When the Spectrum Properties dialog box appears, on the Peak Page tab set Labels to Short or Long. The Short option displays only the element symbol. The Long option displays the element symbol and the KLM lines. Note The None option turns off all Peak ID labeling. If you try to label an individual peak, it will not appear on the spectrum. 3. Click the Peak Label Font button. 4. When the font dialog box opens, set the font parameters as desired and then choose OK. 5. Choose OK to close the Spectrum Properties dialog box. Energy cursor (kev) To turn the energy cursor on, click the Energy Cursor On/Off button on the Elements toolbar. The energy and counts appear in the upperleft corner of the spectrum pane. 118 NSS Spectral Imaging System Handbook

131 Spectral Match Spectral Match lets you identify a spectrum by searching a database of spectra. Using the Database Manager Access the Spectral Match Database Manager by clicking the Match Database button on the Analysis Setup tab for your spectrum. The manager allows you to select the database to search and to manage your databases. When the Database Manager dialog box opens you can create a new data base, add spectra to an existing data base and organize your databases into groups. When you wish to create a new data base, you can import and modify an existing database, create a database from a spectrum, create one manually, or create one from a CSV file. NSS Spectral Imaging System Handbook 119

132 Use the Manual button to enter a known composition for a compound. Parameter Match Name Acceleration and Zero Width voltages Composition Description Enter a descriptive name for the new compound. Enter an acceleration voltage in kv and a width for the zero peak in ev that corresponds to the values for unknown compound spectrum you are matching. Compositions can be entered as weight percent values, atomic percent values, or number of atoms from a stoichiometric formula for each element. After you enter the composition click Show Spectrum to place the simulated data into the spectral display so it can be examined. If you wish to use the simulated spectrum for matching, click Define For Match. If the simulated spectrum is not correct, you can use Clear to erase all composition elements. Once the elements are deleted, a different compound composition can be entered. Use Close to return to the Database Manager. From CSV allows you to select a compound composition from a library of compounds in a CSV (comma separated variable) file format. 120 NSS Spectral Imaging System Handbook

133 Note A CSV file named Match Library.csv is supplied with the NSS system. It is located in the MatchDatabases directory with a backup copy in the bin directory. As necessary, you can change the acceleration voltage or zero peak width values to correspond to the expected values for the spectrum being matched. The zero width value can be found in the Details dialog of the unknown spectrum s attributes. To define a spectrum for a compound in the library, select a compound and then click Define For Match. When only one compound is selected, the Show Spectrum button is active so that the spectrum can be placed in the spectral display for examination. If you wish to use more than one compound from the library, press and hold the CTRL key and then click all of the compounds you wish to use. Once you have selected all the compounds, click Define For Match. Use Close to return to the Database Manager. Setting up a search Follow these steps to search the spectrum displayed in the spectrum pane against a database of spectra: 1. To select the spectral database to search, click the Match Database button on the Analysis Setup tab in the analysis controls pane. NSS Spectral Imaging System Handbook 121

134 2. When the Database Manager appears, select the desired database from Current Database drop-down list box and then choose Close. 3. Specify the maximum number of database spectra to find by setting Max. Number Of Match Results on the Analysis Setup tab. 4. Use Low and High on the Analysis Setup tab to specify the minimum and maximum energy, respectively, used to compare the spectra. 5. Use Chi-square Cutoff to specify a threshold that determines how similar a spectrum from the database must be to the unknown sample spectrum to be considered a match. The lower the calculated Chi-squared value between the sample spectrum and a database spectrum is, the more similar the two spectra are, with a perfect match having a value of 0.0. A greater Chi-squared value indicates a poorer match, so using a larger setting loosens the requirements for the identification. If the lowest calculated value for all the database spectra is greater than the specified value, the sample spectrum is considered unknown to the database. 122 NSS Spectral Imaging System Handbook

135 6. Click the Spectral Match button on the Ident toolbar or choose Match from the Spectrum menu (whenever the spectrum pane is highlighted). The results appear on the Match Results tab in the bottom-right pane. Here is an example: The smaller the match (Chi-squared) value on the Match Results tab, the closer the match spectrum from the database is to the unknown spectrum. For a more direct comparison you can overlay match spectra on the current spectrum by checking the match spectra you want to overlay. (The Match option on the Compare Information tab in the access controls pane is selected automatically when you click the Spectral Match button.) The overlaid match spectra clear any currently displayed comparison spectra. The comparison normalization settings are used to scale the spectra as needed. You can click the Show All button to check all of the match spectra; click the Clear All button to remove all the overlaid match spectra. You can include the results in tabular form in reports by selecting Match Results on the Spectra tab or Point And Shoot tab in the Page Setup dialog box. NSS Spectral Imaging System Handbook 123

136 124 NSS Spectral Imaging System Handbook As with other kinds of results, you can use Export To Word or Export To PowerPoint in the File menu to export the match results to Microsoft Word or PowerPoint and print them (if those programs are installed).

137 Quantifying Spectra A quantitative analysis is performed on an acquired spectrum either from the current automatic peak identification or by performing a manual peak identification. Quantitative analyses are always created from the current periodic table on the Element Setup tab. Preparing the quantitative settings To prepare the quantitative settings, select the quant fit method, define standards (if using a quant fit method with standards) and select a matrix correction algorithm. See the next sections for details. Quant fit method Note On the Analysis Setup tab use Quant Fit Method to select a method to calculate k-ratios. You can switch from one method to the other and click the Quantify Spectrum button on the Ident toolbar again to compare results between methods. The following table describes the available methods. Feature Gaussian Without Standards Filter Without Standards (default) Gaussian With Standards Instructions Uses Kramer s Law to calculate and subtract a theoretical background. This would be a preferred method if you don t have a reference for the peak (for example, radon). Applies a digital top hat filter to remove the background from a spectrum before fitting the spectrum to the reference spectra provided by the software. Uses Kramer s Law to calculate and subtract a theoretical background. This is similar to Gaussian Without Standards except that you use standards developed on your own equipment. See Developing quantitative analysis standards later in this chapter. NSS Spectral Imaging System Handbook 125

138 Feature Filter With Standards Instructions Applies a digital top hat filter to remove the background from a spectrum before fitting the spectrum to the reference that you developed on your own equipment. See Developing quantitative analysis standards later in this chapter. You can use Element X-ray Lines in the Spectrum menu to add or adjust x-ray line intensities for performing quantitative analysis with Gaussian fitting. See Customizing x-ray line energies and intensities in the Identifying Peaks Manually chapter for more information. Matrix correction Matrix correction converts measured peak intensities into quantitative results. These methods calculate differences between elements in pure form and elements in composition. If you use matrix correction, select a calculation method. The following table describes the available corrections. Correction Proza (Phi-Ro-Z) ZAF Cliff-Lorimer Without Absorbance Description Calculates the depth distribution of x-rays emitted from the sample. This method is used in SEM applications, especially for light elements in a heavy matrix. PROZA corrections are based on the methods of Bastin, et al. Corrects peak intensities for average atomic number (Z), absorption (A) and fluorescence (F) factors. Provides metallurgical and biological thin section (MBTS) corrections based on relative elemental K factors (Cliff-Lorimer factors). The correction assumes there is no absorption. Use the Advanced Element dialog box to identify the ratio element. This method is used in TEM/STEM applications. 126 NSS Spectral Imaging System Handbook

139 Correction Cliff-Lorimer With Absorbance Description Same as above, but corrects for absorption in thicker samples. This method requires knowledge of the sample density. Use the Advance Element dialog box to identify the ratio element. This method is used in TEM/STEM applications. Initial quantitative analysis When you acquire spectral data, NSS identifies the elements in the spectrum. An identification (either automatic or manual) marks them in the periodic table on the Element Setup tab in the analysis controls pane. Quantitative analysis uses these identified elements. To change the settings that the software uses for quantification, use the Analysis Setup tab. You can also set the software to automatically perform a quantitative analysis following an automatic identification. In the periodic table, right-click any elements you want excluded in your quantitative analysis results and choose Inactive. Automatic quantification Follow these steps to perform an automatic quantification: 1. Click the Identify Spectrum button on the Ident toolbar. 2. Click the Quantify Spectrum button on the Ident toolbar. Automatic quantification for a series of spectra Follow these steps to perform an automatic quantification for a series of spectra: 1. On the Processing tabbed dialog, choose enable Auto ID and Auto Quant. 2. Choose Quant Analysis from the Batch Processing menu. A dialog box appears. NSS Spectral Imaging System Handbook 127

140 3. Locate and select the files you want to quantify. Hold down the Ctrl key or Shift key when selecting additional files. 4. Choose Open. 5. When the dialog box opens, enter a file name for saving the quant results. 6. If you wish to create a CSV file containing the results, choose Save from the NSS toolbar. A message shows the progress of the quantification. Manual quantification Follow these steps to perform a manual quantification: 1. Mark the elements on the Element Setup periodic table as needed. An elemental energy line (K, L or M) is preselected by the software based on the beam energy. To change to a different elemental line, select the new line in the Quant drop-down list in the Lines Utilized box. If an element is present in the sample, but you wish to exclude it in the quantitative calculation (for example, a coating material), set Quant to Absent. 2. Choose Properties from the Edit menu. The Properties dialog box appears. 3. On the Quant Results tab, check the items you want to appear in the quantitative analysis results. 128 NSS Spectral Imaging System Handbook

141 Specifying quantitative output The Quant Results tab on the Properties dialog (available from the Edit menu) allows you to specify the information you wish reported in the quantitative analysis results. The following items are available. Item Total Weight % Output X-ray Lines Output Precision Line Type Net Counts Net Count Error Intensity Intensity Error Source Description The total weight percentage in the sample for quantitative analysis. The x-ray lines to display for quantitative analysis. The level of precision in which the data is reported. The K-shell, L-shell or M-shell of the x-ray line. The net counts in the peak measured for an x-ray line. The error shown as plus or minus one standard deviation for the measured net counts. The net counts divided by the livetime divided by the beam current to obtain counts per second per nanoampere. The error in the calculated intensity shown as plus or minus one standard deviation. The source of the net count measurement indicated by EDS (standardless EDS), EDS STD (EDS from a standard) and WDS (WDS measurement). NSS Spectral Imaging System Handbook 129

142 Item K-ratio K-ratio Error Z Factor A Factor F Factor ZAF Factor K Factor Weight % Weight % Error Normalized Weight % Norm. Weight % Error Atom % Atom % Error Chemical Formula Compound % Normalized Compound % Number Of Cations Standard Name Description The ratio of the measured net counts divided by the net counts from a pure element sample. The one-standard-deviation error in the K-ratio. The atomic-number correction for an x-ray line. The absorption correction for an x-ray line. The fluorescence correction for an x-ray line. The product of the atomic-number correction (Z), the absorption correction (A) and the fluorescence correction (F) for an x-ray line. The Cliff-Lorimer K factor for an x-ray line. The calculated weight concentration expressed as a percentage for an element in the sample. The one-standard-deviation error for the Total Weight % value. The calculated weight concentration for an element normalized so that the total weight concentration for all elements equals the Total Weight % value. The error in the normalized weight concentration shown as plus or minus one standard deviation. The atomic percentage of an element in the sample. The error in the atomic percentage shown as plus or minus one standard deviation. The chemical formula used for calculating an element s concentration by stoichiometry. The percentage of the compound in the sample represented by the chemical formula. The percentage of the compound in the sample normalized, so the total of all compound percentages equals the Total Weight % value. The number of cations for an element based upon a number of oxygen atoms defined by the user. The base name of the standard used to obtain quantitative results for an x-ray line. When you are finished, choose OK to accept the output settings and close the dialog. Choose Cancel to exit the dialog without changing settings. 130 NSS Spectral Imaging System Handbook

143 Once the output settings are in place, you can choose the Quantify Spectrum button on the Ident toolbar to begin quantifying your data. When the software completes the analysis, click the Quant Results tab in the analysis controls pane to view the results. Rerunning quantitative analysis Follow these steps to requantify a spectrum: 1. Edit the Element Setup periodic table in the analysis controls pane as necessary. 2. Click the Quantify Spectrum button on the Ident toolbar. The Quant Results tab information changes to reflect the new quantitative analysis. Note For proper quantitative analysis results, click the Quantify Spectrum button any time you change the Element Setup periodic table. Ratioed elements To select a ratio element, you must be using one of the Cliff-Lorimer matrix correction methods. Specify the matrix correction on the Analysis Setup tab. Only one element can be a ratioed element. Follow these steps: 1. Select the element you want to ratio in the Element Setup periodic table. 2. Choose Advanced. 3. Check the Is Ratio Element box. This normalizes the k-ratio for that element to 1. Calculating weight percentage You can specify the weight of an element within a sample as a percentage or have the weight calculated. Follow these steps: 1. On the Element Setup periodic table, click the element for which you want to define the weight. NSS Spectral Imaging System Handbook 131

144 2. Choose Advanced. 3. Select Calculated or Fixed in the Quantification Of Weight % box. If you select Calculated, the software will calculate the percentage of the sample and show the percentage in the Quant results. If you select Fixed, enter a fixed percentage. The software will assume the sample contains that percentage of the element and take that into account when figuring the quantitative results for other elements. 4. Choose Close. Developing quantitative analysis standards Usually running a quantitative analysis without standards is sufficient to meet the needs of most analyses. However, in some situations you may prefer to develop your own standards. Developing your own standard can be more accurate, since the standard and the samples are acquired under the same conditions (assuming that the take-off angle and the beam current are the same between runs). Use the following guidelines to make your standards as accurate as possible. Aim for 10,000 integrated counts in the standard s peak. This would result in a one percent error rate. Limit the dead time to less than 30% by adjusting the beam current or changing the pulse processor. Count when the microscope s beam current is stable, and the beam current changes (during the acquisition) are no greater than one percent. The standard should be well characterized with known weight percentages and homogeneous in the region of analysis. The sample for the standard should be polished (smooth). Use a fixed-pulse processor rate instead of auto when doing quantitative analysis with user-defined standards. Always use that time constant when you perform quantitative analysis; otherwise, the Chi-squared fitting results will be too high. 132 NSS Spectral Imaging System Handbook

145 Note The samples you compare with your standards should be acquired under the same conditions as the standard. The exception to this rule is that beam intensity can vary, as the software adjusts for beam intensity differences. However, you should use a fixed pulse processor rate instead of auto when performing quantitative analysis using standards. You can create standards for pure elements and multi-elements. Note If you do not create a standard for every element in a multi-element standard that you are analyzing, the software uses the factory standards for those elements without custom-defined standards. Getting ready to create a standard Follow these steps to prepare to create a standard: 1. Prepare the sample (that you re using to develop a standard). 2. Click the Spectrum icon in the navigation pane. 3. Open the project in which you want to create a standard. See Opening a project and Creating a new project in the Getting Started chapter. 4. Click the Start Acquisition button. 5. Click the Identify Spectrum button. 6. Choose Properties from the Edit menu. The Properties dialog box appears. 7. On the Quant Results tab check the options that you want to display in the final Quant Results report. NSS Spectral Imaging System Handbook 133

146 8. Choose OK. Selecting properties for a standard Follow these steps to select properties for a standard: 1. On the Analysis Setup tab, in the Quant Fit Method area, select either Gaussian With Standards or Filter With Standards. See Quant fit method earlier in this chapter. 2. Set Correction Method to the desired method. See Matrix correction earlier in this chapter. 3. Select the Element Setup tab in the analysis controls pane. If some of the identified elements (green) are not in the standard (such as carbon from a carbon coating), you may want to mark them absent for quantitative analysis. In the Lines Utilized area, select Absent from the Quant drop-down list box. Repeat this until only the elements in the standard have lines selected in the Quant area. 134 NSS Spectral Imaging System Handbook

147 Creating a standard Follow these steps to create a standard: 1. Select (outline in red) the element for which you are creating the standard. 2. On the Standards tab in the lower-right pane, click the Add Standard button. The Add Standards dialog box appears. Note If you make a mistake defining a standard, you cannot edit the standard. Instead, erase the standard with the mistake and start again. NSS Spectral Imaging System Handbook 135

148 3. Choose New Standard. The New Standard dialog box appears: The Element listed in the Element and Line area should be the element for which you are defining a standard. (The ratio element for a TEM multi element standard should be defined first.) If it is not, choose Cancel and return to the Element Setup tab to highlight the required element. 4. If your standard has more than one element, check the Multi Element Standard box. 5. Set Concentration Data Type to the desired type. Enter the elements and the known composition in the boxes that appear. 136 NSS Spectral Imaging System Handbook

149 For multi-element standards, you can select a concentration data type from among weight %, atomic % or atom count. 6. If necessary, adjust the Energy Range values either by manipulating the grid lines on the spectrum or by manually typing in values. The energy range should include only peaks from the element. If peaks from other elements overlap, remove the check mark in the From Current Spectrum check box. In this case the filter method s reference shape for the element will be obtained from the built-in reference library. 7. If you want to adjust element calibration values for standardless analysis, select Use As Standardless Reference and then enter the desired Proza and ZAF calibration factors. For correction methods without standards, a factor greater than 1.0 enhances the weight percent for the element; a factor less than 1.0 reduces the weight percent. 8. If desired, change the name of the standard. When naming a standard, consider the following issues: When you create a multi-element standard, do not name the standard by the name of a single element. In the example above, you would not want to name the standard copper. When you create a multi-element standard, keep the standard name the same for all the elements in the standard. As long as the name is the same, when you select the next element to define (in the Periodic Table), the New Standard dialog box displays all the elements defined previously. NSS Spectral Imaging System Handbook 137

150 When you create standards, an NSS Standards folder is created in the folder defined by the path on the SERVICE Instrument Configuration page, the default location is C:\NSS Libraries. This folder contains all the created standard files. These files have the element being defined in the standard at the beginning of the base standard name and the file extension.std at the end of the base standard name. In the example above, the file name for the Cu-K standard in the NSS Standards folder is Cu-K-Cu Au mixed.std. 9. Choose OK. The Add Standards dialog box appears with the new standard listed at the top of the database list. You can set up multiple standards for the same element. 10. If you are creating a multi-element standard, select the next element in the periodic table, and then return to step 1. Repeat this procedure until you have done all the elements in your multi-element standard. Note If you do not create a standard for every element in a multi-element standard that you are analyzing, the software uses the factory standards for those elements without custom-defined standards. Using standards for quantification Follow these steps to use your standards for quantification: 1. On the Standards tab in the lower-right pane, click the Add Standard button. The Add Standards dialog box appears: 138 NSS Spectral Imaging System Handbook

151 2. Select (highlight) all of the standards you wish to use for quantification. 3. Choose Add Selected. The standards appear in the Standards In Use area. 4. Click the Quantify Spectrum button on the Ident toolbar. 5. When the software completes the analysis, it beeps and lists the results. Click the Quant Results tab in the analysis controls pane to view the results. Note The lower the Chi-squared value, the better is the fit. A fit that is within counting statistics, on average, is 1.0. As a general rule, try to keep the Chi-squared value under 10. NSS Spectral Imaging System Handbook 139

152 Standardless references The Add Standards dialog also can be used to view and select standardless references that you have defined. Choose User Defined Standardless References to view a list of the standardless references available for that spectrum. Batch processing quantitative analyses Batch processing allows you to perform a quantitative analysis and/or peak identification for a series of spectra. 1. Save all spectra to be analyzed in the project directory. Batch processing cannot be applied to spectra in the ~temp directory. 2. Select the type of quant analysis to be conducted. Choose Auto ID to identify peaks. Choose AutoQuant to perform a quantitative analysis using the process parameters. Choose Auto Match identify elements and compounds using spectral match. 3. Choose Quant Analysis from the Batch Processing menu. 140 NSS Spectral Imaging System Handbook

153 4. When the dialog box appears, select the spectral files to be processed and then choose Open. 5. If the Auto Quant is enabled, use the dialog box that appears to select the quant results you wish saved. Choose Save to save the results and exit the dialog box. Choose Cancel to exit the dialog box without saving the quantitative analysis results. When processing is complete the spectra and results are placed in the ~temp directory. When you close the project, you can choose to save either the original spectra or the reprocessed spectra. NSS Spectral Imaging System Handbook 141

154 Using a MagnaRay Spectrometer This chapter explains how to operate the MagnaRay Wavelength Dispersive X-ray Spectrometer with NSS software, including special features added when the system is installed. The information in the rest of this manual also applies to the MagnaRay with the exceptions described here. See the site and safety guide that came with your system for information about safe use of the spectrometer. The MagnaRay is a WDS spectrometer containing a patented hybrid parabolic focusing optic, up to six diffractors (four standard) and a sealed Xe proportional counter, mounted on a 3-axis motorized slide. Because of the focusing action of the hybrid optic, all alignments and quantitative analyses should be performed using an SEM magnification in excess of 10000X. Qualitative analyses can be performed at lower magnifications. Manual spectrometer control and status Starting the spectrometer This section explains how to start, insert, control and align the MagnaRay spectrometer and check its status. To start the spectrometer: 1. Turn on the WDS chassis. 2. Start NSS. 3. Select Spectrometer Control on the WDS Tool tab in the lowerright pane. 4. Click the Initialize button. This brief motor-homing operation needs to be performed only once each time you turn on the spectrometer. 142 NSS Spectral Imaging System Handbook

155 Controlling the spectrometer and checking its status In either Spectrum mode or Point & Shoot mode, select Spectrometer Control on the WDS Tool tab in the lower-right pane to access features for controlling the spectrometer and checking its status. The current settings of the spectrometer appear: The following table describes the available features. Feature Current Element Diffractor Energy Bias, LLD (lower-level discriminator) and ULD (upper-level discriminator) Description The elemental line that the spectrometer is currently positioned for, if any. The currently selected diffractor and its energy range. The x-ray energy that can be analyzed with the current spectrometer settings. Changing the setting by typing a new value or by using the up and down arrow buttons changes the position of the spectrometer accordingly. You can set the speed at which the buttons change the energy by using the drop-down list box to the right. The settings of the x-ray detection electronics of the spectrometer. In general, you should not need to change these values from the factory defaults, but editing is possible if you need full control. NSS Spectral Imaging System Handbook 143

156 Feature Ratemeter display Locate Peak button Go To Element button Insert button Initialize button Tune Detector button Description Indicates the current output of the x-ray detection system. It has two different formats depending on the current acquisition settings. The primary mode is a strip-chart recorder (counts versus time) that is useful for viewing the x-ray output as the spectrometer settings change. The other mode is a multi-channel analyzer (MCA) display of counts versus detector energy. This is used primarily for confirming and adjusting the detector settings. Searches around the selected element s energy for the optimized energy location of an elemental peak. This button is available only if an element is selected on the Element Setup tab or WDS Setup tab. Used in conjunction with the WDS Setup tab in the analysis controls pane to align the spectrometer to the selected element. This button is available only if an element is selected on the Element Setup tab or WDS Setup tab. The name of the button changes to show the element that is selected on the displayed tab. Inserts the spectrometer from the retracted, safe storage location into the analytical location. The button then becomes the Retract button, which lets you retract the spectrometer to a safe location when the experiment is completed. This typically takes about 10 seconds but may take slightly longer depending on the motion distance. Homes the spectrometer motors on those rare occasions when the spectrometer chassis power is turned on. This typically takes about 15 seconds. Confirms the x-ray detection performance by beginning collection of MCA data and showing the location of the LLD and the ULD settings. The button changes to the Restart PHA button; you can click it to restart the process. 144 NSS Spectral Imaging System Handbook

157 Feature Clear History button WDS status bar Bias indicator Moving indicator Counting indicator Parked indicator Stop sign button Description Resets the vertical axis of the graph to the limits of the currently displayed data. When you click the Tune Detector button, this button changes to the Ratemeter button; you can click it to return to the Ratemeter display. Displays information about operation of the spectrometer. Shows the state of the bias voltage to the x-ray detector. X-rays can be detected only if this indicator is lit. If the vacuum interface is connected to the SEM, no user input is needed to vary this signal. If a vacuum interface is not present, you must manually flip the Bias Enable switch to enable this indicator. Make sure the switch and bias voltage are engaged only when the vacuum of the SEM specimen chamber is better than 1x10-4 torr. Lights when any motor inside the spectrometer is engaged. Lights when data is being collected from the x-ray detection electronics. Lights when the spectrometer is in a standby (not analytical) condition. After 3 minutes of inactivity, the spectrometer automatically moves itself to the standby location. If you select a WDS operation, the spectrometer automatically comes out of the standby condition and moves to the desired location. Stops the current WDS acquisition. Inserting the spectrometer Note The WDS optic has a focus distance of 20 mm from the sample for acquisitions. To prevent damage to the optic, it is typically retracted from the sample to provide clearance for sample motion. Before using the optic and spectrometer, you need to insert them to the analytical location. To prevent damage to the optic during insertion, you can visually confirm that the sample is clear of the insertion area by using a chamber camera. To insert the spectrometer: 1. Select Align Spectrometer on the WDS Tool tab in the lower-right pane. NSS Spectral Imaging System Handbook 145

158 2. Click the Insert button. This operation typically takes less than 10 seconds. 3. If no vacuum interlock is present, and the chamber is pumped down, turn on the Bias Enable switch. Aligning the spectrometer WDS spectrometers need some alignment to the sample for optimal operation. The MagnaRay aligns itself based on the peaks in the current EDS spectrum. The alignment procedure automatically adjusts the WDS slide to the empirical optimal location based on the intensity of the selected element. In either Spectrum mode or Point & Shoot mode, select Align Spectrometer on the WDS Tool tab in the lower-right pane to access features for aligning the spectrometer. The current settings of the slide appear in the Spectrometer box: 146 NSS Spectral Imaging System Handbook

159 The following table describes the available features. Following the table is an alignment procedure. Feature Current Element Alignment Element Minimum Dwell Time Insert, Pan and Tilt Stage Z Axis Ratemeter display Auto Align button Z Assist button Description See the description in the preceding Controlling the spectrometer and checking its status section. The element to use for aligning the slide of the spectrometer, based on the checked elements on the WDS Setup tab in the analysis controls pane. If you select Auto, the element will be determined automatically from the current EDS spectrum. The minimum time that the spectrometer will collect data at each point during slide alignment. The actual dwell time may increase automatically if the incoming x-ray count rate is not high enough for good statistics. The current location of the spectrometer slide, which will change dynamically as the slide moves. You can set these values to move the slide to a new location, but that is typically not required. The current location of the SEM slide. If this value is not equal to the analytical or design working distance of the WDS detector, optimum data will not be collected. You an optimize collection using the Z Assist button (described below). Indicates the current output of the x-ray detection system in a strip-chart recorder (counts versus time) format. This is useful for viewing the x-ray output as the spectrometer settings change. Aligns the spectrometer slide to the location that provides the greatest x-ray intensity for the spectrometer settings defined by Alignment Element (described above). If SEM stage automation is available, you can use this button to assist in moving the sample Z position to the optimal analytical location. If no stage control is available, this button is disabled and you must manually move the sample to the analytical working distance. NSS Spectral Imaging System Handbook 147

160 Feature Insert button Clear History button WDS status bar; Bias, Moving, Counting and Parked indicators; Stop sign button Description See the description in the preceding Controlling the spectrometer and checking its status section. Resets the vertical axis of the graph to the limits of the currently displayed data. See the descriptions in the preceding Controlling the spectrometer and checking its status section. To align the spectrometer: 1. Click the Edit Acquisition Properties button on the Acquisition toolbar, uncheck Acquire WDS Elements Simultaneously For Quantitative Analysis on the EDS tab in the Acquisition Properties dialog box, and choose OK. 2. Select Align Spectrometer on the WDS Tool tab in the lower-right pane. 3. Set Alignment Element on the WDS Tool tab to Auto. 4. Click the Start Acquisition button on the Acquisition toolbar to begin the EDS acquisition. 5. After the first peak identification, click the Auto Align button on the WDS Tool tab. The software automatically scans the EDS spectrum for the best high-energy peak to use to align the spectrometer. If a suitable peak is found, the spectrometer slide automatically scans the stage pane and tilt axes and collects x-rays for the element. Graphical feedback is provided through the ratemeter display. This operation typically takes 1 to 10 seconds but could take up to 3 minutes if the intensities are low. The WDS status bar displays a message when the alignment successfully finishes. 148 NSS Spectral Imaging System Handbook

161 If the peaks are too low ( WDS element not defined appears in the WDS status bar), you must perform this operation manually: i. On the WDS Setup tab in the analysis controls pane, select the check box for the desired element-line-crystal. ii. On the WDS Tool tab in the lower-right pane, select Align Spectrometer and set Alignment Element to the desired element. iii. Increase the dwell time by setting Minimum Dwell Time. iv. Click the Auto Align button on the WDS Tool tab. Changing or positioning the sample The MagnaRay spectrometer is designed to operate with the sample at the analytical working distance of the SEM. Because it uses a focusing optic, this requirement is much more stringent than for EDS detectors. To aid in this positioning, a coarse SEM stage movement is required. If SEM z-stage automation is available, NSS can assist in this operation: 1. Focus the electron image of the sample. 2. Select Align Spectrometer on the WDS Tool tab in the lower-right pane and then click the Z Assist button. A dialog box displays the current working distance. a. If you do not have column automation, enter the current working distance as it appears on the SEM console. b. Choose OK to automatically move the stage to position the sample at the analytical working distance. c. Refocus the SEM if necessary. NSS Spectral Imaging System Handbook 149

162 If only manual z-stage motion is available, follow these steps: 1. Manually change the working distance to the designed analytical working distance by adjusting the SEM focus until the SEM console readout displays the latter. 2. Refocus the SEM if necessary using the SEM Z-axis (not the focus controls). Ending your MagnaRay microanalysis session When you are finished using the MagnaRay spectrometer, turn off the Bias Enable switch if no vacuum interlock is present. When NSS closes, the spectrometer moves to a standby location and a message asks whether to retract the spectrometer to a safe location within the SEM. You should normally choose Yes. The MagnaRay will retract. Working with WDS Setup The WDS Setup tab, shown below, is available in the access controls pane for all acquisition modes in NSS. It is your primary means to make changes to the WDS spectrometer operation. On this tab you can define and select element-line-crystal sets and perform operations to either acquire or prepare to acquire typical WDS data. The next sections explain how to use the features on the tab. 150 NSS Spectral Imaging System Handbook

163 Setting up peak-to-background measurements Set Parameter Type on the WDS Setup tab in the access controls pane to Peak To Bkg to set up peak-to-background (P/B) measurements for the MagnaRay. These measurements are most useful for determining the existence of trace elements in a sample. Without taking a long time to scan a whole energy peak, a more targeted analysis measuring only the peak and two background locations is more time efficient and typically more accurate. This display lets you set and acquire all of the typical values for the sample. The following table describes the available features. Feature Start button Display Table Element Search Background Counting Description Begins the P/B acquisitions according to the elements selected and the settings in the table below. All Elements displays the complete list of possible elements in the table below. Active Elements displays only the elements you have selected. Enter the symbol of the element to search for in the table below. The cursor will rest on the next copy of that element in the list. The method to use for the background counts for the P/B acquisition. Normal is the default and counts for one-half the dwell time at both the upper and lower background locations. Select Use Last when many P/B measurements are performed at the same beam current and on a similar sample; this speeds the acquisition by measuring only the peaks and not the backgrounds. Background Only measures only the background of the samples so that the values can be used with the Use Last and Measure At Peak options. Measure At Peak lets you ratio the intensities of the selected elements in an unknown versus intensities in a reference material. When this option is selected, the intensities are measured at the peak position for elements, and these intensities are used as the background values for future peak-to-background measurements of unknown samples. NSS Spectral Imaging System Handbook 151

164 Feature Element-Line Diffractor table Diffractor Selection Optimization Description Lists all of the elemental x-ray line and spectrometer diffractor combinations that are possible with the system and displays all of the values relevant to P/B measurements. The Possible and Present values are used for WDS peak identification to determine if the presence of the element is statistically significant. The Rule values (discussed in the Element-line-crystal rules section below) are used to manually control the collection order of the elements. To change any value in the table, click that cell, edit the value in the text box that appears below the table, and then press Enter. To change a whole column of values to the same value, click the first cell in the column, hold down the Shift key and click the last cell in the column, edit the value in the text box below, and then press Enter. You can perform other operations by right-clicking a cell of the table and choosing a command from the shortcut menu: Go To Element sets the spectrometer to the selected row settings. Add Line adds a row to the table for a combination that is not currently available. A dialog box lets you specify the element, x-ray line and diffractor for the element. Delete Line removes a combination from the table. Be careful with this as it cannot be undone. Reset Element Table sets all of the values to the factory default values. Load Parameters, Save Parameters, Load Rules and Save Rules let you load and save values from and to a disk file on the system. Specifies which combination in the table is preferred if more than one is available; that is, more than one diffractor type for the same element-line combination. 152 NSS Spectral Imaging System Handbook

165 Feature Delete Selected button Add Line button Default Parameter button Default All button Set Up Standard button Description Deletes the selected rows from the table. To select multiple rows, hold down the Ctrl key or Shift key when clicking rows. Adds a line combination; see the description of Add Line above. Resets the selected values of a parameter in one or more rows to the factory settings. To select values in multiple rows, hold down the Ctrl key or Shift key when clicking values. Resets the selected rows to the factory settings. To select multiple rows, hold down the Ctrl key or Shift key when clicking rows. Defines a material reference standard for elemental quantification. See Setting up WDS standards later in this chapter for details. Element-line-crystal rules The Rule column in the table on the WDS Setup tab in the access controls pane lets you manually override the ordered list of selections for the WDS acquisition. To specify a Rule option for an element-line-diffractor combination, click the appropriate Rule cell in the table and type the desired entry in the Edit Rule text box below the table. The available options and their entries are described below. Collect This Element First is used for volatile elements that might migrate from the area of analysis with long exposure to the electron beam. The best example of this is Na in geological samples. To enable any element to follow this rule, enter an exclamation point,!. You can select more than one element as first, but the final acquisition order is not guaranteed. NSS Spectral Imaging System Handbook 153

166 Collect This Element Only is used when an element should be analyzed only if one or more other elements are present in the sample. The elemental symbols are used to designate these elements. The Boolean operators of + and, are available as and and or operators for combinations of elements. Spaces in the rule are ignored. The following examples describe the rules options: Element Rule Description C-Ka1-NiC80 B Collect C only if B is detected. Na-Ka1-TAP! Collect Na as the first element in the analysis. P-Ka1-PET O+Si Collect P only if both O and Si are detected. O-Ka1-TAP Fe Collect O only if Fe is detected. K-Ka1-PET O, Fe, Si Collect K only if O or Fe or Si are detected. Setting up x-ray detection Detector parameters are set at the factory and normally do not need to be viewed or changed. However, if you wish to try to optimize them and fully control the x-ray detection process, set Parameter Type on the WDS Setup tab in the access controls pane to Detector, and refer to the information in the preceding Setting up peak-to-background measurements section. Be aware that there is no undo function for any changes you make, so be sure to save the initial table before editing. To save the table, use Windows Explorer to locate the project and save WDS Element Data.csv using a new file name. Setting up peak search Rarely, the peak location for an element will drift from the theoretical location. In these cases it may be useful to have the software find the energy that produces the maximum x-ray intensity: Set Parameter Type on the WDS Setup tab in the access controls pane to Peak Search, and refer to the information in the preceding Setting up peak-to-background measurements section and the descriptions below. Feature Peak kev Low kev and High kev Step ev Dwell Secs Description The peak location. The search range for the peak location. The granularity of the search. The amount of time to measure data at each energy step. 154 NSS Spectral Imaging System Handbook

167 Setting up and acquiring standards Quantitative composition analysis is a primary function of WDS analysis. To perform analyses with the greatest precision, you must make elemental measurements from standard reference materials at a suitable statistical level. To set up and acquire elemental measurements of standard reference materials for quantification, set Parameter Type on the WDS Setup tab in the access controls pane to Standards, and refer to the information in the preceding Setting up peak-to-background measurements section and the descriptions below. Feature Start button Auto Align Description Begins the standards acquisitions according to the elements selected and the settings in the table below. Aligns the spectrometer slide for each element in the analysis. If large distances must be traversed on the sample, auto alignment is crucial. If all of the standard samples are near each other on the stage, auto alignment may not be needed for every acquisition after an initial manual alignment is performed. NSS Spectral Imaging System Handbook 155

168 Feature Element-Line Diffractor table Set Up Standard button Description Lists all of the elemental x-ray line and spectrometer diffractor combinations that are possible with the system and displays all of the values relevant to the measurement of standard reference materials. Order is an advanced option that is necessary only if the element to be analyzed may decrease in intensity with time under the beam. In this case, set its order to a low integer so that its data is collected first. Min Sec, Max Sec and Stat % are collection time settings that determine how long the system should acquire the data. Stat % permits a dynamic time in order to terminate the acquisition when a given statistical level of the data has been collected. Standard (kv) selects the current definition of the standard reference material to be used for comparison quantification. The options for selection are determined by what standards have been defined by the Set Up Standard button below. Date shows the last date that the standard data was collected. P Srch (Peak Search) and Avg Cal (Average of Calibrations) are advanced options to permit optimum data collection of difficult samples. P Search forces a peak search to be performed before intensities are determined. Avg Cal allows multiple measurements on the scan standard to be averaged together. Peak kev, Bkg1 and Bkg2 are the peak, lower background, and upper background energies associated with the acquisitions. You should normally not change these values. Defines a material reference standard for elemental quantification and a stage location for the standard. See Setting up WDS standards later in this chapter for details. 156 NSS Spectral Imaging System Handbook

169 Setting up quantification of unknown samples Once you have collected standards from reference materials and selected the corresponding elements for quantitative analysis, set the software for collecting elemental information for quantification of unknown samples: Set Parameter Type on the WDS Setup tab in the access controls pane to Unknown, and refer to the information in the preceding Setting up peakto-background measurements and Setting up and acquiring standards sections. Confirming elements using WDS Confirming elements with manual scans As explained in the next sections, you can confirm elements using WDS manually or automatically. Automatic WDS validation of the existence of characteristic elemental peaks is useful, but visual confirmation can be the most satisfying result. You can perform a manual WDS energy scan as a final confirmation. A diagrammatic overlay on the EDS spectrum illustrates the energy range limits of the diffractors. If you need an extensive energy scan, include multiple diffractors if necessary. The software selects the lowest number of diffractors to perform the scan. To acquire a WDS energy scan in Spectrum mode: 1. Enable KLM markers (optional). To do this, right-click the spectrum pane, select Show KLMs on the KLM Page tab in the Spectrum Properties dialog box, and choose OK. 2. Select the desired element on the Element Setup tab in the access controls pane to display for visual selection (optional). 3. Click the WDS Scan button on the Ident toolbar. The WDS Acquisition dialog box appears, and the diffractor energy ranges are indicated by red dashed lines in the spectrum pane. Note You can toggle the display of the diffractor energy range lines by typing Ctrl+D. NSS Spectral Imaging System Handbook 157

170 4. Set the low and high energy limits for the acquisition. You can enter numerical values in the dialog box or drag the slider bars on the spectrum. (The position of the slider bars is reflected by the low and high limits.) 5. Edit the dwell time as needed. Adjust the dwell time to acquire a peak with sufficient amplitude to observe the features of interest. The total acquisition time will be adjusted accordingly. 6. Edit the step size. The step size is automatically adjusted based on the predicted peak width. Increasing or decreasing the value will change the resolution and acquisition time accordingly. 7. Click the Start button. The acquired WDS spectrum is collected and updated periodically with the base EDS spectrum as an overlay. (If this does not appear, manually select the EDS spectrum on the Compare Information tab in the analysis controls pane.) When the scan is finished, the spectrum is automatically saved in EMSA ASCII format. Confirming elements automatically Qualitative analysis in EDS, defined as peak identification, is one of the most experience-dependent abilities in microanalysis. As good as software routines have become, the wide spectral peaks of EDS do not provide much confidence that peak overlaps are either occurring or not. WDS can help in this regard because its spectral resolution and peak-to-background values are so much better than EDS that identifications are nearly trivial to perform. However, the time to collect WDS spectra covering all of the overlapped EDS peaks can be quite time consuming. MagnaRay automatically determines problematic EDS peak identifications and provides WDS confirmation of the elemental contributions to each peak. The fast motor speed of MagnaRay permits all of this validation during the EDS acquisition without the need to perform any actions. 158 NSS Spectral Imaging System Handbook

171 To perform a WDS qualitative analysis in Spectrum mode: 1. Click the Edit Acquisition Properties button on the Acquisition toolbar, uncheck Acquire WDS Elements Simultaneously For Quantitative Analysis on the EDS tab in the Acquisition Properties dialog box, and choose OK. 2. Right-click the spectrum pane, set Labels to Long on the Peak Page tab in the Spectrum Properties dialog box, and choose OK. 3. On the WDS Tool tab in the lower-right pane, select Spectrometer Control for graphical feedback. 4. On the WDS Setup tab in the analysis controls pane, uncheck all the listed elements. Note If you want to determine whether some elements with very low concentrations are present, check those elements. 5. Enable Auto ID on the Processing tab in the analysis controls pane. 6. Enable WDS ID on the Processing tab. 7. Display the WDS Acquisition Status tab in the analysis controls pane. This lets you view textual feedback. NSS Spectral Imaging System Handbook 159

172 8. Click the Start Acquisition button on the Acquisition toolbar to acquire the EDS spectrum. After an EDS peak identification has occurred and whenever the software needs to validate a peak overlap, the WDS spectrometer automatically moves to those elements and validates each element in turn. You can monitor the WDS progress by watching the status on the WDS Tool tab and the WDS Acquisition Status tab. When the acquisition is finished, the peak identification labels in the spectrum pane indicate the WDS confirmation of the selected elements; for example, Si Kα (WDS). Quantitative analysis using combined WDS and EDS acquisitions Since there is no standardless WDS analysis, every quantitative analysis requires measurement from well characterized standard samples, including beam current measurements, before you analyze unknown materials. NSS lets you mix EDS and WDS quantification into a single acquisition, with EDS used for isolated, high-composition elements, and WDS used for difficult or low-composition elements. You can also perform standardless EDS quantification if at least one EDS element is collected with standards. (This is a limitation of the fundamental matrix correction algorithm.) All of these operations are automated as much as possible to make WDS quantitative analyses as easy as standardless EDS quantitative analyses. If you will be using EDS standards, collect and set them up in the normal fashion for NSS. Also, verify two additional settings before the EDS acquisition: check Acquire WDS Elements Simultaneously For Quantitative Analysis and select Measure Beam Current Before EDS Acquisition on the EDS tab in the Acquisition Properties dialog box. Setting up WDS standards To set up the WDS standards: 1. On the Analysis Setup tab in the analysis controls pane, set Quant Fit Method to Filter With Standards. 160 NSS Spectral Imaging System Handbook

173 2. On the WDS Setup tab in the analysis controls pane, set Parameter Type to Standards and then use the Set Up Standard button to set up each standard material. In the Define Standard Composition dialog box, enter the standard sample name and known composition of each element. If your stage is automated, move to the standard and then click the Read Position button to record the SEM stage location for that standard. Choose Save to save the definition for the standard. Repeat this process for each standard. 3. Set Display Table to All Elements and then select the check box for each element-line-crystal to be collected. Scroll the table to the right to see more options. The primary ones of interest are Peak Search and Average Calculation. Peak Search searches for the peak energy to compensate for any calibration or chemical energy shifts and sets the peak location accordingly. Average Calculation permits any number of acquisitions to be collected to compensate for sample variations. For each selected element-line-crystal, click the cell in the Standard column and use Select Standard below the table to associate the appropriate element with that combination. Acquiring standards data Once the table is fully populated with all of the WDS standard elements to be collected, you are ready to acquire them: 1. Select Spectrometer Control on the WDS Tool tab in the lowerright pane to enable visual feedback of spectrometer status. 2. If the beam current is not automated, measure the beam current. 3. On the WDS Setup tab in the analysis controls pane, set Parameter Type to Standards and then click the Start button in the Acquire Stds box. If your stage is not automated, respond appropriately to the prompts that appear. NSS Spectral Imaging System Handbook 161

174 4. Display the WDS Acquisition Status tab in the analysis controls pane to view the acquisition progress. For each element standard, the following actions occur: The SEM stage moves to each standard material in turn. The spectrometer is aligned. The beam current is measured. The quantitative data is collected and stored. The acquisition time is automatically adjusted for optimal statistics. Setting up the unknown sample To set up the unknown sample: 1. Move the SEM stage to the unknown sample. 2. Choose Properties from the Edit menu, select Source on the Quant Results tab in the Properties dialog box and choose OK. 3. Click the Add Standard button on the Standards tab in the lowerright pane. In the Add Standards dialog box, select the standards that will be analyzed for any EDS or WDS elements, choose Add Selected and then choose OK. 4. Enable Auto Quant on the Processing tab in the analysis controls pane. This turns off WDS ID if it is active. Note If you are working only with WDS elements, disable Auto ID on the Processing tab in the analysis controls pane. 5. If you need to verify alignment at each unknown sample location, on the WDS Setup tab in the analysis controls pane set Parameter Type to Unknown and set Auto Align to On. 162 NSS Spectral Imaging System Handbook

175 6. Click the Edit Acquisition Properties button on the Acquisition toolbar. Select Acquire WDS Elements Simultaneously For Quantitative Analysis on the EDS tab in the Acquisition Properties dialog box. If the beam current is automated, also select Measure Beam Current Before EDS Acquisition. Choose OK when you are finished. 7. Confirm that the correct line is specified for each WDS element. To do this, select the element in the periodic table on the Element Setup tab in the analysis controls pane and then verify the setting of Quant in the Lines Utilized box. Acquiring unknown sample data To acquire unknown sample data: 1. Display the WDS Acquisition Status tab in the analysis controls pane. This lets you view results feedback. 2. Select Spectrometer Control on the WDS Tool tab in the lowerright pane to view the WDS progress. 3. If the beam current is not automated, measure the beam current. 4. Click the Start Acquisition button on the Acquisition toolbar. An EDS spectrum is collected, starting with a beam current measurement. The WDS acquisition begins by automatically aligning the spectrometer and then collecting all of the unknown elements at that location. Watch the WDS Tool window to see the current WDS acquisition progress. Watch the WDS Acquisition Status tab in the access controls pane to follow the results progress. When the acquisitions are finished, click the Quant Results tab in the access controls pane to view the completed WDS quantitative results. NSS Spectral Imaging System Handbook 163

176 It is also possible to use the Analysis Automation tab in the access controls pane to perform WDS quantitative analyses for unknown samples. Both points and grids have been tested. It sometimes helps to manually align the spectrometer once: set Auto Align on the WDS Setup tab to Off to shorten the total acquisition time if you have confidence that the sample is flat enough over the total stage range of motion. Combining Point & Shoot analysis with WDS You can perform WDS analyses in Point & Shoot mode, although the quality of the results depends upon the magnification of the SEM. The limitation is that the auto alignment feature of the slide must compensate for the limited x-ray spot size at lower magnifications and is restricted in how much compensation is possible. Quantitative analyses are not recommended in Point & Shoot mode at SEM magnifications below 5000X. At lower magnifications, the spatial distribution is non-uniform and can contribute to inconsistent results. At higher magnifications, the x-ray detection is more consistent and quantitative measures will provide better precision. You can perform qualitative analyses at magnifications as low as 500X using small area scans or points, because the auto alignment feature will optimize x-ray collection for these analyses. Performing linescan and spectral image acquisitions with WDS WDS linescan and mapping acquisitions are only slightly different from acquiring an additional EDS element. You must select an element-linediffractor, move the spectrometer to that location, select WDS for input, and then start the acquisition. All other settings are taken care of automatically by the software, and the data is stored just like that of an additional EDS element. Quantitative WDS linescans are available with SEM stage automation (NSS600 and NSS-AUTO). Large Area Linescan (LALS) is available through Analysis Automation. To perform a qualitative linescan or Spectral Imaging acquisition: 1. On the WDS Setup tab in the analysis controls pane, select the desired element-line-diffractor combination in the table, right-click that row and choose Go To Element. 164 NSS Spectral Imaging System Handbook

177 2. On the Element Setup tab in the analysis controls pane, select the MagnaRay check box. 3. Click the Start Acquisition button on the Acquisition toolbar to begin the combined EDS-WDS acquisition. The WDS data will be collected in parallel with the EDS data and saved directly to disk. You can monitor the progress on the WDS Tool tab in the lower-right pane, although there is little to see because the WDS spectrometer is stationary. NSS Spectral Imaging System Handbook 165

178 Finding Phases With XPhase The XPhase option lets you find phases using any map in Spectral Imaging, Compass or Spectral Imaging modes. If you create phases from Spectral Imaging maps or Compass components, the underlying spectrum is extracted from the original Spectral Imaging data for each phase. You can overlay a phase on the electron image and generate a report showing the results. In a manual phase analysis you select the elements or components to include and the image peaks to use for the phase calculation. If you only want to select the elements or components, you can perform an automatic phase analysis. XPhase does not appear in the software unless it was purchased and installed. To obtain XPhase, contact your sales representative. To perform a phase analysis with XPhase: 1. Acquire or open a map set in Spectral Imaging, Compass or Spectral Imaging mode. 2. On the Phase Analysis tab in the analysis controls pane, specify the elements (for map data) or components (for Compass data) to include in the analysis. The items that are checked will be included. If you want to perform an automatic phase analysis, skip to step 8. If you want the found phases automatically searched against a database, specify the database and set the parameters in the Match box on the Analysis Setup tab as explained in Searching a database with Spectral Match in the Identifying Spectra With Spectral Match chapter. Also, make sure Match is active on the Processing tab. If a match is found for a phase, its name will appear above the phase map in the map pane instead of an automatically numbered name. Any phases that have the same match will be combined. 166 NSS Spectral Imaging System Handbook

179 3. To perform a manual phase analysis, click the Manual button on the Phase tool bar The Manual Phase Editor dialog box appears. It gives you the choice of selecting peaks in the histograms of any or all of the elements, components or phases being used for input in the phase calculation. 4. To create a histogram segment for a peak, select the input map from the drop-down list box and click the button. Two vertical lines appear on the map histogram in default intensity locations. Drag these lines to isolate a peak as the segment. You can specify more segments for the input map by clicking the button again. Colors are used to identify the segments and their corresponding vertical lines in the histogram. To delete a segment, select it in the list and then click the on the keyboard. button or press the Delete key Use the techniques described above to specify segments for the other available input maps. If you want the software to create segments for all the maps automatically, click the Auto Segment Images button. 5. To eliminate small noise phases, set Minimum Area % to the minimum percentage of a map s area that a phase needs to cover to be considered a valid phase. 6. Click the Auto Create Phases button. The resulting binary phase maps appear in the map pane. You can make changes to your settings and click the Auto Create Phases button again to create new phase maps. NSS Spectral Imaging System Handbook 167

180 7. When you are satisfied with the phase maps, click the Close button to close the Manual Phase Editor dialog box and go to step To perform an automatic phase analysis, click the Auto button on the Phases tool bar. The resulting binary phase maps appear in the map pane. 9. Work with the phase maps as explained below. To change the color and other properties of a map, right-click the map and then use the Map Properties dialog box to make the desired changes. To overlay a phase map on the image, click the name above the map. To remove the overlay, click the name again. To rename a phase, double-click either the map name, type a new name in the text box that appears, and then choose OK. In Spectral Imaging mode, you can display spectra from the phase maps. These come from extractions on the original Spectral Imaging data using the phase map as the extraction region. Any settings selected on the Processing tab in the analysis controls pane will be applied (for example, Auto ID, Quant or Match). To display the spectrum for a phase, click the phase map; the spectrum appears in the spectrum pane. You can process and modify the spectra in the same manner as for traditional spectra (for example, by using toolbar buttons or right-clicking the spectrum to access the Spectrum Properties dialog box). In Spectral Imaging mode, you can click the Maps and Phases buttons to toggle between the display of phase maps and x-ray maps. When Compass is selected you can click the Components and Phases buttons to toggle between the display of phase maps and component maps. Information about the found phases appears on the Phase Analysis tab. The Area % column shows the percentage of the total map area occupied by the phase. The Combinations column shows which source maps have been used to create the phase. 168 NSS Spectral Imaging System Handbook

181 To manually combine two or more phases, first select them by holding down the Ctrl key while clicking their rows. Set Into Phase to the name of the phase you want to use for the resulting combination and then click the Combine button. The phase maps in the map pane and the information on the Phase Analysis tab are updated for the combination. To set up a report including the phase analysis results, use the Phase tab in the Page Setup dialog box. NSS Spectral Imaging System Handbook 169

182 Analysis Automation Analysis Automation is an option that lets you automatically perform repetitive acquisitions on large-scale analyses without the need for user input once the initial parameters are defined. Note Analysis Automation does not appear in the analysis controls pane unless it was purchased and installed. Contact your sales representative to purchase Analysis Automation. Analysis Automation performs the given analysis at selected stage locations. These are defined using one of the following methods: user points, a grid (an area of interest), a circular sample or a linescan set up using the Analysis Automation tab in the analysis controls pane. The acquisition parameters and data acquired depend on the current settings and acquisition mode. The system returns the stage to the starting position and proceeds to acquire the appropriate data. When all data is acquired at the first position, the stage is moved to the next position or frame, and the process continues until all selected areas are processed. You can save the stage positions and reload them from a file for reuse if standard patterns of analysis are required, or if reanalysis of a single sample is desired. Note Use the Edit Microscope Parameters button on the Acquisition toolbar to specify the correct magnification, kv and working distance before beginning an acquisition. Analysis Automation and Drift Compensation Analysis Automation is designed to work with Simple Drift Compensation when the analysis area is the same area used for determining the amount of drift that has occurred. However, Advanced Drift Compensation, which uses separate tracking and analysis areas, is not supported with Analysis Automation. If you wish your automated sequence to be drift compensated, make sure that the Enable Drift Compensation button on the Acquisition toolbar is active when you click the Start button. This tells the automation controller to use drift compensation during the automation sequence. 170 NSS Spectral Imaging System Handbook

183 Analysis Automation with Point & Shoot operation and linescans If you notice a problem with point registration when using Point & Shoot mode or linescans in conjunction with Analysis Automation, there are two possible problems: Backlash in the stage is not being corrected for properly. Check to see if the stage automation purchased for the microscope supports backlash correction. If it does, consult with the manufacturer of the stage to ensure that it has been set up properly. If the stage itself does not support backlash correction, contact technical support about enabling the software backlash correction within the automation routines of NSS. You did not properly remove backlash before acquiring the reference image and indexing the points. Index the stage location in the points table, tell the software to return to the previously defined stage position, acquire your image, index your points, and update the previously set location. If you are combining Point & Shoot operation or linescans in Analysis Automation along with Drift Compensation, be sure to use the Enable Drift Compensation button to acquire the reference image at each position. You cannot mix stage positions that have some fields using drift compensation and others that do not. Setting Analysis Automation parameters The parameters on the Analysis Automation tab in the analysis controls pane define the locations on a sample to be acquired. The next section explains how to set the parameters. NSS Spectral Imaging System Handbook 171

184 Using Selected Areas Use the Selected Areas option on the Analysis Automation tab to select multiple user points to be acquired in series without further user input. This option is available for all acquisition modes. The following table describes the available parameters for this option. Parameter Sequence Name Location list Automation Controls Description This name is combined with the base name to create the data file name. The selected stage locations are shown here. Right-clicking any of these locations displays a menu containing Save Points File, Load Points File and Clear All. See Working with grid lists below for more information. Select Beam Off to automatically turn off the microscope at the end of the acquisition. Select Use Saved Mag to use the stored magnifications for each stage location. These features are available only if you purchased column automation and they are supported by your system hardware. 172 NSS Spectral Imaging System Handbook

185 Parameter Description Selected Areas Controls Click the Add Or Change Point button to create a new location. In Point & Shoot or X-ray Linescans mode, select the point-and-shoot or linescan location before creating the stage location. Select a stage location in the list and click the Stage To Point button to go to that point. In Point & Shoot mode or X-ray Linescans mode, you should have selected the Point & Shoot or linescan location before creating the location. Click the Remove Point button location. to delete a selected Spectrum Acquisition Analysis Automation Acquisition toolbar While in Spectrum mode, select Center Spot to position the spot in the center of the field of view. Select Microscope Raster to average the acquisition from the entire field of view. This toolbar is similar to the main Acquisition toolbar. Use the buttons to start, pause, stop or abort an automatic analysis, move to points or grid sequences, test the analysis, or acquire a live image. Using Grid and Circular The Grid and Circular options on the Analysis Automation tab let you select the size, quantity and shape (rectangular or circular) of grids to be automatically acquired in series in an area of interest. NSS Spectral Imaging System Handbook 173

186 Grid parameters Circular parameters 174 NSS Spectral Imaging System Handbook

187 The following table describes the parameters for the Grid and Circular options. Parameter Grid List Frame Layouts Automation Controls Frame Progress Spectrum Acquisition Analysis Automation Acquisition toolbar Description Shows grids created for an automated analysis by area (X,Y stage coordinates and Z-axis when available). Use the buttons below the list to edit, delete or create grids. See the next section for instructions. To overlap adjacent frames by a certain percentage, enter a percentage number in the Overlap % box. The software then calculates the movement size. You can also select User Grid and enter whole number values in the X and Y fields to create a specific grid size. The software then calculates the overlap percentage. Select Beam Off to automatically turn off the microscope at the end of the acquisition. Select Use Saved Mag to use the stored magnifications. These features are available only if you purchased column automation and they are supported by your system hardware. The color of the display indicates the acquisition progress. Green indicates selections to be done. Yellow indicates selections currently being acquired. Blue indicates completed acquisitions. While in Spectrum mode, select Center Spot to position the spot in the center of the field of view. Select Microscope Raster to average the acquisition from the entire field of view. This toolbar is similar to the main Acquisition toolbar. Use the buttons to start, pause, stop or abort an automatic analysis, move to points or grid sequences, test the analysis, or acquire a live image. Using the grid list to index rectangular or circular samples The grid list shows grids created for an automated analysis by area (stage coordinates and Z-axis). Use the buttons below the list to edit, delete or create grids. The next sections explain how to use the buttons. NSS Spectral Imaging System Handbook 175

188 Creating a new rectangular grid Follow these steps to create a rectangular grid: 1. Select Grid in the Stage Movement box on the Analysis Automation tab. 2. Move the stage to the analysis starting point, and then click the Create New Grid button. A panel of features appears: 3. Type a label in the Label text box to help identify the grid in the grid list. Note If the Z-axis of your microscope is automated, be careful to adjust the Z-axis to keep the image in focus at all positions. 4. Click the Add Or Change Point button to specify the starting point for the grid. The coordinates and other information about the point appear. 5. Move the stage to the analysis ending point, and then click the Add Or Change Point button to add the second point. 6. If the Z-axis of your microscope is automated, move the stage to a third location on the grid, focus the image, and click the Add Or Change Point button to add that point. 176 NSS Spectral Imaging System Handbook

189 The Z-axis correction is best calculated using a third location as far as possible from the line connecting the first two points of the grid. 7. Click the Accept button to add the current grid to the grid list. Creating a new circular grid Follow these steps to create a circular grid: 1. Select Circular in the Stage Movement box on the Analysis Automation tab. 2. Move the stage to the analysis starting point, and the click the Create New Grid button. A panel of features appears: 3. Type a label in the Label text box to help identify the grid in the grid list. Note If the Z-axis of your microscope is automated, be careful to adjust the Z-axis to keep the image in focus at all three positions. 4. Click the Add Or Change Point button to specify the first point on the circumference on the circle. 5. Move the stage to the second point on the circle s circumference, and then click the Add Or Change Point button to add the second point. NSS Spectral Imaging System Handbook 177

190 6. Move the stage to a third location on the circle s circumference to complete the definition of the circle, and then click the Add Or Change Point button to complete the grid. 7. Click the Accept button to add the current grid to the Grid list. Working with existing grids To use a grid in an analysis, click the grid s check box in the grid list if it is unchecked. Uncheck the box to remove the grid from the analysis. To edit an existing grid, select the grid and then click the Edit Positions button. Use the buttons in the panel of features that appears to edit the grid information: To return the stage to a selected grid position or circular circumference location, highlight the position and click the Return Stage To Point button. To delete a grid position, highlight the position and click the Remove Point button. Working with grid lists To save the grid list for future analysis, right-click it and choose Save Points File from the pop-up menu. To recall an existing grid list, right-click the grid list and choose Load Points File from the pop-up menu. To remove all grids from the list, right-click the grid list and choose Clear from the pop-up menu. 178 NSS Spectral Imaging System Handbook

191 Using Linescan Use the Linescan option on the Analysis Automation tab to set parameters for acquiring linescans using stage automation. The following parameters are available. Parameter Linescan List Description Check the lines that you want to acquire. See Acquiring a large linescan later in this chapter for instructions for adding lines to the list. NSS Spectral Imaging System Handbook 179

192 Parameter Stage Control Automation Controls Linescan Progress Point Time (s) Beam Control Analysis Automation Acquisition toolbar Description Select Step Size to define the linescan by the distance between points on the line. Select Number Of Points to define the linescan by the number of points on the line. If you have selected Microscope Raster in the Beam Control box, you can select Overlap Percent. This option calculates the size of the raster image in the X and Y dimensions and then determines the step size between points based on the specified overlap of the raster areas. A raster area is a rectangular area that is scanned continuously during acquisition of a point. Select Beam Off to automatically turn off the microscope at the end of the acquisition. Select Use Saved Mag to use the stored magnifications. These features are available only if you purchased column automation and they are supported by your system hardware. The color of the display indicates the acquisition progress. Green indicates selections to be done. Yellow indicates selections currently being acquired. Blue indicates completed acquisitions. Enter the number of seconds to acquire data at each point on the line. Select Center Spot to position the spot in the center of the field of view. Select Microscope Raster to average the acquisition from the entire field of view. This toolbar is similar to the main Acquisition toolbar. Use the buttons to start, pause, stop or abort an automatic analysis, move to points or grid sequences, test the analysis, or acquire a live image. Acquiring a large linescan Note If you have the Analysis Automation option with stage automation, you can acquire linescans larger than the field of view in - ay Linescans mode. Before acquiring a linescan, you should have acquired and identified a spectrum in Spectral Imaging, Spectrum, or Point & Shoot mode. Make sure the elements and Acquisition Properties settings have been defined. The time needed to acquire a large linescan is determined primarily by the speed of your automated stage rather than by the software. 180 NSS Spectral Imaging System Handbook

193 To acquire a large linescan: 1. Switch to - ay Linescans mode. 2. Select Linescan on the Analysis Automation tab in the analysis controls pane. 3. Click the Edit Positions button on the Analysis Automation tab. A panel of features appears. 4. Move the stage to the desired start point and click the Add Or Change Point button. The coordinates and other information about the point appear. If the Z-axis of the stage is automated, adjust the focus by using the Z-axis. To specify the magnification for the point, type a value in the Magnification text box or click the Update button to use the current magnification. You can remove the point by clicking its row of information and then clicking the Remove Point button. You can change the point by moving the stage to a new location, clicking the point s row of information and then clicking the Add Or Change Point button. NSS Spectral Imaging System Handbook 181

194 5. Move the stage to the desired end point and click the Add Or Change Point button. The coordinates and other information about the point appear. If the Z-axis of the stage is automated, adjust the focus by using the Z-axis. To specify the magnification for the point, type a value in the Magnification text box or click the Update button to use the current magnification. You can move the stage to either point by clicking the point s row of information and then clicking the Return Stage To Point button. You can remove or change either point as explained in step Click the Accept button. The specified line is listed in linescan list on the Analysis Automation tab. You can specify another line as explained above. 7. Make sure the linescans you want to acquire are checked in the linescan list, and then click the Start button at the bottom of the Analysis Automation tab. The linescan data appears. Either wait until the acquisition terminates according to the criteria set up on the Linescan tab of the Acquisition Properties dialog box, or click the Stop button at the bottom of the tab. To pause the acquisition, click the Pause button the tab. Click the Start button to resume. at the bottom of 182 NSS Spectral Imaging System Handbook

195 Performing an Analysis Automation acquisition The Start, Stop, Pause, Abort and Acquire Live Image buttons on the Analysis Automation tab perform the same functions as the corresponding buttons on the Acquisition toolbar. The Test Mode button on the right allows you to test the sequence without acquiring an image. The Next Point button skips to the next acquisition sequence. The next section explains how to use Analysis Automation to acquire a linescan that is larger than the field of view. Creating an image montage Analysis Automation provides the ability to create a montage of video images, x-ray maps and quantitative maps, including those extracted from Spectral Imaging data by stitching together images acquired as adjacent fields in a grid automation sequence. To create an image montage: 1. If you are in Spectral Imaging mode, select the type of map or data for the montage from the Map/LS Data Type drop-down list box on the Processing tab in the analysis controls pane. 2. Choose Create Montage from the Batch Processing menu. NSS Spectral Imaging System Handbook 183

196 3. When the Create Montage dialog box opens, select the groups of data you wish to stitch together. You can create a montage using video images, x-ray maps and quantitative maps, including those extracted from Spectral Imaging data. 4. To begin processing, click the arrow button. The montage appears at the right. 5. When you are finished viewing the montage, choose Close. Saving a montage If you wish to save a montage, choose the file name from the file list pane. With the montage open in one of the image panes, choose the Save button on the NSS toolbar. Montage files also can be saved by selecting them in the Modified Data dialog box when you close the projected. Minimizing mismatch When stitching images together, you might observe a mismatch at the edges of the images. This can be minimized by ensuring that: 184 NSS Spectral Imaging System Handbook

197 The X-axis of the microscope scan is aligned with the X-axis of the stage. Use the microscope s scan rotation to align these movements together. This can be done by putting a feature at the top of the scan and moving the stage back and forth until the feature remains at the same Y position as the stage is moved. Adjust the scan rotation if this is not the case. The X and Y scan for NSS must be calibrated correctly for magnification. If the pixel size and squareness of the pixels are incorrect, the amount of stage motion associated with the scans field width will be incorrect. Make sure the stage backlash correction has been set up properly (must be done by a qualified service engineer). NSS Spectral Imaging System Handbook 185

198 Drift Compensation A microscope image can drift, or shift, through time in an acquisition, especially in high magnification analyses. When activated, optional Drift Compensation performs a scan control to correct sample drift during acquisition. In Simple Drift Compensation, the feature that you want to acquire and the feature that drift compensation tracks are the same. In Advanced Drift Compensation, you must define both the analysis area and the tracking area. You can use Drift Compensation in the following modes: Spectral Imaging Point & Shoot - ay Linescans The Enable Drift Compensated Acquisitions button appears on the toolbar only if Drift Compensation was purchased and installed. Contact your sales representative to purchase Drift Compensation. Drift Compensation properties Follow these steps to set up acquisition properties for optimizing drift compensation: 1. Click the Edit Acquisition Properties button on the Acquisition toolbar. 186 NSS Spectral Imaging System Handbook

199 2. When the Acquisition Properties dialog box opens, choose the Drift Comp tab and set the parameters for your acquisition. NSS Spectral Imaging System Handbook 187

200 The following properties are available. Field Automatic With Min Time Of Seconds or Manual With Fixed Time Of Seconds Zoom Factor Separate Analysis And Tracking Areas Description The compensation interval determines how often the system should look for shifts in the image position. Automatic With Min Time Of Seconds The software determines how often it needs to correct. It does this by determining the current drift compensation rate and making sure it will not have to correct for more than one pixel shift each time. Manual With Fixed Time Of Seconds You set a fixed time for the drift-adjusting interval. Drift Compensation works by comparing a current greylevel image with the original greylevel image. During a spectral imaging acquisition, a concurrent greylevel image is used for correction. During Point & Shoot or X-ray Linescan acquisitions, the acquisition is paused while a greylevel image is acquired. The newly acquired greylevel image then is used for drift compensation before the acquisition is resumed. To compensate at a faster interval, you may need to decrease the total frame time by either decreasing the resolution or decreasing the time per frame. NSS can acquire images up to 4096 x 4096 in size. Drift Compensation uses this to acquire smaller images within the 4096 x 4096 space. For example, if the smaller image is 1024 x 1024, it starts in the center of the larger 4096 x 4096 area. If the image shifts through time, the 1024 x 1024 image can be moved in X and Y to track any changes. The zoom factor determines the size of the sub-image; in this case it is 4 (4096 divided by 1024). The higher the zoom factor, the more hardware space is available for tracking image shift. The lower the zoom factor, the higher is the possible resolution of the image, map, etc. The zoom factor ranges from 2 to 64 in powers of 2. If this is unchecked, Drift Compensation will analyze and track the center of the image. When this is checked, it will analyze one area and track another. See Advanced Drift Compensation later in this chapter. 188 NSS Spectral Imaging System Handbook

201 3. Choose OK. Simple Drift Compensation When activated, drift compensation acquires a reference image and periodically measures how far the current image shifts from the reference image. If there is a difference in location between the two images, the correction will be made using beam control. To acquire data with Simple Drift Compensation: 1. Click the Enable Drift Compensated Acquisitions button on the Acquisition toolbar and wait until the reference greyline image is acquired. Drift Compensation will attempt to use this image for tracking. 2. Acquire data as you normally would by clicking the Start Acquisition button. Drift compensation will pause the acquisition periodically to acquire a new image and to correct for any drift that has occurred; then it will resume the acquisition. The more frequently drift compensation performs its correction, the longer the overall acquisition process will take. To stop simple drift compensation, click the Enable Drift Compensated Acquisitions button to turn drift compensation off. Drift compensation uses hardware beam control to track small changes through time. In the default configuration, the image can drift totally off the screen to the top, bottom, left, or right and still be tracked. When the hardware can no longer track, drift compensation will quit and display a message that it can no longer correct. The drift compensation status bar gives an indication of the amount of hardware correction still available. If you run out of correction, the status bar turns red. NSS Spectral Imaging System Handbook 189

202 Advanced Drift Compensation Note Some applications analyze areas that have no features with sufficient contrast for Drift Compensation to track. Advanced Drift Compensation lets you analyze a low-contrast area, while tracking a nearby area with more contrast and better features. You must be in Point & Shoot, Spectral Imaging or - ay Linescans mode to use this feature. To use advanced Drift Compensation: 1. Use the Edit Acquisition Properties button on the Acquisition toolbar to make sure Separate Analysis And Tracking Areas is selected on the Drift Comp tab in the Acquisition Properties dialog box. This adds a double rectangle button to the Acquisition toolbar. 2. Click the button. An image is acquired and two rectangles appear. 3. Drag the red rectangle to define the area to analyze, and drag the yellow rectangle to define the area to track. 4. Click the Enable Drift Compensated Acquisitions button on the Acquisition toolbar. The system acquires a tracking image and then an analysis image. You are now ready to acquire drift compensated data with the Start Acquisition button on the Acquisition toolbar. Drift diagnostics Drift diagnostics displays information on what Drift Compensation is doing, such as how the sample has drifted through time, how much compensation space is available, and how the current image compares with the reference image. 190 NSS Spectral Imaging System Handbook

203 To access drift diagnostics, choose Drift Diagnostics from the View menu. There are four major sections in the dialog box: The following table describes these sections. Section Correction Space Reference + Current Images Description This area shows how the image has drifted through time and how much hardware correction is still available. When the path reaches one of the edges, there is no more space available and drift correction stops the acquisition. The current Drift Compensation image (red) is overlaid onto the reference Drift Compensation image (gray). If Drift Compensation is tracking correctly, there should be very little shift between the reference and current images at any time. NSS Spectral Imaging System Handbook 191

204 Section Drift Data Correlation Image Description Drift Data is a detailed history of every correction since drift was turned on. It shows the X and Y shift that was measured, the time that the correction was made and a correlation coefficient. The correlation coefficient tells how well the current image matches the reference image. A value of 1.0 means there was a perfect match. If two images are totally different, the correlation coefficient will be 0.0. If the current image is too different from the reference image, Drift Compensation will stop. This image is the result of the correlation of the reference Drift Compensation image and the current Drift Compensation image. The simplest case is when the reference image and the current image are identical and perfectly aligned. In this case, the brightest spot is in the center of the correlation image and there is no shift. Now, if the image shifts by one pixel to the right, the correlation image will show the brightest pixel one pixel to the right of the center pixel. Drift Compensation uses the correlation image to measure the shift between the reference and current images. Drift Compensation for JEOL STEM microscopes Drift Compensation for JEOL STEM microscopes uses a digital-to-analog converter and real-time box connected to the computer and the microscope to perform all the same functions as the standard Drift Compensation option. 192 NSS Spectral Imaging System Handbook

205 The Drift Comp tab in the Acquisition Properties dialog box contains a special section for this option. The following table describes the provided features. Feature Rotation Angle Sensitivity Description Some microscopes show an image shift in X and Y when the stage is moved only in the X direction. The rotation angle compensates for this image rotation. Set this angle so moving the stage only in the X direction produces an image shift in X on the microscope CRT. When the reference image is compared with the current image, sometimes the current image is noisy. The sensitivity factor is used to reduce the amount of noise in the current image. Each pixel in the current image is multiplied by the sensitivity factor. A setting of 1.0 means use the current image as is with no noise suppression. A setting of 0.5 means to divide each pixel value by two before comparing the current and reference images. NSS Spectral Imaging System Handbook 193

206 Electron Backscatter Diffraction Electron Backscatter Diffraction (EBSD) is a scanning electron microscope (SEM) technique used to characterize the crystallographic structure of crystalline materials. EBSD uses the wave nature of high-energy electrons and the crystalline nature of the sample to provide a diffraction tool to identify the sample s microstructure. The SEM provides the stationary electron beam that produces backscattered electrons in the sample. These electrons interact with the atomic planes in crystalline material, as described by Kikuchi. The emitted diffracted electrons fluoresce a phosphor screen. The digital camera of the EBSD system records the image of the diffraction pattern. It is then analyzed to identify the specific crystallographic structure of the sample. EBSD is a crystallographic technique complementary to EDS chemical analysis. You can acquire EDS and EBSD data concurrently. The system will use the complimentary information to arrive at a result with higher confidence. Getting started with EBSD Sample preparation This section describes sample preparation, sample positioning in the SEM, and the EBSD navigation pane. EBSD is a highly surface-sensitive technique. Degraded image quality can come from many factors, some (but not all) of which are: specimen damage, surface contamination, and small grain size. Handle your sample carefully. The sample must have: Note A crystalline structure A flat and deformation-free surface No, or only a thin, conductive coating A grain size equal to or greater than twice the electron beam interaction volume. You must also know the crystal type (for example, FCC or BCC), because you will need to identify it later in the calibration process. 194 NSS Spectral Imaging System Handbook

207 Follow standard metallurgical sample-preparation techniques to prepare your EBSD samples through to the polishing step. Each material requires a specific protocol for deformation removal, so a universal method cannot be described here. It is crucial to completely remove all surface deformation caused by the last polishing step. Consult a specimen preparation expert to determine the preparation requirements of your specific sample material. Sample positioning The geometry of the diffraction experiment must be fully characterized and described to the software so that accurate and precise measures can be made. Orientations for the crystals that are measured in EBSD require a frame of reference. Typically that reference frame is the sample as it is placed in the chamber for the acquisition. The naming conventions for the reference directions for this reference frame are Normal for the sample normal, Rolling for the direction down the inclined sample surface, and Transverse for the lateral direction on the sample surface. These are illustrated in the following figure. Normal Sample Transverse Rolling When placing the sample into the chamber, these designations may be important for subsequent analyses. For many randomly oriented samples, these directions do not have any specific meaning. However, for material rolling applications, aligning the sample consistent with the above reference will make interpretation of the results easier. The optimal sample tilt angle for producing the best signal is 70 degrees. This angle yields the brightest patterns, highest intensities, and least signalto-noise ratios and requires the shortest collection times. The tilt can be NSS Spectral Imaging System Handbook 195

208 provided by the SEM stage if its tilt axis is perpendicular to the EBSD camera axis. If it is not, then use a pre-tilted sample holder. The more directly the sample points at the phosphor screen, the better the intensity and analytical results will be. Align the tilt axis of the sample with the x-axis of the SEM image for the best tilt-correction results. Adjust the SEM image rotation until the highest part of the image is at either the top or bottom of the SEM image and the lowest part is on the opposite side. EBSD navigation pane The EBSD navigation pane appears on the left side of the screen. You can access the EBSD modes by clicking the EBSD task bar. The mode you are presently in appears on the topmost taskbar of the navigation pane in boldface type. The three modes are described in the following table. Icon Description EBSD Setup mode, for calibrating the camera and for configuring the camera for sample analysis. EBSD Point & Shoot mode, for surveying a sample spot-by-spot. This mode is best used to discover the crystal structure, orientation and chemistry using a technique known as phase analysis. EBSD Mapping mode, for determining the crystal type and orientation at each location within a scanned region on the surface of the sample. This mode is most useful when investigating the grain and grain boundary nature of an area of the sample. 196 NSS Spectral Imaging System Handbook

209 File list name pane The file name you wish to be used to store the next analysis is entered in the box in the file name pane. Each successive acquisition appends an increasing number in parentheses to provide a unique file name. All files, including both pure EBSD files and combined EDS/EBSD files, associated with the current mode are listed below the base name in the file list pane. In addition to managing your data in projects, you have the ability to assign a base file name for your data before acquisitions. In the file name pane, you can change the default base file name to something more specific to your application. Acquisition Properties for EBSD Follow these steps to set the acquisition properties for EBSD. 1. Click the Edit Acquisition Properties button on the Acquisition tool bar. The Acquisition Properties dialog box appears. NSS Spectral Imaging System Handbook 197

210 2. On the EBSD tab, set the parameters for your acquisition. These parameters are available: Parameter Acquire EDS Data Save Patterns to Disk SEM Image Resolution Map Resolution Tilt Correction Description Acquire EDS data at the same time as EBSD data. Save the raw diffraction patterns. You can reprocess them using new pattern analysis settings if desired. Patterns are very large and by default they are not saved. The resolution of the reference electron image to be acquired. This parameter is set on the Imaging tab. The resolution of the EBSD map to be acquired. This parameter is set on the Spectral Imaging tab. If you are using tilt correction, select the tilt type. This value is set on the Sample Geometry tab. 198 NSS Spectral Imaging System Handbook

211 3. To return settings to their original values, click Defaults. 4. Click OK. EBSD display sizing When several data displays are shown at once, the upper-right quadrant of the screen can appear crowded and the data can be difficult to see. For better visibility, you can show the data displays in three successively larger views: equal, dominant, and exclusive. Double-click on the data title in the Equal view to display it in the Dominant view. Double-click on the title again in the Dominant view to display the data in the Exclusive view. Double-click on the title once more to display the data in the Equal view again. Note If you print the data displays, they will all be the same size. Equal In the Equal view, all data displays are shown at the same size. This is the default view. This example shows three data displays, but there is no limit to the number of displays that may be shown in this pane at one time. NSS Spectral Imaging System Handbook 199

212 Dominant In the Dominant view, one data display is shown larger than all others, which are shown as miniatures. From the Equal view, double-click on the title of a data display to show it in the Dominant view. Double-click on the title of a miniature data display to move it into the dominant display location. This example shows three data displays, but there is no limit to the number of displays that may be shown in this pane at one time. You can also cycle through the data displays to easily bring each one into the Dominant view by rolling the mouse scroll wheel forward or backward. 200 NSS Spectral Imaging System Handbook

213 Exclusive In the Exclusive view, one large data display is shown and all others are hidden. From the Dominant view, double-click on a data display title to show it in the Exclusive view. To return to the Equal view, double-click on the data display title again. You can also cycle through the data displays to easily bring each one into the Exclusive view by rolling the mouse scroll wheel forward or backward. EBSD Setup mode Calibration In this mode, you can setup the calibration of the software and camera, described next, and the analysis of your sample, described later in this chapter. The camera must be calibrated for each new sample because the quality of the measured data is very sensitive to the sample-to-phosphor geometry. To acquire the highest quality data and optimize your analysis results, you must adjust the calibration whenever you analyze a new sample or significantly change the position of the current sample with respect to the phosphor. The electrons diffract from a point on the sample. The ultimate goal of calibration is to determine the shortest distance from this point on the sample to the phosphor. This distance is called the calibrated L value. The point on the phosphor where the shortest distance intersects is called the calibrated (X, Y) location. NSS Spectral Imaging System Handbook 201

214 To calibrate, it is necessary to acquire a high resolution diffraction pattern with the background removed. This pattern is then analyzed to get calibration values for L, X, and Y. Click the Calibration button to display the camera calibration settings. You will see the following tabs in the Calibration settings view: Sample Geometry Camera Background Correction Immersion Lens Correction (optional) Pattern Center 202 NSS Spectral Imaging System Handbook

215 Sample Geometry tab From this tab, you can define the tilt method and tilt angle of the sample, acquire a reference electron image, and insert or retract the camera. 1. Click the Sample Geometry tab. The top left pane displays the reference electron image; in the top right pane is a diagram of the currently defined geometry for the camera and sample; and at the bottom are the geometry settings. Note that the graphic is for instructional purposes. It is not a dimensionally accurate representation of the microscope chamber. 2. Move the EBSD camera into position by using (a) the on-screen buttons or (b) the remote accessory. a. To move the camera using the on-screen buttons: Click the IN arrow button to insert the camera. NSS Spectral Imaging System Handbook 203

216 The camera moves into the correct analysis position. In the diagram in the upper-right pane of the screen, the blue bar (which represents the camera) moves to the left towards the black line (which represents the tilted sample). Click the OUT arrow button to retract the camera. The camera moves back out and stops when fully retracted. Click the STOP button to stop the camera. The IN and OUT buttons are enabled when the camera is not moving. These buttons are disabled when the camera is moving either in or out. Because the IN and OUT buttons are enabled when the camera is not moving, you can still click the IN button when it is fully inserted. The camera will back up slightly then and re-insert itself. When the camera is completely retracted, clicking the OUT button will have no effect. The STOP button is enabled only when the camera is moving. This button is disabled when the camera is not moving. 204 NSS Spectral Imaging System Handbook

217 b. To move the camera using the remote accessory: You can insert and retract the camera either in small steps/increments or in one step by using the EBSD remote camera accessory. There are two buttons available: one for inserting and one for retracting the camera. An LED condition indicator is located on the front of the accessory. To insert or retract the camera incrementally: Press the insert or retract button repeatedly to move the camera in small incremental steps. To fully insert or retract the camera in one step: Press and hold the insert or retract button until the camera begins to move. The camera will continue to move completely in or out of the chamber. To stop the camera while it is moving: Press either the insert or retract button once. To move the camera to the reference position: The reference position is a special location (close to the insert position) that is used to calibrate the position of the slide. Press NSS Spectral Imaging System Handbook 205

218 and hold both the insert and retract buttons simultaneously until the camera begins to move. The camera will move to the reference position. Notice When the camera slide is powered on, it is possible that the system does not know the camera s actual position along the slide, nor does the onscreen graphic reflect the correct position. Once the camera has been either fully retracted or fully inserted, the system can determine the camera s actual position, and the on-screen graphic will display correctly as well. LED Indicator The LED display is green when the camera is fully retracted. This is the safest position for the camera when it is not being used. The LED display is red when the camera is fully inserted. Use caution when moving the sample or inserting other detectors when the EBSD camera is fully inserted to avoid collisions. The red LED can also indicate that the camera is moving in the area between the reference point and the fully inserted position. The LED display is amber when the camera is moving between the reference point and the fully retracted position. 3. Choose the tilt correction setting. There are three options available: Option Off On Sample Holder Tilt Description No tilt correction is applied to the reference electron image or any EBSD acquisition. Used when the sample tilt axis is not parallel to the x-axis of the SEM image. An image pixel will not have equal x and y dimensions. The sample is located on a tilted holder that is mounted on the stage and the sample tilt axis is parallel to the x- axis of the SEM image. Enter the number of degrees of tilt. An image pixel will have equal x and y dimensions. 206 NSS Spectral Imaging System Handbook

219 On Stage Tilt The sample is mounted directly onto the tilted stage and the sample tilt axis is parallel to the x-axis of the SEM image. If the SEM stage tilt is automated, the number of degrees of tilt is automatically reported. If the SEM stage tilt is not automated, enter the tilt value. An image pixel will have equal x and y dimensions. If tilt correction is enabled, the black-line graphic in the upper-right pane that represents the sample will be adjusted to match the specified tilt angle. 4. Click the Acquire Tilt Corrected SEM Image button. A new reference electron image is collected using the current tilt correction method. This button is a duplicate of the standard acquisition button on the Acquisition toolbar. Camera tab From the Camera tab, you can adjust settings to acquire an image at the quality and speed desired to calibrate the camera for the current specimen geometry. NSS Spectral Imaging System Handbook 207

220 1. Click the Camera tab. In the top left pane, the reference electron image appears; in the top right pane is the diffraction pattern and its corresponding intensity histogram; and at the bottom are the camera settings. 2. Click the Acquire Live from Video Camera button. The top right pane displays live video of the diffraction pattern. The intensity histogram is refreshed for each new diffraction pattern image. This button is a duplicate of the standard acquisition button on the Acquisition toolbar. You can also start an acquisition by moving the acquisition cursor on the reference electron image. To pause the acquisition, click the Pause Acquisition button on the Acquisition toolbar. To resume, click the Pause Acquisition button again. To stop the acquisition, click the Stop Acquisition button Acquisition toolbar. on the 3. Adjust the Camera Settings. These settings are available: Setting Binning Description Binning is combining individual pixels into one larger pixel for faster image acquisition, but reduces pattern quality. 1x1 means every pixel is acquired and processed to provide the best resolution but requires the longest processing time. 2x2 means two pixels across and two pixels down are acquired, but processed as one pixel. Each pixel in this new image is the sum of four pixels: two neighboring horizontal pixels and the vertical pixels just beneath them. 208 NSS Spectral Imaging System Handbook

221 Setting Exposure Time Gain Patterns per second Description This setting results in lower resolution but faster processing times. During calibration, only binning settings of 1x1 and 2x2 are permitted. Higher binning settings are permitted during acquisitions (see Analysis ). The amount of time in milliseconds that the camera acquires data for a frame. Longer exposure times result in better image data and longer acquisition times. A measure of electronic amplification of the image signal. Increase this setting to increase the image signal. This also increases the apparent image noise. The estimated maximum rate that the camera can acquire images at the current settings. Below are examples of EBSPs at different exposure levels. Underexposed EBSP NSS Spectral Imaging System Handbook 209

222 Properly exposed EBSP Overexposed EBSP The best quality image is one with the highest exposure and lowest gain settings, which use the full intensity range of the camera. Start with the binning set to 1x1 and the gain set to as low as possible. Increase the exposure time until just before the image is saturated. The image is saturated when the diffraction pattern displays the saturated areas in red. The histogram will display a red indicator on its right side indicating that some pixels meet the upper intensity limit. If the image 210 NSS Spectral Imaging System Handbook

223 is underexposed and any pixels meet the lower intensity limit, they will be colored blue. If increasing the exposure time alone does not maximize the signal, increase the gain setting until just before the image becomes saturated. Background Correction tab The camera image contains both diffraction information and background intensity. The algorithm that automatically finds the lines works best if the background intensity is removed from the camera image. Optimizing the image processing is an iterative technique. The algorithm that finds the lines in the camera image reports its success using a metric called pattern quality (PQ). The PQ is provided to aid you in selecting the best correction settings and is shown as a green progress bar beneath the corrected image with values ranging from 0 (worst) to 100 (best). It is important to make changes in the processing to improve the pattern quality. If a change in the processing results in a lower pattern quality, return to the previous setting or try different settings. NSS Spectral Imaging System Handbook 211

224 1. Click the Background Correction tab. In the top left pane, the reference electron image appears; on the top right there are three images: two diffraction patterns in various states of correction and the background image; and at the bottom pane are the options to optimize the diffraction pattern and the PQ value. 2. Choose a Background Removal method. The background is accentuated in the diffraction pattern, complicates indexing, and is best removed. The intensity distribution of backscattered electrons from the sample surface is not uniform across the image; it follows a distorted cosine distribution. The diffraction information on top of this background is typically only 5 to 10% of the native backscattered electron intensity. These removal methods are available: Option None Subtraction Division Description No background correction. Typically not used for EBSD analyses, but included for illustration purposes. Uses the image subtraction correction method. To use this method, first acquire a background pattern. The background pattern is subtracted from the uncorrected camera image. The intensity is optimized using an automatic brightness and contrast adjustment. Uses the image division correction method. To use this method, first acquire a background pattern. The background pattern is divided into the uncorrected camera image. The intensity is optimized using an automatic brightness and contrast adjustment. Subtraction and division are two mathematically different methods that typically arrive at similar results. 3. Enter the number of images to average when collecting the background image. The background image is obtained by averaging a large number of different diffraction patterns, the amount of which is specified in this 212 NSS Spectral Imaging System Handbook

225 field. The averaging operation smoothes the intensity in each individual pattern. The result is an image that should contain no visible pattern. The number of images to use depends on the beam scan rate of the SEM and the exposure time selected to produce an image with no apparent pattern. The total background-image acquisition time (number of frames times the camera exposure time) should exceed the SEM image scan time. 4. Click Acquire Background. The background image is acquired by averaging the number of camera frames selected using the current exposure. The SEM should be scanning during this operation to collect patterns from many different pixels and patterns. Better quality results are usually obtained by using the fastest slow-scan setting of the SEM rather than by using TV-scan rates. If your resulting background image still has a visible pattern, reduce the SEM magnification by half and reacquire the background image. Be sure to change the SEM magnification setting back to its original value when you are finished with background collection. Keep adjusting settings and reacquiring the diffraction pattern until the pattern quality value is as high as possible. 5. Choose a flat-field correction method. The background removal method described above is only perfectly applied for a single location in the scanned area. At low SEM magnifications, deviations from this ideal location can introduce additional intensity variations in the background-corrected patterns. Flat-field correction removes these variations from the patterns for higher pattern quality and better diffraction analysis later. You can perform flat-field correction with or without background removal. NSS Spectral Imaging System Handbook 213

226 The flat-field correction options are: Option None FFT Parabolic Description No background correction. Typically not used except to achieve maximum speed. The Fast Fourier transform method is a form of high-pass filter, assuming that the background is low frequency and the diffraction patterns are at a higher frequency. The image is analyzed in the frequency domain and the lower frequencies are removed. Enter the strength value that provides the best correction. The higher the strength value, the greater the number of low frequencies that are removed. The Parabolic method models the background of each pattern as a paraboloid and then removes the modeled background. 6. Click the Acquire Diffraction Pattern button. The diffraction pattern is acquired at the current image cursor location based on the current settings. Click the cursor in the image to change the source location of the acquired pattern. Adjust the settings and reacquire the diffraction pattern until the PQ value is as high as possible. Immersion Lens Correction tab (optional) When an EBSP is collected in an immersion lens SEM, the pattern is distorted due to the emerging magnetic field. This results in curved Kikuchi bands in the diffraction pattern. These curved lines will impair the ability to find lines and to get accurate indexing results. The correction provides a diffraction pattern with straightened lines that results in improved indexing. 214 NSS Spectral Imaging System Handbook

227 Here is an example of band distortion: The immersion lens correction feature calibrates the amount of curve in the system at a given geometry and applies the correction automatically to each diffraction pattern between collection and analysis. Enabling Immersion Lens Correction If you are operating your SEM in immersion lens mode, you can enable lens correction in the EBSD Service mode on the Service navigation pane. A new Immersion Lens Correction tab is added to EBSD Setup Calibration. NSS Spectral Imaging System Handbook 215

228 Using Immersion Lens Correction Note To apply immersion lens correction to subsequent analyses, for example, Pattern Center Calibration, Point and Shoot, Mapping, etc, check Use Immersion Lens Correction. 1. Turn off the immersion lens mode on the microscope and acquire a diffraction pattern. This pattern will appear normal and without any curved bands. Also check that your Calibrated WD and KV values match your Current WD and KV values. 2. Turn on the immersion lens mode on the microscope and acquire a diffraction pattern. 3. Place the pink guideline on the Magnetic Field OFF non-distorted pattern. Move the straight pink line to align with the edge of a nearly vertical band. 216 NSS Spectral Imaging System Handbook

229 4. Align the green line on the same band on the Magnetic Field ON distorted pattern. Use the handles to define the curve. Since most distortion is at the top of the pattern, you can place more handles towards the top. Handles do not have to be equally spaced. NSS Spectral Imaging System Handbook 217

230 5. Calculate the correction by clicking the arrow in the Step 5 pane. The corrected diffraction pattern is displayed. In the example above, the image required a corrective shift to the right. This results in a triangular wedge on the upper left hand corner. Pattern Center tab The pattern center is the location on the phosphor screen whose normal points to the electron beam location on the tilted sample. The normal is represented by L in the diagram below. 218 NSS Spectral Imaging System Handbook

231 Settings on this tab are used to store the current calibration parameters of (X, Y, L) for the current diffraction geometry of the sample relative to the phosphor screen. To calibrate correctly and accurately, use a sample with a known crystal structure. 1. Click the Pattern Center tab. In the top left pane, the reference electron image appears; in the top right pane, the diffraction pattern appears optionally with pattern quality and index quality scores below it; next to the diffraction pattern is a graphic representation of the crystal orientation; and at the bottom is the settings pane. The table in the Pattern Center pane shows the parameters for the specific pattern center that you are calibrating. The first time you perform calibration for each sample, NSS automatically populates the X, Y, and L fields with approximate values. The calibration routine will adjust these values for better indexing results. You can adjust these settings manually if necessary. NSS Spectral Imaging System Handbook 219

232 The pattern center parameters are: Parameter X (mm) Y (mm) L (mm) Pattern Qual (%) Index Qual (%) WD (mm) Date (dd/mm/yyyy) Description The lateral calibration location of the pattern center. The vertical calibration location of the pattern center. The sample-to-phosphor distance of the pattern center. The score of the clarity of the Kikuchi bands in the diffraction pattern used for calibration. Read-only.. The score of how closely the indexed bands match the measured band used for calibration. Read-only.. The working distance, which is the nominal SEM focusing distance to the sample. Readonly. When a pattern center calibration is modified, this field is updated to the current date. Readonly. 2. Acquire a new diffraction pattern by clicking on a different location on the reference electron image or click the Acquire Pattern button to acquire a pattern at the current active cursor location on the reference image. 3. Determine how many pattern centers to use for calibration. At high SEM magnifications (above 500x), only one calibration setting is required for high precision diffraction measurement. To calibrate using a single pattern center, see Single pattern center calibration below. At low SEM magnifications (500x and below), three pattern centers provide the most accurate orientation measurements. Under these conditions, the pattern center calibration values vary enough between the corner scan locations that the resulting diffraction measurements are distorted. This option calibrates the pattern center values for the 220 NSS Spectral Imaging System Handbook

233 planar surface of the sample and provides optimized calibration values at every pixel scan location. Each pattern center must be calibrated individually. To calibrate using three pattern settings, see Triple pattern center calibration below. Single pattern center calibration: a. Make sure the Use 3 Pattern Centers check box is not checked. Leaving this option unchecked selects the single point calibration method. You will see a single labeled cross-hair on the reference image corresponding to the current position at which the diffraction pattern will be acquired. b. Proceed to the To calibrate the pattern center section and follow steps 1-5. Triple pattern center calibration: c. Check the Use 3 Pattern Centers check box. Check this option to calibrate three pattern centers for the sample. You will see three labeled cross-hairs on the reference image corresponding to the current positions at which diffraction patterns will be acquired. d. Choose Pattern Center 1 for calibration. e. Proceed to the To calibrate the pattern center section and follow steps 1-5. f. Choose Pattern Center 2 for calibration. g. Proceed to the To calibrate the pattern center section and follow steps 1-5. NSS Spectral Imaging System Handbook 221

234 h. Choose Pattern Center 3 for calibration. i. Proceed to the To calibrate the pattern center section and follow steps 1-5. To calibrate the pattern center: 1. Click the Acquire Diffraction Pattern button. A diffraction pattern is generated based on the current settings. The pattern lines and the indexed lines are displayed using the current settings. The calculated pattern lines should match the underlying pattern very well but the indexed lines will match only if the pattern center values are accurate. If the pattern is not of sufficient quality, you may select a new location by clicking at a new location in the image. For the most accurate calibration results, select a location near the default location. For a single pattern center calibration, the cursor location should generally be in the middle of the image. For a triple pattern-center calibration, there should be one cursor in three of the four corners of the image. 2. Choose the crystal structure of the sample from the Change Selected Crystal drop down box. NSS uses the sample s crystal structure for calibration. Because the crystal structure of your sample is known, it is the standard used for the calibration. 3. Click Find to locate the pattern lines. Pattern lines are the lines that the Radon transform finds in the corrected diffraction pattern. This function is used when the Radon parameters are adjusted and a new calculation is made using the current diffraction pattern. Whenever you collect a new diffraction pattern, NSS automatically performs a find operation. 222 NSS Spectral Imaging System Handbook

235 Show Lines Display the pattern lines on the diffraction image. Flash Lines Intermittently display and hide (blink) the pattern lines on the diffraction pattern. 4. Click Index to determine the index lines. Index lines are the lines that the indexing routine returns after comparing the pattern lines and the crystal structure using the calibration values. This function is used when the indexing parameters are adjusted and a new calculation is made using the current diffraction pattern. Whenever you collect a new diffraction pattern, NSS automatically performs an indexing operation. Show Lines Display the index lines on the diffraction image. Flash Lines Intermittently display and hide (blink) the index lines on the diffraction pattern. 5. Choose Fine Calibration, Medium Calibration, or Coarse Calibration. The system uses mathematical algorithms that adjust the pattern center values to make the index lines match the pattern lines as closely as possible. Fine Calibration: This algorithm is local and fast. Use fine calibration when you believe that the current calibration is close to optimal. This algorithm follows the maximum gradient in the Indexing Quality to identify the best calibration settings. Medium Calibration: This algorithm searches wider and a little slower. Use medium calibration followed by fine calibration when the fine calibration alone does not match the index lines to the pattern lines as closely as you expected, but indexing does occur. This algorithm searches near the current calibration settings for the best indexing quality. NSS Spectral Imaging System Handbook 223

236 Coarse Calibration: This algorithm is an exhaustive, slow search over a large area. Use this option when the indexing quality is low. This can occur when the current geometry (SEM working distance or sample-todetector distance) is far from the current calibration settings. This algorithm searches a large range of calibration settings for the best indexing quality. This operation could take a few minutes to complete. The final step includes a fine calibration. Continue to adjust the settings on the Pattern Center tab until you have maximized the pattern quality of the diffraction image. Note If the pattern is still not indexing, ensure that the crystal type is correct. If the crystal type is correct and there are still issues with indexing, it may be necessary to hand modify the found lines and then re-index. To edit the Advanced Processing and Display Option settings: Additional settings are available for calculation and display, but they are not a mandatory part of the workflow. 1. Click Advanced on the Pattern Center tab. The Advanced Processing and Display Options dialog box appears: 224 NSS Spectral Imaging System Handbook

237 2. Adjust the settings as necessary. The settings are: Setting Number of Radon Lines Show Radon Image Type: Show Pattern Quality Show Index Quality Coarse Search Range Defaults Description Enter the maximum number of Radon lines to measure and display on the diffraction pattern. The default value changes based on the symmetry of the current crystal structure. Fewer lines allow for faster processing but at reduced orientation precision. We recommend using at least four lines. Check this box to display the Radon image of the sample in the calibration pane. Style of Radon Lines to display. Bands: Displays parallel lines on the edges of the Kikuchi bands. Center: Displays a single line in the middle of the Kikuchi bands. Check to display the pattern quality score below the pattern. Check to display the index quality score below the pattern. Defines calibration limits and steps for X, Y, and L values when performing automatic coarse calibration on pattern and index lines. Parameter units are min (mm), max (mm), and number of steps Return all settings to factory default values. To load previous calibration settings: If the current calibration settings are not optimal for the current geometry and more optimal settings were saved during a prior experiment, these values may be loaded from a pattern center file. This method of coarse calibration is especially helpful if you routinely operate the system with a non-standard geometry. NSS Spectral Imaging System Handbook 225

238 1. Right-click anywhere on the Pattern Center tab and choose Load Calibration from the popup menu. The Open EBSD Pattern Center File dialog box appears. 2. Select the pattern to load and click Open. The settings in the selected file are loaded into the pattern center parameter fields. To save the current pattern calibration settings: If you have calibration settings you would like to be able to use for future calibrations, you can save these settings. 1. Right-click anywhere in the Pattern Center tab and choose Save Calibration from the popup menu. The Save EBSD Pattern Center File dialog box appears. 2. Rename the file if desired and click Save. 226 NSS Spectral Imaging System Handbook

239 Editing found lines The Editable Lines feature allows you to improve the index quality (IQ) score of an EBSD pattern by manipulating the found lines that are displayed on a diffraction pattern. You can add, move, and delete the lines on the pattern, and move the pattern center in Calibration mode. You can add bands to patterns where bands may be missing. You can change the endpoint of a found band to match the Kikuchi pattern. You can rotate a band to change the angle to match with a band s edges in the pattern. You can delete found bands that don t match anything on the pattern, that are not useful, or bands that you have added. Editing found lines is enabled in the EBSD Setup and Point & Shoot modes where a diffraction pattern is available. Editing lines is not available in the Mapping mode. Note Once you make a change to a band or move the pattern center, it cannot be reversed. There is no Undo function available with this feature. However, clicking Find Lines will automatically recalculate the original line positions. Editing found lines toolbar There are four tools available on the editable lines toolbar: Move the pattern center (available in the Setup mode only) Add a new band to the pattern Move a line on an existing band Delete a band The tool you select will remain chosen until you choose another tool or click on the toolbar button to deselect the tool. If the toolbar is unavailable, click anywhere on the diffraction pattern display so that it is highlighted, and the toolbar will become active. The NSS Spectral Imaging System Handbook 227

240 following image shows the pattern display area highlighted by a yellow box and the toolbar active. For better visibility, you can set the display mode of the pattern image to the exclusive view so that the pattern appears larger on your screen. This can help with editing bands and making more precise movements. You can also choose not to show the index lines so that only the editable lines appear on the pattern (shown in green in the image above). Editing found lines cursors The tool you choose will determine how your cursor changes while performing an action. Once your cursor is placed close to a line or hovers on a line, your cursor will change to one of these described below: No tool has been selected, or the Move the Pattern Center tool has been selected but the cursor is not in the region to move the pattern center. The Add a new Band to the Pattern tool is selected or in use. The Move a line on an existing band tool is selected or you are moving or rotating a line. 228 NSS Spectral Imaging System Handbook

241 The cursor is in the region to move (not rotate) a line. The cursor is in the region to rotate a line, extend a band, or move the pattern center. The Delete a band tool is selected. The cursor is in the region to delete a band. Moving the pattern center You can move the pattern center only when you are in the EBSD Setup Mode on the Pattern Center tab of the Calibration page. 1. Click the arrow button to select the Move the pattern center tool. The image below shows the Move pattern center tool selected. The cursor (white arrow) is near the pattern center (red cross) but not in the region to move it: NSS Spectral Imaging System Handbook 229

242 When the cursor is close enough to the pattern center or hovered over the pattern center, it changes into the crossed arrows cursor and the pattern center can be moved: 2. Click and drag to move the pattern center. The mouse cursor changes back to an arrow. The original position of the pattern center is visible for reference until you drop the pattern center marker in its new location. 230 NSS Spectral Imaging System Handbook

243 3. Move the pattern center in small increments until you are satisfied with the IQ score. The pattern center is shown its new location below. Notice that the IQ score has changed. Note If the IQ score does not improve after making changes to lines, press the Find button to automatically find the lines again. This will bring the default lines back for the pattern. If the IQ score does not improve after making changes to the pattern center, press one of the calibration buttons to return to the default pattern center for the pattern. If you have moved the pattern center far from its original position, you may need to run the coarse calibration. NSS Spectral Imaging System Handbook 231

244 Adding a new band to the pattern You can add lines along the band edges in the diffraction pattern. 1. Click the pencil button to select the Add a new band to the pattern tool. The following image shows that the Add a new band tool is activated. Place the mouse cursor at the location to start the line. 2. Click and drag your mouse to draw the line along the edge of a band. 232 NSS Spectral Imaging System Handbook

245 When you release the mouse, the line turns red to indicate that it is not part of a band yet: 3. Click on the opposite edge of the band in the diffraction pattern to add a line parallel to the one you just added. NSS Spectral Imaging System Handbook 233

246 After you add the second line, a band is created and both lines turn green: Notice that the IQ score has changed. In this case, adding the band has increased the IQ score. Moving a line on an existing band You can move a line in two ways: you can rotate it to change its angle relative to the band in the diffraction pattern, or you can move the line towards or away from the band edge. Click the hand button tool. to select the Move a line on an existing band There are two types of mouse cursors that can appear when hovering over a line while in the move mode. The cursor that appears depends on the position of the cursor relative to the end of the line: Crossed arrows : This cursor appears when it is within the first 15% of either end of the line. This cursor indicates that you can change the endpoint of the line. The line rotates with the opposite end fixed as the pivot point. The second line adjusts automatically to remain parallel to the first line after it is moved. Band lines will adjust to remain parallel to each other. 234 NSS Spectral Imaging System Handbook

247 Hand : This cursor appears when it is within the middle 70% of the line. This cursor indicates that you can move the entire line towards or away from its parallel partner line. With this tool, just one line moves; the parallel line does not adjust to move with the first line. The following image shows that the tool to move a band is selected, but that the cursor is not in the region to move or rotate any line. Moving a line s endpoint Moving a line s endpoint will change the angle of the line pair relative to the band in the pattern. 1. To move a line s endpoint, hover your cursor over the end of the line you want to move, as shown in the following image. NSS Spectral Imaging System Handbook 235

248 2. Click on the line s endpoint to capture it and drag it to the desired position. The opposite end of the line stays stationary as if the line were attached to the pattern. The cursor changes to the arrow as shown in the following image: 236 NSS Spectral Imaging System Handbook

249 Once you release the mouse, the other line adjusts to become parallel with the first one. Notice that the IQ score has increased in this case. This is because the lines are now aligned better with the band in the diffraction pattern. Widening or narrowing a band You can either widen or narrow a band. 1. Hover your mouse cursor closer to the middle of the line so that the hand cursor appears. NSS Spectral Imaging System Handbook 237

250 2. Click on the line to select it and move it to the desired position. The mouse cursor changes to the one shown in the image below. The original position is shown with a white line and the new position is shown with a green line. 3. Release the cursor at the desired position. The line will turn green and the cursor changes back to a hand. 238 NSS Spectral Imaging System Handbook

251 Notice that the IQ score increased. This is because the line was moved closer to the band edge in the diffraction pattern. Quickly extending or shortening a band You can lengthen or shorten a band quickly. 1. Hover the cursor at the location to where you would like to extend or shorten the band. The crossed arrows cursor must be displayed to change the band length to that point. Both lines in the band will be lengthened or shortened. In the following image, the crossed arrows cursor is shown past the end of a band to lengthen it. NSS Spectral Imaging System Handbook 239

252 2. Click the location while the crossed arrows cursor is displayed and both ends of the band will automatically lengthen or shorten. Deleting bands You can delete bands from the image. If the line is part of a pair that forms a band, both lines will be deleted. You can also delete a single line that is not part of a pair, such as one you just added. You cannot delete one line of a band pair, nor can you undo deleting a band. 1. Click the button to select the Delete a band tool. When the Delete a band tool is active, your cursor will become an arrow with a black eraser next to it as shown in the following image. 240 NSS Spectral Imaging System Handbook

253 When your cursor is close enough to the line, the cursor will change to an arrow with a white eraser and motion marks as shown in the following image. NSS Spectral Imaging System Handbook 241

254 2. Click the line that you want to delete. The line will disappear and you will see a white box momentarily as you click. 3. Release the cursor. The white box disappears and so does the line that is parallel to the one you deleted. The cursor changes back to an arrow with a black eraser and the original band is removed. 242 NSS Spectral Imaging System Handbook

255 Displaying zone labels You can choose to display the zone labels for found lines and index lines as shown in the following image. 1. Click Advanced to display the Advanced Processing and Display Options dialog box. 2. Check Numeric Pattern Labels and click OK. To hide the zone labels, remove the check from the Numeric Pattern Labels box and click OK. NSS Spectral Imaging System Handbook 243

256 Analysis The goal of the previous section was to calibrate the X, Y and L values by analyzing a high-resolution diffraction pattern. Having a well-calibrated pattern center is necessary for EBSD analysis. In the Analysis mode, you optimize the acquisition speed while maintaining the necessary image quality for indexing patterns. Speed is needed to minimize overall acquisition time of maps. Quality is needed to ensure accurate indexing of the patterns and determining the crystal structure of your sample. You can collect a diffraction pattern, correct the background of the diffraction image, and analyze the Kikuchi bands with potentially different settings during analysis than those used during calibration. You can select any number of crystal structures to determine the orientation of your sample. Once you have identified all of the useful crystal structures, you can continue to the Mapping mode or the Point and Shoot mode for analysis. The process to acquire an image and correct the background is the same for both the calibration stage and the analysis stage, except that during analysis, you can select a higher binning setting for faster image acquisition. Click the Analysis button to display the camera settings. You will see the following tabs: Camera Background Correction Find Crystals 244 NSS Spectral Imaging System Handbook

257 Camera tab From the Camera tab, you can acquire a reference electron image 1. Click the Camera tab. In the top left pane, the reference electron image appears; in the top right pane is the diffraction pattern and its corresponding intensity histogram; and at the bottom are the camera settings. 2. Click the Acquire Live from Video Camera button. The top right pane displays live video of the diffraction pattern. The intensity histogram is refreshed for each new diffraction pattern image. This button is a duplicate of the standard acquisition button on the Acquisition toolbar. You can also start an acquisition by moving the acquisition cursor on the reference electron image. To pause the acquisition, click Pause Acquisition on the Acquisition toolbar. To resume, click Pause Acquisition again. To stop the acquisition, click Stop Acquisition toolbar. on the Acquisition NSS Spectral Imaging System Handbook 245

258 3. Adjust the Camera Settings. These settings are available: Setting Binning Description This setting provides the ability to trade off between image resolution and speed. Individual pixels are combined into one larger pixel for faster image acquisition, but this results in lower pattern quality. A setting of 1x1 means every pixel is acquired and processed, providing the best resolution but requiring the longest processing time. 2x2 means two pixels across and two pixels down are acquired, but processed as one pixel. Each pixel in this new image is the sum of four pixels: two neighboring horizontal pixels and the vertical pixels just beneath them. This setting results in lower resolution but faster processing times. The available settings are 1x1, 2x2, 4x4, and 8x8. Higher binning is offered in analysis mode to allow for higher frame rates and faster acquisition times. Exposure Time Gain Patterns per second The amount of time in milliseconds that the camera acquires data for a frame. Longer exposure times result in better image data and longer acquisition times. A measure of electronic amplification of the image signal. Increasing this setting increases the image signal, but also increases the apparent image noise. The estimated maximum rate that the camera can acquire images at the current settings. Depending upon the type of analysis you will perform, you may want to acquire at higher frame rates. To do this and maintain a high index quality, you need a combination of higher binning, higher beam current, shorter exposure time, and higher gain. As you modify the exposure time and gain, pay attention to the diffraction pattern and associated histogram. For the best signal quality it is important 246 NSS Spectral Imaging System Handbook

259 to use the full range of the camera, but at the same time, not to saturate the image. The histogram displays the entire range of pixel values. Choose an exposure time and gain setting that will just span the entire range of the histogram. If any of the pixel values are too intense (overexposed), they will appear red on the image and the histogram will display a red indicator on the right side. Pixel values that are not intense enough (underexposed) will appear blue on the image and the histogram will display a blue indicator on the left side. Mapping If you are going to perform an EBSD Mapping acquisition, the speed required to acquire a large map of data points is more important than producing a high quality pattern. This acquisition mode requires a very flat, smooth surface that should produce patterns at every pixel location during the map acquisition. In this mode, the rate of pattern collection is very important to minimize total acquisition time. Typically you can set the patterns-per-second rate rather high (with a short exposure time).the quality of the patterns will be reduced at these higher rates, so care must be taken to maintain a minimum pattern quality for accurate indexing. Point and Shoot When preparing for Point and Shoot mode acquisitions, the pattern quality is more important than the acquisition speed. A limited number of very high-quality diffraction patterns acquired at specific locations in the sample are all that is needed. These locations can be representative visible grains or interesting particle features. Sometimes, the sample surface can be too rough for mapping, but individual points can still be acquired that produce good patterns. In this mode, select a limited number of points (fewer than 20) and use a long exposure time (low collection rate). For example, if each exposure takes two seconds, the complete acquisition would last less than one minute. NSS Spectral Imaging System Handbook 247

260 Background Correction tab The camera image contains both diffraction information and background intensity. The algorithm that automatically finds the Radon lines works best if the background intensity is removed from the camera image. Optimizing the image processing is an iterative technique. The algorithm that finds the Radon lines in the camera image reports its success as a metric called pattern quality (PQ). The PQ is provided to aid you in selecting the best correction settings and is shown as a green bar beneath the corrected image, with values ranging from 0 (worst) to 100 (best). It is important to make changes in the processing to improve the pattern quality. If a processing change results in a lower pattern quality, which is insufficient to correctly locate the lines, return to the previous setting or try different settings. 1. Click the Background Correction tab. In the top left pane, the reference electron image appears; on the top right there are three images: two diffraction patterns in various states of correction and the background image; and in the bottom pane are the options to optimize the diffraction pattern and the PQ value. 248 NSS Spectral Imaging System Handbook

261 2. Choose a Background Removal method. The background intensity dominates the diffraction pattern, complicates indexing, and is best removed. The intensity distribution of backscattered electrons from the sample surface is not uniform across the image; it follows a distorted cosine distribution. The diffraction information on top of this background is typically only 5 to 10% of the native backscattered electron intensity. These removal methods are available: Option None Subtraction Division Description No background correction. Typically not used for EBSD analyses, but included for illustration purposes. Uses the image subtraction correction method. To use this method, first acquire a background pattern. The background pattern is subtracted from the uncorrected camera image. The intensity is optimized using an automatic brightness and contrast adjustment. Uses the image division correction method. To use this method, first acquire a background pattern. The background pattern is divided into the uncorrected camera image. The intensity is optimized using an automatic brightness and contrast adjustment. Subtraction and division are two mathematically different methods that typically arrive at a similar result. 3. Enter the number of images to average when collecting the background image. The background image is obtained by averaging a large number of different diffraction patterns, the number of which is specified in this field. The averaging operation smoothes the intensity in each individual pattern. The result is an image that should contain no visible pattern. NSS Spectral Imaging System Handbook 249

262 The number of images to use depends on the beam scan rate of the SEM and the exposure time selected to produce an image with no apparent pattern. The total background-image acquisition time (number of frames times the camera exposure time) should exceed the SEM image scan time. 4. Click the Acquire Background button. The background image is acquired by averaging the specified number of camera frames using the current exposure settings. The SEM should be scanning during this operation to collect patterns from many different pixels and patterns. Better quality results are usually obtained by using the fastest slow-scan setting of the SEM rather than by using TV-scan rates. If your resulting background image still has a visible pattern, reduce the SEM magnification by a factor of 2 and reacquire the background image. Remember to return the SEM magnification setting back to its original value when you are finished with background collection. 5. Choose a flat field correction method. The background removal method described above is only perfectly applied for a single location in the scanned area. At low SEM magnifications, deviations from this ideal location can introduce additional intensity variations in the background-corrected patterns. Flat-field correction removes these subtle intensity variations from the patterns for increased pattern quality and better diffraction analysis later. You can perform flat field correction with or without background removal. 250 NSS Spectral Imaging System Handbook

263 The Flat Field options available are: Option None FFT Parabolic Description No background correction. Typically not used except for maximum speed. Use the fast Fourier transform method. This method is a form of high-pass filter, assuming that the background is at low frequencies and the diffraction patterns are at higher frequencies. The image is analyzed in the frequency domain and the lower frequencies are removed. Enter the strength value that provides the best correction. The higher the strength value, the greater the number of low frequencies that are removed. Use the parabolic method. This method models the background of each pattern as a paraboloid and then removes the modeled background. 6. Click the Acquire Diffraction Pattern button. This acquires the diffraction pattern at the current image cursor location based on current settings. Clicking the cursor in the image will change the source location of the acquired pattern. Find Crystals tab This tab is where you determine the crystal structure and orientation of your sample. NSS Spectral Imaging System Handbook 251

264 1. Click the Find Crystals tab. In the top left pane, the reference electron image appears; in the top right pane, the diffraction pattern appears optionally with pattern quality and index quality scores below it; next to the diffraction pattern is a graphic representation of the crystal orientation; and at the bottom is the settings pane. 2. Either use the current diffraction pattern or acquire a new one by clicking on a different location on the reference electron image, and click the Acquire Pattern button. A diffraction pattern is generated based on the current settings. The Radon lines and the indexed lines are displayed using the current settings. The Radon lines and the indexed lines should match the underlying pattern or Kikuchi bands very well. If the indexed lines do not match and the calibration values are good, then it is possible that the sample has a crystal that you have not specified yet. 3. Choose the crystal structures from the Select Crystals To Use drop down box. When you reacquire the diffraction pattern, NSS will compare the pattern to the crystal structure(s) chosen and return an index quality 252 NSS Spectral Imaging System Handbook

265 score. The highest score indicates the most likely crystal structure of your sample. If the pattern quality is high, but none of the selected crystals give a good match, you may need to add more crystals to your analysis. 4. Click Find to locate the Radon lines. Radon lines are the lines that the Radon transform finds in the corrected diffraction pattern. This function is used when the Radon parameters are adjusted and a new calculation is made using the current diffraction pattern. Whenever you collect a new diffraction pattern, NSS automatically performs a find operation. Show Lines: Display the Radon lines on the diffraction image. Flash Lines: Intermittently display and hide (blink) the Radon lines on the diffraction pattern. 5. Click Index to locate the index lines. These are the lines that the indexing routine returns after comparing the Radon lines and the crystal structure using the calibration values. This function is used when the indexing parameters are adjusted and a new calculation is made using the current diffraction pattern. Whenever you collect a new diffraction pattern, NSS automatically performs an indexing operation. Show Lines: Display the index lines on the diffraction image. Flash Lines: Intermittently display and hide (blink) the index lines on the diffraction pattern. Note You can edit the found lines by referring to Editing found lines in the Calibration section. NSS Spectral Imaging System Handbook 253

266 Advanced settings Additional settings are available for calculation and display, but they are not a mandatory part of the workflow. 1. Click the Advanced button on the Find Crystals tab. The Advanced Processing and Display Options dialog box will appear: 2. Adjust the settings as necessary. The settings are: Setting Number of Radon Lines Show Radon Image Description Enter the maximum number of Radon lines to measure and display on the diffraction pattern. The default value changes based on the symmetry of the current crystal structure. Fewer lines allow for faster processing but at reduced orientation precision. Check this box to display the Radon image of the diffraction pattern. 254 NSS Spectral Imaging System Handbook

267 Type Show Pattern Quality Show Index Quality Coarse Search Range Defaults Style of Radon Lines to display. Bands: Displays parallel lines on the edges of the Kikuchi bands. Center: Displays a single line in the middle of the Kikuchi bands. Check to display the pattern quality score below the diffraction pattern. Check to display the index quality score below the diffraction pattern. These settings do not apply to analysis. Return all settings to factory default values. EBSD Views tab There are several ways to display EBSD data. There are displays for pixel information, map information, and histograms. The data can be phase information, orientations, misorientations, grain boundaries, and phase boundaries. The views are displayed in the upper-right quadrant of the screen. The specific options vary slightly between analysis modes, but the general operation is identical for all modes. Data displays for all modes are grouped into two categories: Common and Phases. The Common category contains display options for data that is common to the acquisition and valid for all of the analyzed phases in the data sets. The Phases category contains data that is unique for each crystal phase selected during the acquisition setup. The data display is labeled with both the crystal name and the data type. NSS Spectral Imaging System Handbook 255

268 Selecting views Each EBSD analysis mode has different views available, which are described below. Unless noted otherwise, a view is available in the EBSD Point and Shoot and Mapping modes. Chosen views are automatically saved and kept checked for each project by mode. 1. Click an EBSD analysis mode button in the navigation pane. 2. Click the EBSD Views tab in the lower left quadrant of the screen. The data types accessible for the selected mode are listed in an expanding and collapsing tree structure. As an example, the tree structure below shows all of the views available in the EBSD Mapping mode. The tree is completely expanded and all views are selected for display. 256 NSS Spectral Imaging System Handbook

269 3. Select the data to display by checking the corresponding checkbox. Check item/clear item: To select an item for display, check the box next to the item. To clear an item from the display, clear the checkmark from the box next to the item. NSS Spectral Imaging System Handbook 257

270 Check all/clear all: Check the box next to a group. All of the checkboxes in that group are checked. Click Apply to display all selected data displays in the upper right quadrant of the screen. To clear all checkboxes in a group, clear the checkbox next to the group name. Expand all groups/collapse all groups: Click the + (plus) next to the group to expand it; click the (minus) to collapse the group. 4. Click Apply. The displays in the upper-right quadrant are updated to reflect the new selections. This final set of display options is automatically saved for the current project. You can also edit the display properties for many of the views. Right-click on the view to display the property panel if one is available for the particular display. The property panel for each view is explained following its description below. Common view types When EBSD data is acquired and analyzed, there is basic information that applies to all phases, and there is also phasespecific information. The views in the Common group show the basic information and are described below. The phase-specific information is available by phase at the bottom of the tree structure and is described following descriptions of the Common views. 258 NSS Spectral Imaging System Handbook

271 Pattern This is the display of the processed EBSD diffraction pattern for the current cursor location on the reference image. The cursor on the diffraction pattern itself identifies the pattern center location. Right-click on the diffraction pattern to display the following property panel: NSS Spectral Imaging System Handbook 259

272 The following table describes the properties that you can change: Property Color Scheme Gradient color bar Mode Brightness Contrast Description Controls the color display mode of the image or diffraction pattern. There are several color schemes available: Red, Green, Blue, Cyan, Magenta, Yellow, and Grey. The colors range from black to the specified color. The default color is grey. Earth: The colors simulate a landscape, ranging from sea (dark blue to light blue), which represents the lowest pixel intensity; to beach (white), which represents medium pixel intensity; to mountains (light brown to dark brown), which represents the highest pixel intensity. Custom: Colors blend from one color to another. Click on the colored boxes on either side of the gradient color bar to select which colors to blend. Thermal: Colors range from blue to red to mimic cold (low intensity) and hot (high intensity) areas. Clipping: Based on the Grey color scheme except that the lowest value is blue and the highest value is red. With this coloring it is easier to see if any histogram values are potentially out of range. Displays the color range of the current color scheme that represents the pixels from low to high intensity. Specifies the method to set the brightness and contrast values. The modes are: Manual: You can change the settings yourself. Auto: Brightness and contrast are automatically set and not editable in this mode. Hot Pixel Suppression: This mode ignores 1.5% of the highest and lowest-intensity pixels to provide better, more accurate image contrast. Brightness and contrast are not editable in this mode. Adjusts the overall lightness or darkness of an image. Brightness can only be changed in manual mode. Adjusts the difference between the black and white levels of an image. Contrast can only be changed in manual mode. 260 NSS Spectral Imaging System Handbook

273 Smooth Pixels Pattern Quality/ Found Lines Index Quality/ Simulated Lines Cursor Load Camera Image Save Camera Image Save Processed Image Smoothes visual transitions between pixels. Patterns can be very pixelated if the binning is set at a high level. This option creates more visually appealing patterns. Clear the check box to view pixelated patterns. This option is for display purposes only and does not affect the underlying data. Controls the color of the pattern lines on a pattern and the pattern quality bar. The default color is green. If this property is not applicable to an image, this property is unavailable. Controls the color of the index lines on a pattern and the index quality bar. The default color is cyan. If this property is not applicable to an image, this property is unavailable. Controls the cursor color, which is used to mark a location on some images. The default color is red. This property is available only in the EBSD Setup mode. Loads a previously saved camera image. This property is available only in the EBSD Setup mode. Saves the current unprocessed camera image. Saves the current processed pattern. This option is available for all processed images. Both 8-bit and 16-bit image formats are saved. The boxes on either side of the gradient color bar and to the right of the Decoration Colors properties show the current color settings. Click on a box to change the color of its respective property. A color selection grid will appear. Click on a color in the grid and the button will change to that color. NSS Spectral Imaging System Handbook 261

274 Example of a diffraction pattern with different color settings: This property panel illustrates the settings for the previous pattern. 262 NSS Spectral Imaging System Handbook

275 Orientation Cell This view shows the name of the crystal and its orientation. Here is an example of an orientation cell: The notation (81, 37) describes the (x, y) location of the pixel in an EBSD map. A 3D unit cell is shown in its current alignment using the orientation values measured for the current pattern. This display also has a table with the orientation description in HKL, UVW, and Euler angle notations. Right-click on the view to display the following property panel: NSS Spectral Imaging System Handbook 263

276 The following table describes the properties that you can change: Property Face Color Reset to Defaults Description The color of the cube face. Click the color box to change the color. Choose a new color from the grid that appears. The default color is blue. Changes all values back to the original factory settings. Pattern Quality Map This map indicates the quality of the diffraction patterns. This view is available only in the EBSD Mapping mode. Lighter pixels indicate where high-quality diffraction patterns were acquired. Darker pixels indicate where poor quality diffraction patterns were acquired. This can occur due to pattern overlaps at boundaries, a rough surface, surface contamination, or surface scratches. Purple pixels indicate that no pattern was received from the camera. Orange pixels indicate that no measured (Radon) lines were found in the acquired pattern. 264 NSS Spectral Imaging System Handbook

277 Right-click on the map to display the following property panel: The following table describes the properties that you can change: Property Color Scheme Gradient color bar Description Controls the color display mode of the image or diffraction pattern. There are several color schemes available: Red, Green, Blue, Cyan, Magenta, Yellow, and Grey. The colors range from black to the specified color. The default color is grey. Earth: The colors simulate a landscape, ranging from sea (dark blue to light blue), which represents the lowest pixel intensity; to beach (white), which represents medium pixel intensity; to mountains (light brown to dark brown), which represents the highest pixel intensity. Custom: Colors blend from one color to another. Click on the colored boxes on either side of the gradient color bar to select which colors to blend. Thermal: Colors range from blue to red to mimic cold (low intensity) and hot (high intensity) areas. Displays the color range of the current color scheme that represents the pixels from low to high-intensity. NSS Spectral Imaging System Handbook 265

278 Mode Brightness Contrast Show Legend Unacquired Data Low Quality Data Reset to Defaults Selects the method to set the brightness and contrast values. The modes are: Manual: You can change the settings yourself. Auto: These settings are automatically set and not editable in this mode. This is the default mode. Hot Pixel Suppression: This mode ignores 1.5% of the highest and lowest-intensity pixels to provide better, more accurate image contrast. Brightness and contrast are not editable in this mode. Adjusts the overall lightness or darkness of an image. Brightness can only be changed in manual mode. Adjusts the difference between the black and white levels of an image. Contrast can only be changed in manual mode. Displays the color definitions on the map. The pixel color that indicates where no pattern was received from the camera. The default color is purple. The pixel color that indicates no indexing was possible because no Radon lines could be found. The default color is orange. Changes all values back to the original factory settings. Index Quality Map This map indicates the quality of alignment between the Radon lines and the crystal simulation lines. This view is available only in the EBSD Mapping mode. Lighter pixels indicate that there was good indexing for that pattern. Darker pixels indicate that there was poor indexing for that pattern, but a solution was found. Purple pixels indicate that no pattern was received from the camera. Orange pixels indicate that no indexing was possible because there was no solution. This usually occurs when there is not enough band information in a pattern to find a solution or the correct crystal was not selected as a potential match. 266 NSS Spectral Imaging System Handbook

279 Right-click on the map to display the following property panel: The following table describes the properties that you can change: Property Color Scheme Description Controls the color display mode of the image or diffraction pattern. There are several color schemes available: NSS Spectral Imaging System Handbook 267

280 Red, Green, Blue, Cyan, Magenta, Yellow, and Grey. The colors range from black to the specified color. The default color is grey. Earth: The colors simulate a landscape, ranging from sea (dark blue to light blue), which represents the lowest pixel intensity; to beach (white), which represents medium pixel intensity; to mountains (light brown to dark brown), which represents the highest pixel intensity. Custom: Colors blend from one color to another. Click on the colored boxes on either side of the gradient color bar to select which colors to blend. Thermal: Colors range from blue to red to mimic cold (low intensity) and hot (high intensity) areas. Gradient color bar Mode Brightness Contrast Show Legend Unacquired Data Low Quality Data Reset to Defaults Displays the color range of the current color scheme that represents the pixels from low to high-intensity. Selects the method to set the brightness and contrast values. The modes are: Manual: You can change the settings yourself. Auto: These settings are automatically set and not editable in this mode. This is the default mode. Hot Pixel Suppression: This mode ignores 1.5% of the highest and lowest-intensity pixels to provide better, more accurate image contrast. Brightness and contrast are not editable in this mode. Adjusts the overall lightness or darkness of an image. Brightness can only be changed in manual mode. Adjusts the difference between the black and white levels of an image. Contrast can only be changed in manual mode. Displays color definitions on the map. The pixel color that indicates where no pattern was received from the camera. The default color is purple. The pixel color that indicates no indexing was possible because no solution/match could be found. The default color is orange. Changes all values back to the original factory settings. 268 NSS Spectral Imaging System Handbook

281 Strain Map Many times the orientation differences between pixels within a grain are more important than the specific pixel orientations. For these analyses, the misorientation of the pixel with respect to the average orientation of the grain is plotted. This measure is simply a misorientation angle. This map indicates that the range of misorientations exceeds 12 degrees but there are very few pixels at this level. For a particular grain, the areas that are black are closely aligned to the average grain orientation and the areas that are white have the highest deviation from the average grain orientation. NSS Spectral Imaging System Handbook 269

282 Right-click on the map to display the following property panel: The following table describes the properties that you can change: Property Color Scheme Description Controls the color display mode of the image or diffraction pattern. There are several color schemes available: Red, Green, Blue, Cyan, Magenta, Yellow, and Grey. The colors range from black to the specified color. The default color is grey. Earth: The colors simulate a landscape, ranging from sea (dark blue to light blue), which represents the lowest pixel intensity; to beach (white), which represents medium pixel intensity; to mountains (light brown to dark brown), which represents the highest pixel intensity. Custom: colors blend from one color to another. Click on the colored boxes on either side of the gradient color to select which colors to blend. Thermal: colors range from blue to red 270 NSS Spectral Imaging System Handbook

283 to mimic cold (low intensity) and hot (high intensity) areas. Gradient color bar Mode Brightness Contrast Show Legend Displays the color range of the current color scheme that represents the pixels from low to high-intensity. Selects the method to set the brightness and contrast values. The modes are: Manual: You can change the settings yourself. Auto: These settings are automatically set and not editable in this mode. This is the default mode. Hot Pixel Suppression: This mode ignores 1.5% of the highest and lowestintensity pixels to provide better, more accurate image contrast. Brightness and contrast are not editable in this mode. Adjusts the overall lightness or darkness of an image. Brightness can only be changed in manual mode. Adjusts the difference between the black and white levels of an image. Contrast can only be changed in manual mode. Display color definitions on the map. NSS Spectral Imaging System Handbook 271

284 Orientation Phase Map An orientation phase map illustrates the distribution of crystal phases. The map is useful only when multiple crystals are used to analyze diffraction patterns. The map displays the best crystal match for each location. The following map shows the distribution of FCC and BCC material in a sample. Right-click on the map to display the following property panel: 272 NSS Spectral Imaging System Handbook

285 The following table describes the properties on the Map Properties dialog box. Property Crystal Color Show Legend Reset to Defaults Description The specific crystal structure. This value cannot be changed. The color assigned to represent the crystal structure. Display crystal and color definitions on the map. Change all values back to the original factory settings. Orientation Phase Boundary Map This is a map of the boundaries separating each crystal phase. It is derived from the Orientation Phase map. The following Phase Boundary map is derived from the Phase map in the previous section. NSS Spectral Imaging System Handbook 273

286 Right-click on the map to display the following property panel: The following table describes the properties that you can change: Property Color Thickness Reset to Defaults Description The color used to draw the boundary lines. Width in pixels of the line drawn at the axis grain boundary. The default thickness is one pixel. Changes all values back to the original factory settings. Overlay Map You can overlay certain maps on top of each other for further analysis. There are three logical display layers in this display: a base map, multiple transparent overlay maps, and an opaque overlay boundary map. Optional opaque overlay boundary map Optional transparent overlay map #n Optional transparent overlay map #2 Optional transparent overlay map #1 Opaque base map 274 NSS Spectral Imaging System Handbook

287 Right-click on the map to display the following property panel: For the base map, select a map as the primary map for display. This map is typically shown in the gray-scale color scheme. With the boundary map, you can display a single grain boundary representation on top of the other displays. The grain boundary map is an opaque overlay. From the Additional Maps area, you can select one or more maps to transparently overlay onto the base map if desired. Boundary maps are not included in this set. NSS Spectral Imaging System Handbook 275

288 The following table describes the properties that you can change: Property Title Base Map Boundary Map Show Legend Additional Maps Transparency Load Save Description The name of the overlay map to create. This is automatically generated based on your selections. You can optionally change the name of the map. The map you start with; the underlying map. The type of map that is placed on top of the base and additional map(s) that delineates grain boundaries. The boundary map is an opaque overlay. You can optionally display a list (legend) of the maps used in the overlay. This list is displayed below the overlay map. Displays the available transparent maps that you can overlay onto the base map. There is no limit to the number of maps that can be selected. The currently selected base map will not appear in this list, but all other base maps will. Controls the transparency level of the additional map(s). Load a previously saved overlay map configuration from disk. Save the current overlay map configuration to disk for future use. 276 NSS Spectral Imaging System Handbook

289 The following maps are used to create the resulting overlay map. The Pattern Quality Map is selected as the opaque base map. The FCC Euler Map is selected as a transparent overlay map. NSS Spectral Imaging System Handbook 277

290 Here is the resulting overlay map: Phase view types Orientation Maps These views show information specific to the phases that were analyzed (one phase per crystal). Orientation maps show the different pixel orientations based on Euler angles, sample normal direction, and sample transverse direction. These maps are available only in the EBSD Mapping mode. 278 NSS Spectral Imaging System Handbook

291 Euler This map shows the orientation of each pixel in red, green, and blue, respectively, representing the three Euler angles. This map is useful for viewing the orientation and extent of each grain in a unique manner. Right-click on the map to display the following property panel: The following table describes the properties that you can change: Property Show Legend Reset to Defaults Description Displays color definitions on the map. Changes all values back to the original factory settings. NSS Spectral Imaging System Handbook 279

292 Normal Direction This map shows the orientation of each pixel with respect to the sample normal direction, colored with the inverse pole figure red-green-blue color scheme. This map is useful for viewing the orientation relative to the sample normal direction. Grains with similar orientations are easy to associate by similar coloring. Right-click on the map to display the following property panel: The following table describes the properties that you can change: Property Show Legend Reset to Defaults Description Displays color definitions on the map. Changes all values back to the original factory settings. 280 NSS Spectral Imaging System Handbook

293 Transverse Direction This map shows the orientation of each pixel with respect to the sample transverse direction colored using the inverse pole figure red-green-blue color scheme. This map is useful for viewing the orientation relative to the sample transverse direction. Grains with similar orientations are easy to associate by similar coloring. Right-click on the map to display the following property panel: The following table describes the properties that you can change: Property Show Legend Reset to Defaults Rolling Direction Description Displays color definitions on the map. Changes all values back to the original factory settings. NSS Spectral Imaging System Handbook 281

294 This map shows the orientation of each pixel with respect to the sample rolling direction, colored with the inverse pole figure red-green-blue color scheme. This map is useful for viewing the orientation relative to the rolling direction. Grains with similar orientations are easy to associate by similar coloring. Right-click on the map to display the following property panel: The following table describes the properties that you can change: Property Show Legend Reset to Defaults Description Displays color definitions on the map. Changes all values back to the original factory settings. 282 NSS Spectral Imaging System Handbook

295 Schmid This map displays the variation of the resolved stress for simple tension in a sample. The Schmid Factor indicates how easy slip can occur for a particular slip system or how likely a deformation is to occur at a boundary. This view is available only in the EBSD Mapping mode. In the following example, the legend shows the slip system {1,1,1}<1,1,0>, a color ramp, and the range of Schmid values in the map. NSS Spectral Imaging System Handbook 283

296 Right-click on the map to display the following property panel: The following table describes the properties that you can change: Property Slip System Color Scheme Description The combination of the slip plane and direction in which a slip may occur. This is dependent on the crystal type. Controls the color display mode of the image or diffraction pattern. There are several color schemes available: Red, Green, Blue, Cyan, Magenta, Yellow, and Grey. The colors range from black to the specified color. The default color is grey. Earth: The colors simulate a landscape, ranging from sea (dark blue to light blue), which represents the lowest pixel intensity; to beach (white), which represents medium pixel intensity; to mountains (light brown to dark brown), which represents the highest pixel intensity. Custom: Colors blend from one color to another. Click on the colored boxes on either side of the gradient color bar to select a custom destination 284 NSS Spectral Imaging System Handbook

297 color. Thermal: Colors range from blue to red to mimic cold (low intensity) and hot (high intensity) areas. Gradient color bar Mode Brightness Contrast Show Legend Unacquired Data Low Quality Data Reset to Defaults Displays the color range of the current color scheme that represents the pixels from low to high-intensity. Selects the method to set the brightness and contrast values. The modes are: Manual: You can change the settings yourself. Auto: These settings are automatically set and not editable in this mode. This is the default mode. Hot Pixel Suppression: This mode ignores 1.5% of the highest and lowest-intensity pixels to provide better, more accurate image contrast. Brightness and contrast are not editable in this mode. Adjusts the overall lightness or darkness of an image. Brightness can only be changed in manual mode. Adjusts the difference between the black and white levels of an image. Contrast can only be changed in manual mode. Displays color definitions on the map. The pixel color that indicates where no pattern was received from the camera. The default color is purple. The pixel color that indicates no indexing was possible because no Radon lines could be found. The default color is orange. Changes all values back to the original factory settings. Texture Histograms These histograms show the pixel distribution in different types of orientation spaces. Inverse Pole Figures: IPF-Normal, IPF-Transverse, IPF-Rolling The three displays below are histograms of the pixel orientations in inverse pole figure (IPF) space with respect to the sample normal direction, sample transverse direction, and rolling direction. Clusters in these histograms indicate pixels of similar orientation or grains. NSS Spectral Imaging System Handbook 285

298 The cursors change in each histogram as the cursor is moved in a map. Normal Direction: Transverse Direction: 286 NSS Spectral Imaging System Handbook

299 Rolling Direction: Right-click on any of the inverse pole figures to display the following property panel: > NSS Spectral Imaging System Handbook 287

300 The following table describes the properties that you can change: Property Display Style Description Controls how the PF is shown, either Discrete or Smoothed. Discrete: Gun-shot/spatter pattern distribution, dots represented individually Smoothed: Gradient fill showing the distribution Discrete Settings (enabled when Display Style is set to Discrete): Dot Size (% display width) Minimum Dot Size (pixels) Controls size of the dots of the individual points. Relative to the displayed or printed size of the control The smallest a dot is allowed to be. If dot size is set to a value that results in a dot size smaller than the minimum dot size, the dot will be shown at the minimum dot size. Smoothed Settings (enabled when Display Style is set to Smoothed): Smooth Radius (º) Color Scheme Gradient color bar Controls the color display mode of the PF. There are several color schemes available: Red, Green, Blue, Cyan, Magenta, Yellow, and Grey. The colors range from black to the specified color. The default color is grey. Earth: The colors simulate a landscape, ranging from sea (dark blue to light blue), which represents the lowest pixel intensity; to beach (white), which represents medium pixel intensity; to mountains (light brown to dark brown), which represents the highest pixel intensity. Custom: Colors blend from one color to another. Click on the colored boxes on either side of the gradient color to select which colors to blend. Thermal: Colors range from blue to red to mimic cold (low intensity) and hot (high intensity) areas. Displays the color range of the current color scheme that represents the pixels from low to high-intensity. 288 NSS Spectral Imaging System Handbook

301 Color Range Minimum Value Maximum Value Show Legend Use entire color range or use a smaller range. Can raise min value to see major peaks. Auto: These settings are automatically set and not editable in this mode. This is the default mode. Manual: You can change the settings yourself. Lowest setting/value on the low / left color range (on one side) Enabled only when Color Range is set to Manual. Same as above, but high / right, on the other side Enabled only when Color Range is set to Manual. Display color definitions on the map. PF-{100}, PF{110}, PF{111} Each display below is a histogram of the pixel crystal orientations in the sample mapped in pole figure space. There is a separate pole figure for the most useful crystal poles for the specified crystal and an option for a userdefined set of poles. NSS Spectral Imaging System Handbook 289

302 Right-click on any of the pole figures to display the following property panel: The following table describes the properties that you can change: Property Miller Indices Display Style Description Not available Controls how the PF is shown, either Discrete or Smoothed. Discrete: Gun-shot/spatter pattern distribution, dots represented individually Smoothed: Gradient fill showing the distribution Discrete Settings (enabled when Display Style is set to Discrete): Dot Size (% display width) Minimum Dot Size Controls size of the dots of the individual points. Relative to the displayed or printed size of the control The smallest a dot is allowed to be. If dot size 290 NSS Spectral Imaging System Handbook

303 (pixels) is set to a value that results in a dot size smaller than the minimum dot size, the dot will be shown at the minimum dot size. Smoothed Settings (enabled when Display Style is set to Smoothed): Smooth Radius (º) Color Scheme Gradient color bar Color Range Minimum Value Maximum Value Show Legend Controls the color display mode of the PF. There are several color schemes available: Red, Green, Blue, Cyan, Magenta, Yellow, and Grey. The colors range from black to the specified color. The default color is grey. Earth: The colors simulate a landscape, ranging from sea (dark blue to light blue), which represents the lowest pixel intensity; to beach (white), which represents medium pixel intensity; to mountains (light brown to dark brown), which represents the highest pixel intensity. Custom: Colors blend from one color to another. Click on the colored boxes on either side of the gradient color to select which colors to blend. Thermal: Colors range from blue to red to mimic cold (low intensity) and hot (high intensity) areas. Displays the color range of the current color scheme that represents the pixels from low to high-intensity. Use entire color range or use a smaller range. Can raise min value to see major peaks. Auto: These settings are automatically set and not editable in this mode. This is the default mode. Manual: You can change the settings yourself. Lowest setting/value on the low / left color range (on one side) Enabled only when Color Range is set to Manual. Same as above, but high / right, on the other side Enabled only when Color Range is set to Manual. Display color definitions on the map. NSS Spectral Imaging System Handbook 291

304 Orientation Distribution Function (ODF) An ODF is an orientation histogram of the Euler angles of each pixel in an orthogonal space. You can display the data as a 3D representation and as a user-selected slice through the 3D volume. This display shows the concentration of different crystal orientations within the sample. Options are available in the primary display to adjust the current view: Slice Position (text and slider): Drag the slider to adjust the current angular position of the slice. Smoothing level (text and slider): Drag the slider to adjust the amount of parabolic smoothing (in degrees) to apply to the data. 292 NSS Spectral Imaging System Handbook

305 Right-click on the histogram to display the following property panel: The following table describes the properties that you can change: Property Slice Thickness Slice plane direction Slice position (phi#) Slice view options Description Thickness of the slice of the 3D ODF data cube (in degrees). Specifies ODF slice plane direction (phi1, PHI or phi2) in the 3D ODF data cube. The slice moves in the direction normal to the plane. Position of the ODF slice in degrees along the selected slice plane direction. Specifies how the data in the ODF slice is displayed: Scatter points each orientation represents a dot in the slice view. Gradient A colorful gradient representation of the ODF function (similar that of relief/topographical map). Red represents high density (clusters) of the specific NSS Spectral Imaging System Handbook 293

306 orientations, while blue is the lower density and white color represents areas of the orientation point omission. Contour Similar to gradient, except that contours are drawn instead of the transitional coloring. Smoothing level (diameter) Reset to Defaults Copy to Clipboard Level of smoothing in degrees, which is the diameter of the smoothing (convolution) kernel. The smoothing algorithm uses a parabolic kernel. Changes all values back to the original factory settings. Copy the ODF slice image to the Windows clipboard. Grain Boundary Maps These maps show the differences in the orientations between neighboring pixels. Axis The axis grain boundary map is colored by the common rotation axis between neighboring grain pixels. The axis coloring scheme is based on the inverse pole figure. 294 NSS Spectral Imaging System Handbook

307 Right-click on the map to display the following property panel: The following table describes the properties that you can change: Property Thickness Show Legend Reset to Defaults Description Width in pixels of the line drawn at the axis grain boundary. The default thickness is one pixel. Shows line definitions on the legend. Changes all values back to the original factory settings. NSS Spectral Imaging System Handbook 295

308 Angle This is a grain boundary map colored by the angle of rotation between neighboring grain pixels. You can define how to display lines for grain boundaries to reflect their misorientation angles. The different colors represent different angle ranges. In the example map below, white represents the smallest difference between angles, from 0 degrees to 2 degrees. The thin red line represents all of the angle differences between 2 degrees and 55 degrees. The thicker black line represents all of the angle differences greater than 55 degrees. The colors and angle ranges may be changed using the property panel. 296 NSS Spectral Imaging System Handbook

309 Right-click on the map to display the following property panel: Each row in the table contains the characteristics of the line that delineates a grain boundary. To edit the line characteristics, highlight the corresponding row and change the settings in the Values area. Set the limits of the degree range by entering the values into the Minimum and Maximum fields. To set the line color, click on the color selector box and select a color. The color of the first band determines the background color of the map and the minimum threshold for displayed boundaries. To set the line thickness, enter the pixel width in the Thickness field. A characteristic is unavailable if its value cannot change or does not apply to the selected item. The following table describes the properties that you can change: Property Color Minimum Maximum Description Color of the line drawn at the grain boundary. For increased visibility, assign a different color to each line. Lowest value in degrees of the defined range. The lowest value of the first band cannot be changed from 0 (zero). Highest value in degrees of the defined range. The highest value of the last range specified is set by the symmetry of the crystal and cannot be NSS Spectral Imaging System Handbook 297

310 changed. Thickness Split Delete Show Legend Reset to Defaults Width in pixels of the line drawn at the grain boundary. The default thickness is one pixel. This option splits selected range in half and creates a new row in the table. Edit high and low values of new range as needed and select a different color or line thickness. This option removes the selected row. Assigns the range values of the deleted parameter to the range neighbor with the largest angular range. Shows line definitions on the map. Changes all values back to the original factory settings. Coincidence site lattice (CSL)/Special A Coincidence Site Lattice (CSL) map is a grain boundary map that describes a special relationship between two grains relative to each other. These special orientations exist at boundaries where the orientations of the lattice structures of the two crystals align in such a way that they create a special pattern. Some points of the lattices will coincide, creating a new pattern from both lattices, called a CSL. Each lattice point in the CSL map is described by a value called Sigma, which specifies the relation between the two grains. Values for cubic materials are always odd numbers (3, 5, 7, up to 31.), with the most common being NSS Spectral Imaging System Handbook

311 The conditions which define these special boundaries are a common axis of rotation and the angle of rotation around this axis. The conditions for cubic materials are listed in the following table. In NSS, the CSL map displays the boundaries for each pixel where a CSL condition exists. The boundary is made up of two lines: one is located to the right of the pixel, indicating the boundary between the pixel in question and the pixel to its right in the X direction, and the other line is located below the pixel, indicating the boundary between the pixel and the one below in the Y direction. These lines are color coded and of a certain thickness to represent a specific Sigma value. The color and line thickness can be modified from the property panel for the CSL map. NSS Spectral Imaging System Handbook 299

312 300 NSS Spectral Imaging System Handbook Below are two maps: the Grain Boundary Angle map and the CSL map. Notice the relationship between these maps. The CSL is a subset of the Grain Boundary map indicating only those boundary locations that satisfy the CSL conditions.

313 Right-click on the map to display the following property panel: The following table describes the properties that you can change: Property Color (column) Sigma Value (column) Color Thickness Show Legend Reset to Defaults Description The current setting of the line color and thickness that represents the corresponding Sigma value. The corresponding Sigma values represented by a specific line color and thickness. Always an odd number. Starts at 3 and ends at 31. The lower the value, the higher degree of coincidence in the special pattern between the two grains. Color of the line representing the Sigma value at that location. Width in pixels of the line representing the Sigma value at that location. Shows the current settings of the Sigma value line colors and thicknesses on the map. Changes all values back to the original factory settings. NSS Spectral Imaging System Handbook 301

314 Histograms/Plots A histogram is a graphical representation of the frequency distribution of data. Grain Sizing Analysis Histogram Many times you will wish to understand how grain sizing parameters of the sample correlate to the properties of the material. A number of grain sizing parameters are available which provide different descriptions of the grain structure of the sample. Histograms of these parameters are available for display for analysis purposes. 302 NSS Spectral Imaging System Handbook

315 Right-click on the histogram to display the following property panel: The following table describes the properties that you can change: Property Units Data Item Description Choose the units for the results. Choose the type of sizing parameter to use: Total Particles*: The total amount of particles in the grain. Frame #*: Number assigned to the frame containing the particle. Particle #*: Number assigned to the particle, cumulative across multiple frames. * Total Particles, Frame #, and Particle # are part of the data but are not really useful for histograms. Area: Particle area, as the number of pixels in the particle times Pixel_Area, in current units squared. Perimeter: Sum of the distances between centers of adjacent pixels on the particle perimeter, measured in current units. Circularity: Perimeter squared divided by (4 Pi times NSS Spectral Imaging System Handbook 303

316 Area), unitless. Proj: Min: Minimum particle projection (minimum caliper dimension), as the smallest separation between points on the particle convex perimeter, in current units. Proj: Max: Maximum particle projection (maximum caliper dimension), as the largest separation between points on the particle convex perimeter, in current units. Proj: Mean: Average of 360 radial particle projections (mean caliper dimension), in current units. Proj: Std. Dev.: Standard deviation of the 360 radial particle projections (caliper dimension), in current units. Orientation: Angle between the positive X axis and the maximum particle projection, in degrees. Clockwise rotation from the X axis is a positive orientation angle. Length: Derived length of particle, after it is straightened into a rectangle of equal area and perimeter, in current units. Width: Particle projection perpendicular to the maximum projection, in current units. Aspect Ratio: Defined as maximum projection divided by Width. Unitless. Vertical Axis Automatic Full Scale: Select this option to automatically fit the data to the vertical axis. Log Scale: Select this option to display the vertical axis in log scale. Maximum Value: Highest value to display on the vertical axis. This value can only be changed if Automatic Full Scale is not checked. Horizontal Axis Bin Size: the range of values that are grouped together into a single bar. The higher the setting, the wider the bars and less precise the histogram. Minimum Value: Lowest value to display on the horizontal axis. Maximum Value: Highest value to display on the horizontal axis. Display Mode Background Color Data Color Reset to Defaults Copy to Clipboard Controls the appearance of the data. Can be either solid or outlined. Color of the area behind the data. Color of the bars that represent the data. Changes all values back to the original factory settings. Copy the histogram data to the clipboard. 304 NSS Spectral Imaging System Handbook

317 Grain Boundary Angle Histogram Adjacent crystals can have different orientations. The clearest method to describe this difference is to measure the amount of rotation needed for the second pixel to align its crystal axes with the crystal exes of the reference pixel. The Grain Boundary Angle Histogram is a frequency histogram of all of these angles. NSS Spectral Imaging System Handbook 305

318 Right-click on the histogram to display the following property panel: The following table describes the properties that you can change: Property Automatic Full Scale Log Scale Maximum Value Bin Size Minimum Value Maximum Value Display Mode Background Color Data Color Description Select this option to automatically fit the data to the vertical axis. Select this option to display the vertical axis in log scale. Highest value to display on the vertical axis. This value can only be changed if Automatic Full Scale is not checked. The width of each bar in degrees. The higher the setting, the wider the bars and less precise the histogram. Lowest value to display on the horizontal axis. Highest value to display on the horizontal axis. Controls the appearance of the data. Can be either solid or outlined. Color of the area behind the data. Color of the bars that represent the data. 306 NSS Spectral Imaging System Handbook

319 Reset to Defaults Copy to Clipboard Changes all values back to the original factory settings. Copy the histogram data to the clipboard. CSL Histogram The CSL Histogram is a related summary of the data in the CSL Map. Please refer to the CSL Map description to understand how CSLs are defined. The CSL boundaries are described by a Sigma value that is always an odd number and ranges from 3 to 31. For a given map, the CSL histogram shows a frequency distribution of the different Sigma values. NSS Spectral Imaging System Handbook 307

320 Right-click on the histogram to display the following property panel: The following table describes the properties that you can change: Property Automatic Full Scale Log Scale Maximum Value Bin Size Minimum Value Maximum Value Display Mode Background Color Data Color Reset to Defaults Description Select this option to automatically fit the data to the vertical axis. Select this option to display the vertical axis in log scale. Highest value to display on the vertical axis. This value can only be changed if Automatic Full Scale is not checked. Cannot be altered for CSL histograms. Lowest value to display on the horizontal axis. Highest value to display on the horizontal axis. Controls the appearance of the data. Can be either solid or outlined. Color of the area behind the data. Color of the bars that represent the data. Changes all values back to the original factory 308 NSS Spectral Imaging System Handbook

321 Copy to Clipboard settings. Misorientation Linescan Extract Plot Copy the histogram data to the clipboard. This is a linescan plot of the misorientations between pixels across the sample. This display is useful for understanding small orientation variations inside grains (strain) and verifying grain boundary angles. The black lines show the misorientation between the first pixel and the current pixel in degrees. The red lines show the misorientation between the current and previous pixels in degrees. The yellow line shows which pixels have not been indexed: zero degrees means that it was successfully indexed; ten degrees means that it was not indexed. NSS Spectral Imaging System Handbook 309

322 Right-click on the plot to display the following property panel: The following table describes the properties that you can change: Property Automatic Full Scale Log Scale Maximum Value Bin Size Minimum Value Maximum Value Display Mode Description Select this option to automatically fit the data to the vertical axis. Select this option to display the vertical axis in log scale. Highest value to display on the vertical axis. This value can only be changed if Automatic Full Scale is not checked. Cannot be altered for CSL histograms. Lowest value to display on the horizontal axis. Highest value to display on the horizontal axis. Controls the appearance of the data. Can be either solid or outlined. 310 NSS Spectral Imaging System Handbook

323 Background Color View misorientation with respect to the first point View misorientation with respect to the previous point View location of points that could not be indexed Reset to Defaults Copy to Clipboard Color of the area behind the data. This color is editable and shows the color of the first-point reference plot. Check to enable. This color is editable and shows the color of the previous-point reference plot. Check to enable. This color is editable and shows the color of the unindexed pixel plot. Check to enable. Changes all values back to the original factory settings. Copy the histogram data to the clipboard. EBSD Point & Shoot mode The EBSD Point & Shoot mode is used for surveying a sample spot-by-spot. In this mode, you can acquire an image, specify points on the image, and gather data from those points. Each point selected acquires the diffraction pattern at that location. You can click anywhere on the reference image to acquire the pattern. This mode is especially useful if you want to see the diffraction pattern of a specific feature on the image. This mode is best used to determine the crystal structure, orientation, and chemistry of a sample using a technique known as phase analysis. NSS Spectral Imaging System Handbook 311

324 Performing a Point & Shoot acquisition To start a new EBSD Point & Shoot analysis, you will need to acquire an averaged electron image. To acquire new image, click the Acquire An Averaged Electron Image button. In EBSD, you can perform both immediate and batch Point & Shoot acquisitions. An immediate acquisition of data at a point begins when you click a new point on the image. For a batch acquisition, place all of the necessary points on the electron image first and then click the Start button on the toolbar. 312 NSS Spectral Imaging System Handbook

325 Note You must acquire a new image before adding new points if you have switched modes, changed projects, or opened a Point & Shoot file containing points that were previously acquired. If you switch to another mode or open a different project, acquired points will be retained, but you won t be able to add new points to the current data set. To acquire more data, acquire another averaged electron image and then acquire new points. EBSD Point & Shoot toolbar The EBSD Point & Shoot toolbar is a limited version of the EDS Point & Shoot toolbar with only the buttons enabled that apply to EBSD: Button descriptions: immediate/batch acquisition (toggle) image cursor (button) point selector arrow point acquisition EBSD Point & Shoot does not support the following acquisition types: rectangle acquisition, magic wand acquisition, circular acquisition, and polygon acquisition. These buttons are not available on the EBSD Point & Shoot toolbar. Immediate acquisitions Notice An immediate acquisition begins when you click anywhere on the image. When the acquisition is finished, you can click another point to acquire more data. Before performing an immediate acquisition, be sure the Immediate/Batch toggle button on the Point & Shoot toolbar is pressed in. NSS Spectral Imaging System Handbook 313

326 To acquire data from a single point, click the image at the desired location. For best image registration, use an acquisition time that is at least ten microseconds per pixel. To abort an acquisition, click the Abort Acquisition button on the toolbar. To abort the acquisition and immediately begin another one, click a new location before the current acquisition is finished. To keep the current point, wait for the current analysis to complete, and then click a new location to continue acquiring points. Another acquisition begins at the new point using a different file name. There is no method to delete points from a Point & Shoot acquisition once the data has been acquired. Batch acquisitions Notice A batch acquisition lets you place as many points on the image that you wish to collect and then acquire them automatically, one after the other. The system will position the beam and collect and analyze each point in sequence. Before performing a batch acquisition, be sure the Immediate/Batch toggle button below. on the Point & Shoot toolbar is not pressed in, as shown 1. Click on the image at the location(s) to acquire data from. For best image registration, use an acquisition time that is at least ten microseconds per pixel. 2. Click the start button to begin the acquisition from the designated location(s). To abort the acquisition, click abort acquisition on the toolbar. If you wish to add more point(s), return to Step 1 and repeat the process. 314 NSS Spectral Imaging System Handbook

327 There is no method to delete points from a Point & Shoot acquisition once the data has been acquired. EBSD views available in Point & Shoot mode When you click on the EBSD Views tab in the analysis controls pane, the map tree shows the views that are available in the Point & Shoot mode. Refer to the EBSD Views Tab section for view descriptions. NSS Spectral Imaging System Handbook 315

328 EBSD Point & Shoot Analysis Pane Orientation/Phase ID Toolbar Four potential tabs are available for further Point & Shoot analysis in the lower-right quadrant of your screen: Find Crystals tab, Misorientation Summary tab, Spectrum tab, and Phase ID tab. There are two toggle buttons on the toolbar that switch between the Crystal Orientation and Phase ID panes: Crystal Orientation: Click on the toolbar to view the Orientation pane. Three tabs, Find Crystals, Misorientation Summary, and Spectrum, will display (default view). Phase ID: Click on the toolbar to view the Phase ID operation pane. Two tabs, Phase ID and Spectrum, will display. Find Crystals tab This tab is used to adjust some of the processing settings when analyzing the patterns. The same functionality is located on the Analysis page in the EBSD Setup mode and works the same way. It is available here so that you can change the parameters without having to switch back and forth between the Point & Shoot mode and Setup mode. 316 NSS Spectral Imaging System Handbook

329 1. Click Find to locate the Radon lines. Radon lines are the lines that the Radon transform finds in the corrected diffraction pattern. This function is used when the Radon parameters are adjusted and a new calculation is made using the current diffraction pattern. Whenever you collect a new diffraction pattern, NSS automatically performs a find operation. Show Lines: Display the Radon lines on the diffraction image. Flash Lines: Intermittently display and hide (blink) the Radon lines on the diffraction pattern. 2. Click Index to locate the index lines. These are the lines that the indexing routine returns after comparing the Radon lines and the crystal structure using the calibration values. This function is used when the indexing parameters are adjusted and a new calculation is made using the current diffraction pattern. Whenever you collect a new diffraction pattern, NSS automatically performs an indexing operation. Show Lines: Display the index lines on the diffraction image. Flash Lines: Intermittently display and hide (blink) the index lines on the diffraction pattern. Note You can edit the found lines by referring to Editing found lines in the Calibration section. NSS Spectral Imaging System Handbook 317

330 3. Choose the crystal structures from the Select Crystals To Use drop down box. When you acquire the diffraction pattern or click the Index button, NSS compares the pattern to the crystal structure(s) chosen and returns an index quality score for each crystal. The highest score indicates the most likely crystal structure of your sample. If the pattern quality is high, but none of the selected crystals give a good match, you may need to add more crystals to your analysis. Misorientation Summary Tab This tab compares the orientation of the acquired points to a specified reference frame. This reference frame can be defined by the sample, a custom direction, or the orientation of one of the acquired points. Background Misorientation analysis involves comparing the orientation of a selected point with points other than the sample. The selected point s orientation is used as the reference and the different transformations needed to find each point s misorientation are calculated. Calculate Orientation for each point with respect to the sample. T R Reference = Sample Pt 1 Pt 2 Pt NSS Spectral Imaging System Handbook

331 Calculate Misorientation for each point with respect to point 2. T R Sample Pt 1 Reference = Pt 2 Pt 3 A point s misorientation is defined by a three dimensional direction [UVW] and a twist angle. These four values describe the difference between the reference direction and the selected point s direction. The relative misorientation between two points of a sample may provide more information about the sample s structure and related properties for materials analysis. From this tab, you can investigate pixel misorientations by changing the reference axis from the sample reference to a pixel reference. Calculating Misorientations NSS Spectral Imaging System Handbook 319

332 To calculate misorientations, select the reference frame to use. Use the dropdown box to select Sample (default), Custom, or a particular point. The reference orientation values are displayed in two formats: the (HKL) [UVW] pair and the Euler angle triplet. All orientation values are determined with respect to the Misorientation Reference that is specified at the top of the dialog. As you change the reference point, the new misorientation values are automatically calculated. To calculate misorientations using a Custom Reference Frame To use a custom reference frame, first select Custom as the reference frame. Next click Custom Direction. A dialog appears that allows you to enter the direction values. Enter the (HKL) or [UVW] values or the Euler angles to specify the custom reference direction. 320 NSS Spectral Imaging System Handbook

333 As you enter any new value, the other values are automatically modified to maintain an orthogonal reference frame. For example, as you modify the (HKL) values, the [UVW] and Euler values are automatically changed to maintain an orthogonal coordinate system. Viewing the Results The misorientation twist angle and tilt vector for each point are displayed in the table at the bottom of the analysis pane. If a given point was not indexed, then the twist and tilt values for that point are displayed as question marks (? ). If the selected reference point was not indexed, all of the misorientation values in the table are displayed as question marks (? ), indicating that the measurements cannot be calculated. The column headings on the Misorientation Summary tab are described in the following table. Column Point Crystal Tilt -u, -v, -w Twist Angle Description The location of the pixel on the electron reference image. The type of crystal structure of the specified point. The vector required to align this point s axis with the reference axis. In other words, the difference between the reference axis and point axis. The number of degrees around this common axis that the crystal must rotate to become coincident with the reference axes. Misorientations of dissimilar symmetries If the crystal symmetries of the reference point and compared point are the same, no special steps are applied. If the crystal symmetries of the reference point and compared point are different, then the crystal symmetry of the reference point is replaced by the crystal symmetry of the compared point. Then the calculation proceeds normally. NSS Spectral Imaging System Handbook 321

334 Copying the results to the clipboard You can place all of the dialog information onto the clipboard for pasting into a text editor or spreadsheet. To copy the results to the clipboard, right-click anywhere in the table and click Copy. Spectrum Tab This tab displays the EDS spectrum for the current point if the Collect EDS option was selected on the EBSD tab of the Acquisition Properties dialog. This tab appears in both the Orientation view and Phase ID view of the Analysis Control panel. 322 NSS Spectral Imaging System Handbook

335 For more information about spectra, see the Spectral Imaging chapter of this document. Phase ID tab A sample that contains potentially unknown phases can use EBSD to automatically search crystal databases to identify the phases. Phase ID is used to identify an unknown sample using information collected from an EBSD pattern and an EDS spectrum. 1. Before you perform Phase ID: Be sure that Acquire EDS data is selected on the EBSD tab in the Acquisition properties menu. Navigate to Edit > Acquisition Properties > EBSD tab > check Acquire EDS Data. The spectrum appears on the Spectrum tabs available in the Misorientation and Phase ID quadrants of Point and Shoot mode. Enable Auto Peak ID: Navigate to the Processing tab (lower left quadrant) > Spectrum Results pane > click Auto ID ON. Turn off History: Navigate to Element Setup tab (lower left quadrant) > deselect History. (Optional) Disable any elements known not to exist in the sample. 2. Perform an EBSD Point and Shoot acquisition to acquire a pattern and spectrum to determine the elements that are present at that point on your sample. 3. Select the Phase ID icon from the toolbar to display the Phase ID tab. The following dialog box appears in the lower right quadrant. NSS Spectral Imaging System Handbook 323

336 The following table describes the Phase ID tab parameters. Parameter Find the Lines Phase ID Library Phase ID pane Best Phase ID Matches Description This button automatically calculates the Radon lines. The Radon lines are the lines that the Radon transform finds in the corrected diffraction pattern. You can fine tune your line placement before running the database search to get as accurate results as possible. This field specifies which database(s) the search is being performed in. This feature automatically finds the best crystal match based on the diffraction pattern and the chemistry described in the periodic table. It does not use the Active Crystal list, but rather uses the entire crystal database filtered by chemistry. The crystals in this filtered list are then automatically indexed and sorted by IQ for insertion into the Best Phase ID Matches list. This list contains the best Phase ID results sorted by IQ. Show Top 10 or All: You can choose to show all results or 324 NSS Spectral Imaging System Handbook

337 just the top 10 results from the Phase ID, based on the IQ score. Note: Changing the selection to All requires performing another Phase ID operation. Note If you still cannot identify your crystal, it is possible that it may not be in the database. In this case, you may add it to your database by using the Crystal Phase ID Editor. Selected Crystals Once you identify the best matching crystal phase, you can add it to the Selected Crystals list. 4. Click Index Phases to perform the search on the database. The results appear in the table in the Best Phase ID Matches pane. NSS uses the chemistry results to filter the database of crystals and indexes each crystal against the diffraction results. The system returns a list of crystals and their associated Index Quality (IQ) scores, which indicates how closely the crystal phase information found in the database matches the phase information of your crystal. 5. Review the results. Select a crystal in the Best Phase ID Matches list to compare a crystal result to the found lines of your crystal. The indexed lines on the diffraction pattern and the cell orientation will change to reflect the currently chosen crystal. The crystal with the highest IQ score is usually the best match to your crystal. Ideally, you want to select the crystal whose index lines most closely match the found lines of your crystal. 6. Select the best matching crystal and move it to the Selected Crystals list. To use this crystal for further analyses, such as Mapping, you will need to move it to the Selected Crystals list. NSS Spectral Imaging System Handbook 325

338 Highlight the crystal in the Best Phase ID Matches list to select it. Use the arrow button to add, and the delete button to remove, crystals from the Selected Crystals list. The image below shows the selected crystal before being moved to the Selected Crystals list. After the crystal has been moved to the Selected Crystals list: 326 NSS Spectral Imaging System Handbook

339 Selecting crystals Selecting crystals gives you the option to identify a specific crystal from the database and add it to the list of Select Crystals to Use list. When you know something about your sample, such as what element(s) is in your sample, you can narrow down the list of potential crystals in the database. FCC, BCC, FCC-Diamond, and HCP crystal structures are always available because these are most common (generic) and describe the structure of about 80% of crystals. They will always appear on the Select Active Crystals list. The ability to select crystals to use is available from several places within the software: EBSD Setup Mode > Calibration > Pattern Center tab EBSD Setup Mode > Analysis > Find Crystals tab EBSD Point and Shoot Mode > Find Crystals tab EBSD Point and Shoot Mode > Phase ID tab Depending on where you are in the software, click Select Active Crystal or Add Crystal, and the list of currently available crystals appears. The Active column describes which crystals will be used for indexing for the current task. For Pattern Center Calibration, only one crystal can be active at a time, and for all other tasks, multiple crystals can be active at the NSS Spectral Imaging System Handbook 327

340 same time. After clicking OK, the active crystals will be displayed for the task. To select different crystals for indexing, click Expand. The Select Active Crystals dialog expands to the right to display tools that you can use to search the entire crystal database. The crystallographic database included with NSS is very large, containing upwards of 50,000 crystals. Searching for potential crystal matches without any limits applied can require a large amount of time and will produce a list of search results that is too long to be useful. You can reduce the list of potential crystal matches and the search time by applying filters to the database that include or exclude elements. After excluding by elements, you can filter the data by crystal specific data, such as the element name, Bravais Lattice, etc. The total number of crystals in the specified database is displayed in the upper right hand corner of the screen. You can choose to search the standard database or a user-defined custom database by selecting the appropriate database. If a database choice is not enabled, it means that the database is not available, or at least not in the proper location. 328 NSS Spectral Imaging System Handbook

341 Note The location of the database file(s) in Win7 is C:\ProgramData\Thermo Scientific\NSS\NSS Libraries\EBSD\. The location of the database file(s) in WinXP is C:\Documents and Settings\All Users\Application Data\Thermo Scientific\NSS\NSS Libraries\EBSD. This folder contains the database files in XML format. To create a custom database, refer to Editing your Crystal Phase ID database. Viewing crystals in the database is a two-step process. The first is to filter by chemistry and the second is to filter by crystal-specific information. Filtering by Chemistry Specify elements that you know are not present in the sample. Any crystals that contain any of the excluded elements will not appear in the results. Specify elements that you know are present in the sample. Results are further restricted to include only these selected elements. Specify elements that may be present. The results are further restricted to include only those crystals that contain at least one of these elements. In the Record Filter: By Periodic Elements pane of the filter tool, enter the parameters to search on. There are several ways to filter the data: All must be present: Enter elements that you are positive are contained in the sample. All crystals returned must have this element. No others Check this box to exclude all other elements from the search. NSS Spectral Imaging System Handbook 329

342 Any may be present: Specify those elements that may be contained in the sample. The returned results will contain at least one of these elements. Excluding any of: Enter elements to exclude from the search. The results will not contain any of these elements. A default list of typically excluded elements automatically populates this field from the periodic table, but you can edit this field as needed. As you enter filter parameters, the value in the Number of filtered records field changes. This shows you the number of crystals in the database that fit your filter restrictions. The more filters you add, the smaller this value becomes. A periodic table is available for quick and easy element selection. Click the button to display the periodic table. Right-click on an element. A menu with four choices appears. To change the element s status, select the one you would like to apply. In the case above, the element is not used in filtering. 330 NSS Spectral Imaging System Handbook

343 Selecting definite for an element will insert it into the All must be present field on the filter tool. Selecting Possible will turn the element orange and enter the element into the Any may be present field. Selecting Excluded will turn the element gray and enter it into the Excluding any of field. Once you have identified the element(s) to filter by, select OK. Notice that the value in the Number of filtered records changes. To display all the matching crystals, click Load Records. There is a status indicator at the bottom of the screen to indicate when the crystals are loading ( Loading ) and when all crystals have been loaded ( Ready ). Filtering by crystal-specific information You can sort these crystals by any column in ascending or descending order by clicking a column heading. Each column can be further filtered by values specific to that column content. Right-click the column heading to display its specific filter. NSS Spectral Imaging System Handbook 331

344 For example, your initial search on all elements that contain nickel returns 831 crystals: This is still a large number of crystals to choose from, so you decide to filter by element name. To display only those elements with the occurrence of the character string strontium anywhere in the element name field, select..xxx.. from the dropdown list, and enter strontium into the text field. As you enter the letters, you will see that the table automatically filters as you type. As you continue typing the search string the list gets smaller. Entering strontium narrows the list to 15 crystals. Click the green checkmark to apply the filter. The filter definition for that column appears in the column heading. 332 NSS Spectral Imaging System Handbook

345 You can also filter by specific values (where available), such as Bravais Lattice or Laue Symmetry. Right-click on the column heading, and select = (equal to) or <> (not equal to), and a value. For example, to see those crystals with a Bravais type that is not equal to triclinic, select <> from the first dropdown list, and triclinic from the second dropdown list: Your list of crystals will be reduced even further. To remove a filter, right-click on the column heading and click the Remove Filter icon.. To remove all filters, click the Remove all icon Once you ve identified your crystal, add it to the Select Active Crystals list by highlighting the crystal in the table and clicking the Add selected crystal(s) button to move the crystal to the list. NSS Spectral Imaging System Handbook 333

346 To delete a crystal from the Active Crystals list, select the crystal in the left hand list and then click the Remove selected crystal(s) button. This button will not remove crystals from the standard database or the custom database. Click OK when you are finished. Any crystals you added to the list appear in all Select Crystals to Use lists. After clicking OK, the active crystals will be displayed for the task. Select Crystals to Use lists are saved on a per project basis. Editing your Crystal Phase ID database The Crystal Phase ID Editor is intended for advanced users who want to modify their crystallographic database. EBSD comes with a comprehensive crystallographic database from the Crystallographic Open Database (COD), a publicly available source of crystallographic information. You can add a new crystal to the database, edit an existing crystal in the database, or create and edit custom groupings, or subsets, of crystals called libraries. A library could contain crystals that are particular to a scientific discipline, such as geology or metallurgy, in which you can perform a 334 NSS Spectral Imaging System Handbook

347 search. Performing a search within a library narrows your search parameters and requires less time to search than the entire database requires. To open the database, navigate to C:\Program Files\Thermo Scientific\NSS and double-click EBSD_PhaseIdLibEditor.exe. The following screen appears: The database editor toolbar: Click an arrow button or enter a row number to navigate to other entries in the database: Highlight the first record in the database. Highlight the previous record (the row above the active row). press Enter). Highlight a specific record (type the row number and NSS Spectral Imaging System Handbook 335

348 Highlight the next record (the row below the active row). Highlight the last record in the database. Add a new record. Delete a record. The following table lists the database fields and their descriptions. Field Crystal ID Source crystal ID Element name Description The unique ID number of the crystal in your local database. The ID number of the crystal from the external database source that the crystal information was imported from. Name of the chemical element. If the name is too long, click to the right of this field to display an expanded view of the description. Bravais lattice Laue symmetry Space group The Bravais lattice type of the crystal. The Laue symmetry type of the crystal. Note: If you specify both the Bravais and the Laue types, there are a restricted number of valid combinations. For example: Cubic Cubic-O Cubic Cubic-T Tetra-BC Tetragonal-D Tetragonal Tetragonal-D For more combinations, refer to a fundamental crystallography monography, such as. Basics of Crystallography and Diffraction by Christopher Hammond, IUCr, Oxford Science Publications, The number of the crystallographic space group, from 1 to 230, that describes the symmetry of the crystal. For more information, refer to International Tables for Crystallography, Vol A; Space-Group Symmetry, IUCr, Kluwer Academic Publishers, NSS Spectral Imaging System Handbook

349 Field Description Crystal Lattice Cell Parameters: Lengths: Angles: Source database The length in Ångstroms of edges A, B, and C of the crystal unit cell. The measurement of the unit cell s alpha, beta, and gamma angles in degrees. The name of the database that the crystal information was imported from. Click to the right of this field to display an expanded view of the description. Element Compound The chemical element(s) contained in the crystal. If the chemical element text is too long, click to the right of this field to display an expanded view of the description. Comment This field contains notes or comments about the database entry. If the comment text is too long, click to the right of this field to display an expanded view of the description. H K L F Entries A numerical notation that describes the H K L- plane orientation and the structure factor (F), a mathematical description of how that plane of the material scatters incident radiation. There must be at least four entries in this list. Format: H K L F (for example, ). The first three numbers represent the H K L combination and are different within the crystal definition. Each number can be positive or equal to zero. The fourth number represents the structure factor (F) and can be positive or equal to zero. If equal to zero, this means the structure factor is unknown for the crystal. For more information, refer to Basics of Crystallography and Diffraction by Christopher Hammond, IUCr, Oxford Science Publications, Number of HKLFs The number of rows in the Rows of H K L F list. This value is automatically calculated and not user-editable. NSS Spectral Imaging System Handbook 337

350 Editing the database You can add, delete, and edit records in the database. To add a record to the database: Click to add a new record to the database. The Crystal ID number field is populated automatically. It starts at and is incremented by -1 with each new entry (for example: -1001, -1002, ). You can enter a different Crystal ID number if desired. Continue adding crystal data and click Update when you are finished. To save the changes to the database, click File > Save. To delete a record from the database: Place your cursor anywhere in the row you want to delete. Click to delete the record. There is no undo available for this function. If you delete a record, the only way to return the record to the database is to add a new empty record and type the information back in. To save the changes to the database, click File > Save. To edit a record in the database: Make desired changes in the record fields and click Update. This will copy the contents of the editable fields into the table, but will not modify the database. You can continue to make changes to as many records as you would like. To permanently save all the changes to the database, click File > Save. This operation could take some time depending on the size of the database. 338 NSS Spectral Imaging System Handbook

351 Working with COD files You can add existing crystallographic information to your database by importing a COD file. The COD file(s) must already reside on your system or be accessible from a directory located on your network to be imported. COD files are appended with the extension.cif, which stands for Crystallographic Information Framework. Refer to for information about how to download COD files onto your system. To import a COD file: Click File > Import COD File. Navigate to the COD file (in.cif format) to import and click Open. You can import one.cif file at a time using this method. To import all COD files from a directory: Click File > Import COD Files from Directory. Navigate to the directory containing the.cif files and click OK. All the.cif files in that directory are imported. NSS Spectral Imaging System Handbook 339

352 The following image shows the records in the database after importing COD files from a directory: CIF Batch Import Options This tool lets you specify how to receive error messages when importing COD files. Click Tools > Options. The following dialog box appears: 340 NSS Spectral Imaging System Handbook

353 The following table lists the options available and their descriptions. Option Show every problem as a dialog Ignore problems and create a Problem Log file Description Pause the import and display error messages as they occur. Each time an error occurs, you will be notified. Import the records that are valid and create a log file of errors after the import is complete. You will not see any error messages during the import. The log file is located in the same directory as the imported.cif files. Working with libraries To create a library, you can choose crystals from your database to create a subset. The library can include crystals that you have created or edited and crystals that you may have imported from another database or other source. To open an existing library: Click File -> Open. Select the Phase ID Library XML file and click Open. The table on the top half of the screen displays the crystal data. NSS Spectral Imaging System Handbook 341

354 To edit an existing library: Highlight the row you want to edit by clicking in the cell to the left of the Crystal ID, as shown in the following image: The data in the crystal record will appear in the fields in the bottom half of the screen: To make a change, edit the entry in the text field and click Update. 342 NSS Spectral Imaging System Handbook

355 Note You must click Update after updating each row; otherwise you will lose your changes when you move to another row. To save the changes to the library, click File > Save, and then click OK. To save as a new library, click File > Save As and rename the file. Click OK. To create a new library: Click File > New to start a new library. An empty record appears in the editor as shown: Add data to the new library. You can import existing data from a COD file or manually enter the data: To import existing data: Click File -> Import a COD file to import a single.cif file, or Import COD files from directory to import all.cif files in a directory. You can import an unlimited number of COD files into a library. Refer to the Working with COD files section for instructions on how to import a COD file. To add data manually: Enter data into the fields on the bottom half of the screen and click Update after each crystal record you add to the database. The first NSS Spectral Imaging System Handbook 343

356 time you add data to a new library, an empty entry is automatically added to the table. For each subsequent new entry, click to add an empty row to the database. Return to the bottom half of the screen to enter data into the fields. Save the new library by clicking File > Save. Enter a name for the new library and click OK. Show Filtered Subset To view a subset of data within the current library, use the Show Filtered Subset tool. Click View > Show Filtered Subset. The following dialog box appears: The following table lists the filters available and their descriptions. 344 NSS Spectral Imaging System Handbook

357 Field By Space Group By Crystal Lattice/ Symmetry By Chemical Table or Formula Element Description Specify the space group in which to restrict the search. This is a number from 1 to 230 that corresponds to a group that describes the symmetry of the crystal of interest. Specify the lattice type and/or symmetry type in which to restrict the search. Lattice: Choose one of the 14 Bravais lattice types. Symmetry: Choose one of the 11 Laue symmetry types. You can apply either one or both of these filters. Note: If you specify both the Bravais and the Laue types, there are a restricted number of valid combinations. For example: Cubic Cubic-O Cubic Cubic-T Tetra-BC Tetragonal-D Tetragonal Tetragonal-D For more combinations, refer to a fundamental crystallography monography, such as. Basics of Crystallography and Diffraction by Christopher Hammond, IUCr, Oxford Science Publications, Specify the element(s) to include or exclude from the search. By Table Element: Choose this option to filter by periodic table element. For example, Fe. By Formula Element: Choose this option to filter by chemical formula element. For example, Fe203. All must be present: Enter the element(s) that the crystal must contain. No others: Search for crystals that contain only the specified element(s) and no other elements. Any may be present: Enter the element(s) that the crystal may optionally contain. Excluding: Enter the element(s) that the crystal must not contain. NSS Spectral Imaging System Handbook 345

358 By Crystal Name Keywords Specify the keyword(s) to include or exclude from the search. Ignore case in keywords: Do not require search terms to be case-sensitive. No others: Check to return elements that have the specified keyword(s) and no other keywords. All must be present: Enter the keyword(s) that the crystal must contain. Any may be present: Enter the keyword(s) that the crystal may optionally contain. Select the filters to apply by placing a check in the corresponding checkbox, enter any special parameters, and click OK. The search results appear in a popup dialog box like the one shown below: 346 NSS Spectral Imaging System Handbook

359 EBSD Mapping Mode In the EBSD Mapping mode, you can determine the crystal type and orientation at each location within a scanned region on the surface of the sample. This mode is most useful for investigating the grain and grain boundary nature of an area of the sample. Refer to Microanalysis Spectral Imaging for instructions to acquire new data and work with old data. EBSD Views available in the Mapping Mode EBSD Mapping Analysis Pane Xray Maps tab All EBSD views are available to see in the EBSD Mapping Mode. Refer to the EBSD Views tab section for a description, example, and description of the right-click menu (if applicable). Additional tabs are available for further Mapping analysis: X-ray Maps and Spectrum. An x-ray map appears in this tab if a combined EBSD-EDS acquisition was performed. Pure EBSD acquisitions will not produce any data for this tab. For information about this feature, refer to the X-ray Mapping section in the Spectral Imaging chapter of this manual. Spectrum tab A spectrum appears in this tab if a combined EBSD-EDS acquisition was performed. Pure EBSD acquisitions will not produce any data for this tab. For information about this feature, refer to the Viewing the Spectrum section in the Acquiring and Managing Data chapter of this manual. NSS Spectral Imaging System Handbook 347

360 EBSD Mapping Extractions and Filtering Spatial extraction Just as with Microanalysis Spectral Imaging data, you can draw multiple unique shapes on an image to select areas for EBSD data extraction and analysis. The toolbar for EBSD spatial extraction is a limited version of the Microanalysis Spectral Imaging toolbar. If you have acquired EDS data with your EBSD data, you can also generate x-ray maps based on the elements found in the spectra for the subset of the data selected. In EBSD, most electron images have very little contrast to use when making an extraction selection. To aid in selection, a transparent Pattern Quality map is placed on top of the reference image to assist in identifying the grain boundaries and other regions of interest. Using the Pattern Quality map you can create a more accurate extraction area. It appears when you choose an extraction tool. The following image is an example: 348 NSS Spectral Imaging System Handbook

361 It is possible to use the image s transparency factor to better see either the Pattern Quality Map, or the underlying grey level image. Here are some examples of the shapes you can draw: Drawing a rectangle NSS Spectral Imaging System Handbook 349

362 Drawing a polygon Filling a polygon (right-click to fill) 350 NSS Spectral Imaging System Handbook

363 Placing a circle Flood-filling areas with similar intensity NSS Spectral Imaging System Handbook 351

364 To draw a shape on the image for extraction: 1. Click the appropriate cursor button on the Spatial Extract toolbar: Extract Polygon Extract Rectangle Extract Spot Extract shape defined by image intensity Note To extract data, the intensity cursor must be turned off. To turn it off, click the button. 2. Draw the desired shape on the image. To draw a closed shape, use the polygon or rectangle tool. To draw an irregular shape, use the polygon tool. Click on the image to start the shape. You can either drag the cursor to draw a line or click another location to place a straight line that connects the points. Continue drawing or placing lines until you have created the shape you want. To complete the shape and start the extraction, right-click anywhere on the image. To change the size or shape of a rectangular area, drag a side or corner. To draw multiple polygon shapes, hold the Ctrl key down while you draw the additional shapes. To remove an existing shape, left-click once anywhere on the image. To change the circle size for spot extractions, enter a spot size radius (in μm) on the Image Extract tab in the General Properties dialog box for the image. Click the small yellow maximize icon in the upper-right corner of a rectangle to expand it to fill the entire image. To restore the original rectangle, click anywhere inside the maximized rectangle. Drag a side or corner of the maximized rectangle just as you would any other rectangle to reduce it. 352 NSS Spectral Imaging System Handbook

365 Note If you want to isolate a particularly small area, drag the borders of the image pane down and right to increase the image size. 3. Release your mouse cursor to begin the extraction process. Depending on the kind of extraction you are performing and the size of the area you selected, the processing may take a few minutes. The selected data is extracted from the image and all applicable views in the top right quadrant reflect that subset of data. Any data outside of the extraction area is temporarily removed from the views. Here is an example of a polygon-shaped extraction and some corresponding views: Polygon drawn on an image. NSS Spectral Imaging System Handbook 353

366 Original Euler map Extracted Euler map Original inverse pole figure Extracted inverse pole figure Angular filtering Angular filtering enables you to emphasize areas on orientation maps that share similar crystal orientations. These crystal orientations are specified by identifying areas of interest on pole figures and inverse pole figures. With this data, you can analyze a sample to determine how crystals are oriented with respect to the normal, transverse, and rolling directions of your sample. 354 NSS Spectral Imaging System Handbook

367 How Angular Filtering works We use PFs and IPFs to identify orientations of interest. Those results are displayed on the orientation maps. This is done by emphasizing the areas of interest in rich colors and deemphasizing the other areas using pastel colors. Selecting areas on the IPF identifies specific crystal directions. The pixels with the same orientation in the corresponding orientation map will be emphasized (rich colors). For comparison purposes, the same pixels in the other orientation maps will also be emphasized, even though they describe the orientations from a different point of view. Start with a directional map: for example, Orientation Map-Normal. You want to investigate pixels or grains with a specific orientation (represented by a specific color). Display the corresponding IPF for the map, for example, IPF-Normal. Use the selection tools to select/highlight orientations of interest in the IPF. The pixels associated with these selected orientations are used to create a spatial filtering mask that is applied to all of the orientation maps. Only the colors of the corresponding orientation map and IPF will match. The selected pixels in the other orientation maps will maintain their original colors. To perform angular filtering: 1. Click the appropriate cursor button on the Angular Filtering toolbar: Filter data based on a circular area of data Filter data based on a user-defined shape 2. Draw the desired shape on the pole figure or inverse pole figure. To draw a circular shape, click the center location and drag the cursor to the desired radius. To draw a user-defined shape, click on the figure to start the shape. You can either drag the cursor to draw a line or click another location to place a straight line that connects the points. Continue drawing or placing lines until you have created the shape you want. To complete the shape, right-click anywhere on the image. To draw multiple shapes, hold the Ctrl key down while you draw the additional shapes. NSS Spectral Imaging System Handbook 355

368 3. Complete the shape to begin the filtering process. Depending on the kind of filtering you are performing and the area you selected, the processing may take a few minutes. The points specified on the pole figure or inverse pole figure are displayed in the original rich colors on the corresponding Orientation map and all other points are de-emphasized and shown in pastel colors. Example The following table below shows three orientation maps in the first row: Normal, Rolling, and Transverse. An IPF- Normal appears in the second row beneath its corresponding Normal Orientation map. These images demonstrate how the same pixels on each orientation map appear when one particular IPF is used for angular filtering. The Normal IPF has the 111 direction selected. The BCC Normal map has the 111 area emphasized in blue. This same area is emphasized on the Rolling and Transverse maps, although the colors may be different. 356 NSS Spectral Imaging System Handbook

369 Stacking You can perform both spatial extraction and angular filtering at the same time to further analyze a subset of the data. This is called stacking. The order in which you perform the extractions and filtering on the data does not matter. 1. Perform angular filtering on the pole figure or inverse pole figure. 2. Perform spatial extraction on the reference image or orientation map. Example: Here is a reference image with a Pattern Quality map overlaid on top: NSS Spectral Imaging System Handbook 357

370 Here is the original Euler map: Here is the reference image with a circular area selected for extraction: 358 NSS Spectral Imaging System Handbook

371 Here is the Euler map with spatial extraction applied: Here is the IPF with an angular filter shape. NSS Spectral Imaging System Handbook 359

372 Here is the resulting stacked Euler map (spatial extractions + angular filtering): The map pixels corresponding to the specified orientation are emphasized in the Euler map and the other pixels are de-emphasized. 360 NSS Spectral Imaging System Handbook

373 Here are more examples of angular filtering being performed on different areas of the extraction. An Euler map, Normal direction orientation map, and Rolling direction orientation map are shown with their corresponding inverse pole figures and the results of the angular filtering. 1. Spatial extraction performed 2. Angular filtering performed on the inverse pole figure for the preceding orientation map 3. Points on the orientation map corresponding to the points on the IPF are highlighted. NSS Spectral Imaging System Handbook 361

374 EBSD Pixel Enhancement Pixel enhancement is a tool that lets you modify maps to show corrected views of the data. Pixels with low index quality (IQ) are replaced for aesthetic enhancement; noise reduction and data cleanup produce a cleaner-looking map for analysis. Enhancements to a map are not permanent and can be reversed. The raw data is always preserved and enhancements for display are performed as requested. Enhancements will appear on all displays, such as maps, pole figures, and inverse pole figures, because the enhancements are made to the underlying data. This feature is available in the EBSD Mapping mode for all maps. How pixel enhancement works Maps are enhanced by replacing outliers and low-quality pixels with an orientation that is determined to be the closest match to its neighbors. This calculation is based on an algorithm that considers the strength of correction and whether outliers and low-quality pixels are to be replaced. Outliers: Pixels that were acquired and have a good IQ, but their orientations differ from all of their neighbors orientations. The goal is to replace each outlier with the orientation of a nearby pixel. Low-quality pixels: Pixels that were not acquired, do not produce a readable pattern, or do not produce a pattern whose quality is greater than or equal to the Minimum Index Quality threshold setting. There are many reasons for low-quality pixels: The camera missed the frame and no image was acquired. Acquired but no pattern was found due to non-crystalline area or poor sample surface preparation. Acquired but pattern quality is very poor due to inadequate acquisition conditions. Acquired with proper acquisition conditions, but it occurs on a boundary between two grains so it is a mixed pattern. A mixed pattern cannot be indexed. Acquired but the crystal type was not used to index this pattern. 362 NSS Spectral Imaging System Handbook

375 Performing pixel enhancement To perform pixel enhancement on an EBSD map, follow the steps below. 1. Click on the map to highlight it. Click EBSD on the main menu, and then select Enhance Map. The Map Enhancement Settings dialog box appears: The following table describes the Map Enhancement settings. Option Options Description Interpolate Missing Pixels: Replaces low quality pixels. Low quality pixels are those pixels which have an IQ of less than the Minimum Index Quality setting. Remove Outliers: Replaces high quality pixels that have a different orientation than the surrounding pixels. High quality pixels are those which have an IQ greater than or equal to the Minimum Index Quality setting. NSS Spectral Imaging System Handbook 363

376 Minimum Index Quality Maximum Hole Size (Pixels) Strength An image must have a minimum IQ score to be considered for outlier enhancement. Any images whose IQs are below the specified value are considered missing pixels. You can choose a value between 0 and 50. The default value is 10. The maximum width of a poorly indexed feature that will be corrected. Features wider than this value will not be enhanced. This setting is available only when the strength is set to Aggressive. The default value is 4. Strength indicates the amount of correction to be applied to the map. As the strength is increased, larger features will be corrected. More strength typically means that fewer neighboring pixels are required to have similar orientation values. The levels are: No Enhancement (default) Slight Low Medium High Aggressive 2. If desired, check either or both of the boxes next to Interpolate Missing Pixels and Remove Outliers. 3. Specify the Minimum Index Quality. 4. Specify the Maximum Hole Size. 364 NSS Spectral Imaging System Handbook

377 5. Choose a strength level. 6. Click OK to start the enhancement process. This may take several seconds to perform. Note Note To remove all enhancements and return to the original map, set the strength to No Enhancement. All pixel enhancement processing settings are stored and recalled with the dataset. NSS Spectral Imaging System Handbook 365

378 Advanced details The following table displays the actions made by the correction calculation. Correction Strength Minimum number of good neighbors required to perform the replacement. Low Quality Pixel Replacement Features with a width less than or equal to this value will be replaced. Recursive/iterative hole filling? Outlier Replacement Number of good neighbors required to perform the replacement. None Not applicable Not applicable No Not applicable Slight 8 1 No 8 Low 7 1 Yes 7 Medium 6 1 Yes 6 High One iteration of 6 followed by as many iterations of 5 that are needed. 2 Yes One iteration of 6 followed by as many iterations of 5 that are needed. Aggressive One iteration of 6, then one iteration of 5, then as many iterations of 4 that are needed. User defined from 3 to 100; default is 4. Yes One iteration of 6 followed by as many iterations of 5 that are needed. 366 NSS Spectral Imaging System Handbook

379 Examples of pixel enhancement The following series of images demonstrates how pixel enhancement can change the appearance of a map. A Pattern Quality Map and an Index Quality Map are shown in Figures 1 and 2. The tables that follow display several versions of the corresponding Euler map with different types and levels of enhancements applied. Figure 1: Pattern Quality map Figure 2: Corresponding Index Quality map NSS Spectral Imaging System Handbook 367

380 Correction strength variation The following table displays maps with different enhancement strengths applied and both options selected. No enhancement Slight enhancement Interpolate Missing Pixels and Remove Outliers selected Low enhancement Interpolate Missing Pixels and Remove Outliers selected Medium enhancement Interpolate Missing Pixels and Remove Outliers selected High enhancement Interpolate Missing Pixels and Remove Outliers selected Aggressive enhancement Interpolate Missing Pixels and Remove Outliers selected 368 NSS Spectral Imaging System Handbook

381 Remove Outlier and Interpolate Missing Pixels corrections The following table displays maps with different options selected and the same strength applied. No enhancement Interpolate Missing Pixels selected High enhancement Remove Outliers selected High enhancement Interpolate Missing Pixels and Remove Outliers selected High enhancement NSS Spectral Imaging System Handbook 369

382 EBSD Attributes The EBSD Attributes window shows the acquisition conditions of your selected data set. This includes the SEM conditions, EBSD camera settings, and other settings specific to the acquisition type. This menu item is not available for modes that do not support it. 1. To display Attributes of a data set, first click on the data set to select it. A yellow border will appear the outside of the data set to indicate that it is selected. 2. Click the View menu. 3. Click Attributes. Microscope tab The Microscope tab displays the microscope attributes of the selected data set when it was acquired. The Microscope tab is displayed first when this dialog opens. You can edit all of the values on this tab. The Apply button is enabled when changes are made. After you click Apply, the Cancel button becomes unavailable and the OK button changes to a Close button. Changes that are applied cannot be undone. 370 NSS Spectral Imaging System Handbook

383 The attributes on the Microscope tab are: Option Instrument Date/Time Immersion Lens Microscope X (mm) Y (mm) Z (mm) Tilt ( ) Rotation ( ) Bank ( ) Acc. Voltage (KV) Beam Current (na) Magnification Description Name of the instrument or microscope. The date and time that the data was acquired. If an immersion lens microscope was used for acquisition, this box is checked. Microscope stage position along the x axis. Microscope stage position along the y axis. Microscope stage position along the z axis. Microscope stage tilt angle in degrees. Microscope stage rotation angle in degrees. Microscope stage bank angle in degrees. Measurement of the accelerating voltage in KV. Measurement of the beam current in na. The magnification setting of the microscope. NSS Spectral Imaging System Handbook 371

384 Working Distance (mm) Tilt Correction Method Sample Holder Tilt ( ) The nominal SEM focusing distance to the sample in millimeters. The selected tilt correction method. If Stage tilt was the selected method, the tilt angle of the stage was used. If Sample Holder Tilt was the selected method, the Sample Holder Tilt value was used. If a sample holder was used, this is the angle in degrees at which the sample was tilted with regards to the x-axis. This field is unavailable when sample holder tilt is not selected in the Tilt Correction Method field. EBSD tab The EBSD tab displays the EBSD detector geometry, pattern calibration settings, and the acquisition settings for the selected data display. You can edit most of the settings on this tab. The Apply button is enabled when changes are made. After you click Apply, the Cancel button becomes unavailable and the OK button changes to a Close button. Changes that are applied cannot be undone. 372 NSS Spectral Imaging System Handbook

385 The attributes on the EBSD tab are: Option Name Full Resolution Tilt ( ) Azimuth ( ) Sample to Phosphor (mm) Field of View Width (mm) Binning Exposure Time (ms) Gain Removal Technique Flat Field Technique FFT Strength Description Name of the camera used to acquire the data. Not editable. The maximum camera pixel resolution. Not editable. Tilt angle in degrees of the camera from horizontal. Azimuth angle in degrees of the camera with respect to the stage tilt axis. The distance in millimeters between the sample and the surface of the phosphor screen. The width in millimeters of the acquired image. The binning setting of the image when it was acquired. A binning of 1x1 means full resolution; a binning of 2x2 means half the x resolution and half the y resolution. The amount of time in milliseconds that the camera exposed each frame to acquire a diffraction pattern. A measure of electronic amplification of the image signal. The background removal method used on the diffraction pattern. The flat field correction method used on the diffraction pattern. If the flat field technique was FFT, the strength indicates how aggressively the diffraction pattern background was removed. # of Radon Lines to Find The number of Radon lines located and displayed on the diffraction pattern. Crystals Found Use 3 Pattern Centers X (mm) The type of crystal structure(s) identified in the current sample. Not editable. If this box is checked, then three pattern centers were used for calibration; otherwise only one pattern center was used. Lateral calibration location in millimeters of the pattern center. NSS Spectral Imaging System Handbook 373

386 Y (mm) L (mm) Pattern Quality (%) Index Quality (%) WD (mm) Time Stamp Vertical calibration location in millimeters of the pattern center. Sample-to-phosphor distance in millimeters of the pattern center. The score of the clarity of the Kikuchi bands in the diffraction patterns when the pattern center was calibrated. Not editable. The score of how closely the indexed bands match the measured bands when the pattern center was calibrated. Not editable. Working distance in millimeters; the nominal SEM focusing distance to the sample when the pattern center was calibrated. The date the pattern center was calibrated. Map tab This tab shows information about a map. This tab is present only when the selected data is an EBSD map. The Apply button is enabled when changes are made. After you click Apply, the Cancel button becomes unavailable and the OK button changes to a Close button. Changes that are applied cannot be undone. 374 NSS Spectral Imaging System Handbook

387 The attributes on the Map tab are: Option Resolution Pixel Size (µm) Indexing Success Rate (%) Acquisition Rate (fps) Result Rate (pixels/sec) Description Pixel resolution of the acquired map. This resolution should not be confused with the resolution of the video camera or the acquired diffraction pattern. The map resolution reflects how the SEM beam moved in X and Y, acquiring a video camera image at each beam location. Not editable. Size of one pixel in micrometers in the selected map. This value is with respect to the SEM beam movement. Note that the system expects tilt correction (if required) to maintain square pixels. The x and y pixels are assumed to be the same size. The percentage of pixels in the map that were indexed. 100% would mean all pixels were indexed. The number of camera images per second that were acquired while collecting the map. The rate that camera imaged were processed to into orientation information (Hough transform and the indexing rate). This time will always be the same or higher than the Acquisition Rate (previous field). NSS Spectral Imaging System Handbook 375

388 Feature Sizing Feature Sizing is an option that lets you measure, count and identify particles and subparticles (particles touching or surrounded by another particle) of interest in a sample. Feature Sizing includes Chemical Typing, an advanced way to classify particles by matching their quantitative chemical composition to a database of chemical types you create in a chemical library. Basic Feature Sizing lets you analyze and report the size, shape and number of particles and subparticles in selected areas of a sample. You can set dozens of parameters, filters and sieves to tailor your analysis. This can provide valuable information about the sample and help you determine its quality and properties for industrial applications, investigative analysis and more. Chemical Typing helps complete your analysis by quantifying and matching the elements and compounds that make up the particles. Applications for Feature Sizing range from analyzing inclusions in steel and grading the potential of gold ore to detecting asbestos fibers or verifying gun shot residue in samples. 376 NSS Spectral Imaging System Handbook

389 Morphology overview Using Feature Sizing you can define, locate and analyze custom defined particles that may be scattered throughout a sample. Once defined, you can manually move to particles of interest and analyze them or, if your system is equipped with Analysis Automation software, you can direct the software to find and analyze particles without your intervention. The flow chart that follows provides an overview of the process. Helpful tips Keep the following tips in mind when using Feature Sizing: A Backscatter Electron Image (BEI) is ideal for Feature Sizing, because it reduces the effects of a sample s surface anomalies. To accurately return to stage locations later, you should perform a backlash on the stage before acquiring the image to be sized. NSS Spectral Imaging System Handbook 377

390 In chemical typing, if your sample is carbon-coated or you observe carbon polymerizing on the sample, mark carbon as Absent in the periodic table under Element Setup. If you do not mark carbon as Absent, residual carbon could be unintentionally introduced into your analysis, reducing precision. See Removing carbon from chemical typing later in this chapter. Feature Sizing Setup mode Follow these steps to use Feature Sizing Setup mode: 1. Select Feature Sizing in the navigation pane, and then click Setup. 2. On your microscope, move the stage to an area of interest. 3. Acquire an image of your sample, including the particles of interest. Note Use a Backscatter Electron Image (BEI) for best results. 378 NSS Spectral Imaging System Handbook

391 Defining particles to size As you adjust the Threshold slider bars, the image pane displays particles to size in red (binary representation). Particle pixels intersected by the Line Profile cursor that fall within the selected area histogram box are shown as intensities in the video line profile pane at top-right and selected area histogram at bottom-left. Within Feature Sizing Setup mode, you can define as many as 7 sets of thresholds. This allows you to size features of different backscatter intensities during a single analysis. For instance, you could size both dark and light features and ignore the gray between them. You can also analyze phases within a single feature by setting thresholds that associate different video levels with the phases. Then when you size features, the software reports features that are bound together (subparticles) versus free features. The associated chemistry and size information for each phase is displayed along with the total feature data. Follow these steps: 1. Drag or resize the selected area histogram box, as desired, and move the Line Profile cursor to intersect particles of interest. Note The selected area histogram box is most useful when you work with images with sparse particles and mostly matrix material. Selecting an image area provides a better particle-to-matrix ratio. The histogram can then show a large enough peak to represent the particle and let you refine the setup. 2. In the image pane, move the High and Low Threshold slider bars to define the particles to size. Thresholds cannot overlap. NSS Spectral Imaging System Handbook 379

392 To add a new threshold set, click the button in the image and particle processing pane, shown below. The first threshold set is red when it is active and has red triangles on the end points when it is inactive. Similarly, the second threshold set is yellow, and the third set is blue. To delete a threshold set, click the button. When you double-click a threshold set or select it and click the button, it becomes active. You can modify the threshold numerically, accept the settings, or delete the threshold set. Click the check mark, shown below, to accept the threshold limits, or click the X to cancel any changes to the selected threshold. NSS recognizes any feature with an intensity level between the high and low thresholds as a particle. The thresholds are coordinated between the histogram, linescan, and particle processing panes. You can drag the thresholds in the histogram pane left or right to make adjustments. Note You also can move the threshold slider bars in the video line profile pane or enter values under Image Processing in the image and particle processing pane. 380 NSS Spectral Imaging System Handbook

393 3. Specify whether to use threshold tracking and a peak location for the matrix material. Threshold tracking automatically locates a specified matrix material peak in the histograms for subsequent images. The software adjusts the threshold values to compensate for brightness changes based on the peak location. It also adjusts the threshold values for contrast changes by using the Full Width Half Maximum (FWHM) value of the peak. Threshold tracking works best on samples where the particles are a small percentage of the field of view. If you want to use threshold tracking, select Enable and enter the matrix material peak location in the Tracking Peak Location text box. You can also set the location by dragging the matrix target cursor (see the illustration below). Be sure to specify a location associated with the background rather than a peak that defines your particles. This feature works as long as the following is true: You need something that produces a grey level in the images that will stay relatively constant in area fraction between multiple frames. NSS Spectral Imaging System Handbook 381

394 The algorithm uses the intensity and Full Width Half Maximum (FWHM) of the selected grey level peak to adjust brightness and contrast. If the area fraction associated with that peak changes significantly between multiple frames, it will affect the contrast since this directly affects the FWHM of the peak. The technique was developed for cases where the area fraction of particles versus background does not change significantly from one field to the next, such as with inclusions in steels. Selecting guard regions At times, you might want to modify how particles are defined and which particles should be processed. You can use guard regions and image filters to further process particles before they are measured and (optionally) chemically typed. When particles overlap the edges of your image frame, you can set a guard region to omit these partial particles and reduce bias in results. To access this capability, Choose Advanced under Image Processing and then select the Guard Region tab. 382 NSS Spectral Imaging System Handbook

395 The following table describes the available properties. Field None Center Of Mass Stereological (Full Coverage) Guard Region Size Description No guard region will be applied. The software sizes features up to the borders of the image frame. Ignores particles whose centers of mass fall inside the guard area. Use for random, manual spot-checking of images where frames are unlikely to overlap. Applies a guard region along two edges in a size you set. Use this in acquisitions controlled by optional Analysis Automation for full coverage of a sample. Sets the guard region size in micrometers and calculates the percentage of image width covered. For automated analysis, match the frame overlap percentage to the percentage of image width covered by the guard area. Set the guard region to half the maximum particle size. This helps to ensure that all particles are analyzed when you do full coverage and use an overlapping frame stage motion. The guard region appears as a blue border in the image pane. You can drag this border to resize the guard region. Selecting filters At times, you might want to modify how particles are defined and which particles should be processed. You can use guard regions and image filters to further process particles before they are measured and (optionally) chemically typed. NSS Spectral Imaging System Handbook 383

396 To access the filters available for image processing, choose Advanced under Image Processing in the image and particle processing pane and then select Filters. You can now choose a filter and then close the dialog box. The table that follows describes the filters available to you. Field Remove Particles With Area Less Than Or Equal To Fill Holes Description Removes particles from analysis when their area is less than or equal to the number of pixels you specify. The particle area can be of any shape and orientation. Fills holes in particles for analysis, ensuring that whole particles will be processed. 384 NSS Spectral Imaging System Handbook

397 Field Separate Touching Particles Description Erodes or dilates borders of touching particles to isolate particles for analysis. If this is active, also select the Low, Medium, High, or Custom separation mode to apply. Custom mode lets you enter Erode and Dilate values, explained below. Erode settings -1: The borders are eroded until there is no further change. 0: No erosion is performed. 1 or greater: The borders are eroded the specified number of times. Dilate settings -1: The borders are dilated until there is no change when the dilated image is masked with the original image. 0: No dilation is performed. 1 or greater: The borders are dilated the specified number of times. Defining processing parameters and setting acquisition criteria The Advanced Particle Processing dialog box lets you control what you want to measure in a sample, define parameters used during chemical typing, set particle sieves, manage spectra and image acquisitions for extended acquisitions, and set termination criteria for automated analysis. Morphology tab Morphology refers to the size, shape and measurements of the particles you want to size. NSS Spectral Imaging System Handbook 385

398 Follow these steps to set the parameters on the Morphology tab: 1. Under Particle Processing, click the Advanced button and then select Morphology. 386 NSS Spectral Imaging System Handbook

399 2. Select the desired Morphology properties. The following table describes the available settings. Field Area Dimensional (in Particle Parameters box) Location Feret Fiber/Stringer Projections Internal Description Measures particle area, as the number of pixels in the particle times the pixel area, in current measurement units squared. This is a default parameter. Measures the perimeter, which is the sum of the distances between the centers of adjacent pixels on the particle perimeter times the pixel width in current measurement units. Also measures circularity, which is the perimeter squared divided by the value 4 pi times the area. The circularity is unitless. A perfect circle will have a value of 1.0. Displays the X and Y center of mass, as the average value of particle pixel X or Y coordinates. Also displays the calculated location for a single spot x-ray acquisition, in case the particle has a hole in the center of mass. This is a default parameter. Displays the projection of the particle along the X-axis and Y-axis. Applies parameters best suited to fiber or stringer analysis, including length, width, aspect ratio and orientation for fibers in filter paper or stringers in metal alloys. Measures the largest and smallest separation between points on the particles convex perimeter. Also calculates an average of all triangle altitudes drawn between pixels on the convex perimeter and the standard deviation (sdv) of the measurements. Measures the sum of the distances between centers of adjacent pixels on the particle inclusion multiplied by the pixel width. Measures the number of non-particle pixels completely surrounded by particle pixels multiplied by pixel area, in current measurement units squared. Lists the number of discrete inclusions. NSS Spectral Imaging System Handbook 387

400 Field Convex Description Calculates area as the number of pixels inside the particle s convex perimeter multiplied by pixel area, in current measurement units squared. Calculates circularity as the convex perimeter squared divided by the value 4 pi times the convex area. Calculates length as the length of a particle or fiber after it is straightened into a rectangle of equal area and perimeter, in current measurement units. Calculates perimeter as the sum of the distances between the centers of adjacent pixels on the particle's convex perimeter multiplied by pixel width, in current measurement units. Dimensional (in Frame Parameters box) Particles Microscope Image Analyze Subparticles Return To Particle Measurement Units Displays the summary per frame of the percentage of the total area and factional area covered by particles. Displays the summary per frame of accepted and rejected particles, based on your selected sieves. Displays the microscope state during acquisition. Displays the image resolution in the X and Y dimensions and the size of an image pixel. Measures the morphology and chemistry of a feature and any subparticles attached or contained within the feature. To use this measurement mode, you must set up multiple threshold to identify the different phases. You can use this measurement only if the feature s subparticles can be distinguished by video intensity. Acquires the stage and beam information needed to put the particle in the center of the field of view after analysis. Set to micrometers (µm) or nanometers (nm). By default, the software measures and reports particle area and stage location, including partial particles. Select other parameters based on the sample and kind of analysis you want to conduct. For example, to analyze fibers in filter paper or stringers in metal alloys, select Fiber/Stringer. The software will then apply parameters best suited to fiber or stringer analysis, including length, width, aspect ratio, and orientation. 388 NSS Spectral Imaging System Handbook

401 Note The Return To Particle setting automatically selects Location and Microscope parameters. This ensures that the software acquires the stage and beam information it needs to visit a particle after analysis is complete. Feature Sizing Analysis mode provides a Move To feature to move the stage to put the desired particle in the center of the field of view. NSS Spectral Imaging System Handbook 389

402 Chemistry tab Follow these steps to set the parameters on the Chemistry tab: 1. Under Particle Processing, click the Advanced button and then select Chemistry. 390 NSS Spectral Imaging System Handbook

403 The following table describes the available properties. Field Learn Unknown Measured Particles Remove Background Classify Element Rich Types First and Classify Multi-element Types First Description Sets the software to learn chemical types automatically during analysis from unknown measured particles. The types are added to the current chemical typing library under the names of Learn 1, Learn 2, and so on. Once they are acquired, you can use the chemical typing editor to rename or merge the typing files. Set Learn Variance (sigma) to the desired value. By default, the software excludes elements that are less than 5% of a particle s composition. When you acquire spectra from small particles, the matrix spectrum might also be present in the acquired spectra. The background spectrum can be mathematically removed. To do so, you must provide a pure background spectrum. You also need to provide an element and line in the matrix that will be used for normalization. The normalization element must not be present in any of the particles. Distinguishing the background allows the software to properly ratio the contribution of the substrate to the particle. If you acquire a matrix spectrum, use an acquisition time that is long enough to ensure that the spectrum is statistically valid. Usually 50 to 100 seconds is adequate. Use these parameters to classify element rich types or multi-element types first. The software maintains the selected order in the particle and frame analysis results. NSS Spectral Imaging System Handbook 391

404 Field Minimum Element Concentration Cut Off (WT%) Acquisition Time Maximum Peak Counts Raster and Spot Ignore Spectra With Insufficient Data Store Spectra Description This parameter allows you to specify the minimum concentration in WT% which must be detected to classify an element as present in the particle. Since acquisition times are generally short during chemical typing, noise can cause false element identification. This parameter lets you direct NSS to ignore the noise. Sets the amount of time spent on acquiring an EDS spectrum for each particle. The higher the time, the greater the accuracy, but the longer the processing will take. The default of 2 seconds is usually sufficient. Terminates acquisition when the number of counts in any spectral channel exceeds this value. Select Raster (more common) to scan the entire particle or Spot to scan one point on the particle. For irregularly shaped particles, Spot applies XREF and YREF to define the point for acquisition. Raster scans 1 micrometer in from the particle borders. If the elements in a particle do not exceed the number of counts, the software marks the particle as Insufficient Data. With Store Spectra enabled, spectra acquired for chemical classification are retained for each particle. Selecting a particle from the list of particles restores the spectra for viewing. Sieves tab To speed up analysis, you might want to reject particles with certain characteristics. For example, you could create a sieve to reject any particle whose area is greater than 4 pixels but less than 20. Parameters include area, circularity, aspect ratio and many more. You can apply multiple sieves as tests. Particles must pass all sieve criteria to be accepted. Follow these steps to set the parameters on the Sieves tab: 1. Under Particle Processing, click the Advanced button and then select Sieves. 392 NSS Spectral Imaging System Handbook

405 2. Select a particle parameter from the center drop-down list box. 3. Select the desired Boolean operators from the drop-down list boxes beside the particle parameter. NSS Spectral Imaging System Handbook 393

406 4. If you selected a parameter other than Chem Classification, enter values in the text boxes. If you selected Chem Classification, select the chemical type you want used as the sorting criterion. Selecting a parameter determines the unit that appears, if any. If you selected Chem Classification, a new drop-down list box appears containing the chemical types in the chemical type library that has been associated with the data. After you select a chemical type, you can sort on an equal to or not equal to basis. 5. Click the button to add the condition. To delete a condition, select it in the list and click the button. 6. Create additional sieves, as desired. To edit a sieve, select the sieve, modify the values, and click the button. To delete a sieve, select the sieve and click the button. 7. Choose Apply or OK to apply your conditions. The conditions are saved in the project folder when you save or close a project. Extended Acquisitions tab During Feature Sizing analysis, you can mark particles for closer examination when they meet any of the criteria you establish under Extended Acquisitions. The software can automatically acquire a normal EDS spectrum or a magnified image of particles that meet your criteria. The images and spectra are displayed in the graphics pane in Feature Sizing Analysis mode and can be reviewed along with other results. 394 NSS Spectral Imaging System Handbook

407 Follow these steps to set the parameters on the Extended Acquisitions tab: 1. Under Particle Processing, click the Advanced button and then select Extended Acquisitions. This tab lets you set conditional operators for acquiring and saving images and spectra of the particle under analysis. You can set the software to acquire images or spectra whenever any of the conditions you specify are true. The top list controls image acquisitions, while the bottom list controls the acquisition of spectra. 2. In the upper or lower box, select a particle parameter from the center drop-down list box. 3. Select the desired Boolean operators from the drop-down list boxes beside the parameter. NSS Spectral Imaging System Handbook 395

408 4. Enter values in micrometers, degrees, pixels, etc. as warranted by the selected parameter. 5. Click the button to add the condition. To edit a condition, select it, modify the values, and click the button. To delete a condition, select the condition in the list and click the button. 6. Choose Apply or OK to apply your conditions. The conditions are saved in the project folder when you close a project. Termination tab You can tell NSS to terminate Feature Sizing analysis when any of a set of specified conditions are met. For example, you can terminate processing when statistically sound samples of 1,000 particles are analyzed. Termination is especially useful in analysis automation where Feature Sizing will terminate and the software can move on to analyze the next sample. 396 NSS Spectral Imaging System Handbook

409 Follow these steps to set the parameters on the Termination tab: 1. Under Particle Processing, click the Advanced button and then select Termination. 2. Use the center drop-down list box to select particle or frame parameters. Frame # and Total Particles are available by default. To select from about 30 total parameters, first select Use ALL Parameters. 3. Select the desired Boolean operators from the drop-down list boxes beside the parameters. 4. Enter values in the text boxes. The selected parameter determines the unit that appears, if any. NSS Spectral Imaging System Handbook 397

410 5. Click the button to add the condition. To edit a condition, select it, modify the values, and click the button. To delete a condition, select it in the list and click the button. 6. Choose Apply or OK to apply your conditions. The conditions are saved in the project folder when you save or close a project. Feature Sizing Analysis mode Once Feature Sizing setup is complete, you can begin Feature Sizing analysis: 1. Click the Analysis button under Feature Sizing in the navigation pane. 2. Acquire and image. 398 NSS Spectral Imaging System Handbook

411 3. With the image in the image pane and your particle parameters defined, click the Start Acquisition button toolbar. on the Acquisition The software sizes features based on your setup. Particle and frame data appear in the results pane. Generated histograms and extended images or spectra appear in the graphics pane at top-right. Feature Sizing Analysis mode 4. For manual analysis, move the stage to a new location, acquire a new backscatter electron image, and then click the Start Acquisition button to run Feature Sizing again. Results for the next frame are appended to the current results. Managing Feature Sizing results Once you acquire Feature Sizing data, you can chart, sort, filter, reclassify and report results, as well as drive the microscope stage for a live review of a particle of interest. NSS Spectral Imaging System Handbook 399

412 The top list on the Particles tab in the bottom-right pane shows particle attributes based on Morphology parameters you defined in Feature Sizing Setup mode under Advanced Particle Processing. The bottom list shows general statistics, including mean, median and standard deviation. You can further refine the display of results by choosing Setup Filters to set conditional operators to omit data from display. When the filters are ready, choose Apply. The Results box shows the results of your analysis. Note When you run subsequent scans, results of particle analysis are appended to the list. Particles are referenced by Frame # and Particle #. The Frames tab in the bottom-right pane displays results of frames analyzed in your sample. The Particle Count Summary tab in the bottom-right pane provides two simple summaries of the Feature Sizing data for each chemical type. The first summary shows the number of particles found in the analysis for each chemical type, the percentage of particles for each type based on the total number of particles, and the percent of the total sample area that is associated with each chemical type. The second summary gives you a way to create tabular histograms for all the chemical types based on any one of the morphological parameters. Select the desired parameter from the drop-down list box below the table. Note You can create a graphical histogram for a single chemical type by using the Histogram tab. To set the number of bins in the histogram and their sizes, choose Edit Ranges. The Edit Ranges dialog box lists the bins and their range limits. To add a bin, type the desired limits in the text boxes and click either button. To delete a listed bin, select it and click either button. To edit the limits for a listed bin, select it, type new limits and click the Set button. The low limit of the first bin and the high limit of the last bin cannot be changed. 400 NSS Spectral Imaging System Handbook

413 Viewing Feature Sizing graphics Note The top-right pane contains the Histogram, Spectrum and Image tabs. The histogram renders data from the results lists. Spectra and images appear only if you set up Feature Sizing to capture such data during extended acquisitions. To view Feature Sizing graphics: 1. On the Histogram tab, click any column heading in a Feature Sizing results list. The histogram graphs data from the selected measurement using the column heading for the title. Here is an example showing data for the Area column: 2. Repeat this for other measurement types, as desired. Sorting results In a Feature Sizing results list, the first time you click a column heading, the data is charted as a histogram. Clicking the same heading repeatedly sorts the data in ascending or descending order. You can sort on any column. Filter the display of results Follow these steps to filter the display of results: 1. On the Particles tab in the bottom-right pane, choose Setup Filters. You can filter your results to display only features with specific characteristics. NSS Spectral Imaging System Handbook 401

414 2. When the Display Filters dialog box appear, specify the desired parameters and conditional operators, and then click the button to add the filter to the list. Note To view results for features with subparticles, select Sub Particles and!=, enter 0, and then click the button. 3. Create additional filters, as desired. The software retains the data set but displays only the particles that meet all tests. To edit a filter, select it, modify the values, and click the button. To delete a filter, select it in the list and click the button. 4. When you are finished, choose OK and then select Apply Filters on the Particles tab to filter the results. 402 NSS Spectral Imaging System Handbook

415 Examining particles To examine a particle, you can select a particle in either the results list on the Particles tab in the bottom-right pane or the current image. Follow these steps: 1. In Feature Sizing Analysis mode, activate the image intensity cursor by clicking the image pane and then clicking the Intensity Cursor button on the Extract toolbar. 2. Click a particle in the image pane. The row for that particle is highlighted in the results list. You can also click any row for a particle displayed in the current image. The cursor goes to that particle in the image pane. This technique works only if the particle is in the last-acquired frame. Previous frames images are not stored. Note If images or spectra were stored for the selected particle, they will be displayed on the Image or Spectrum tabs in the top-right pane. Moving the stage to a particle Follow these steps to move the stage to a particle: 3. In the results list on the Particles tab in the bottom-right pane, select a particle in any frame in which you performed Feature Sizing. It need not be a particle shown in the current image pane. 4. Click the Move To button. The software drives the stage and returns the microscope to a view of the selected particle. This is useful when you need to confirm a particle s features with a live analysis. Note To enable driving the stage, be sure to select Return To Particle on the Morphology tab in the Advanced Particle Processing dialog box in Feature Sizing Setup mode. NSS Spectral Imaging System Handbook 403

416 Saving Feature Sizing results When you close a project, you are given the opportunity to save your work. Results are stored in a.siz directory using your current base name. But you can also save Feature Sizing data at any time. When you save results, you can save unique data in a file. You can also append results from multiple analyses and save the combined data into one file. To save Feature Sizing results: 5. In Feature Sizing Analysis mode, click the Save button on the NSS toolbar. The software saves the current project, including any Feature Sizing data. 6. To acquire and save unique results in a new file, first click the Close button on the Particles tab in the bottom-right pane to clear all earlier particle and frame data from the lists. Note If you don t clear the results first, data from your new analysis will be appended to Feature Sizing data acquired earlier in the session. 7. Click the Start Acquisition button on the Acquisition toolbar and acquire, sort and filter Feature Sizing results, as desired. 8. Click the Save button to store the new file. Your new files are saved using the base name and a unique number. Once you generate data, images and spectra, you can print reports or export data for later use. 404 NSS Spectral Imaging System Handbook

417 Feature Sizing Chem Lib mode To use Chemical Typing, you must set up a Chemical Typing library. This library can have previously defined elements, or it can be empty. To add new chemical types to the library, the software can automatically create types as it goes, you can define a type from a spectrum, or you can manually enter elements and their concentrations. If you already have set up a Chemical Typing library and are satisfied with its content, see Feature Sizing with Chemical Typing later in this chapter. Otherwise, follow the instructions below to create or edit a Chemical Typing library. Under Feature Sizing in the navigation pane, click Chem Lib to go to that mode. Feature Sizing Chem Lib mode Creating a chemical library Follow these steps to create a chemical library: 1. In Chemical Libraries Explorer, right-click the ChemLib folder and select New Library. NSS Spectral Imaging System Handbook 405

418 2. On the Chemical Library tab in the chemical library attributes pane, rename the default New Library name to something that represents your library. Examples are Steels and Fibers. The name is updated immediately in Chemical Libraries Explorer. Note Once you create chemical types, you can save, edit, copy, paste, and merge them, including between chemical libraries. Right-click any chemical type in Chemical Libraries Explorer to manage types. You also can modify the chemical type library; for example add a new chemical type or change the chemistry of an existing chemical type, and then have the software automatically re-classify the particles in the database based using the modified chemical type library. Creating chemical types You can create chemical types in any of three ways: Manually entering elements, weight percentages and sigmas in the Chemical Typing Editor to create element-rich or multi-element types. Learning chemical types from spectra. Learning the composition of unknown measured particles automatically during Feature Sizing analysis of a frame. Once you create chemical types and add them to a typing library, you can use them in Feature Sizing Analysis mode. To activate a Chemical Typing library, see Feature Sizing with Chemical Typing later in this chapter. The next sections explain how to create chemical types using the three techniques. 406 NSS Spectral Imaging System Handbook

419 Manually creating chemical types You can manually create either Element Rich or Multi-Element chemical types. To begin, set up a chemical type as described below and then follow the steps for the desired composition. 1. Create and name a new project. 2. In the navigation pane, under Feature Sizing, click Chem Lib to activate that mode. 3. In Chemical Libraries Explorer, create and name a new library by right-clicking the ChemLib folder and choosing New Library. For example, if you are analyzing precious metals, create a Precious Metals typing library. 4. On the Chemical Type tab in the chemical library attributes pane, enter a name for your new type. An example would be Gold. Now follow the steps below to set up either an element-rich or multielement type. NSS Spectral Imaging System Handbook 407

420 Creating element-rich chemical types Use element-rich to define a chemical type, such as gold. The assumption is that you are not concerned with a sample s composition other than its main element. For example, you can set your gold chemical type to 70% weight percentage. Any sample containing 70% or more gold would be identified as element-rich for gold when you run Feature Sizing Analysis. To create an element-rich type: 1. Select Element Rich on the Chemical Type tab. 2. Beside Element, click the drop-down arrow and select an element from the periodic table that appears. 3. Enter the minimum weight percentage for the element in the Minimum Wt. % text box. For example, you could set gold to a 70% minimum weight. 4. Click the Create Type From Spectrum button. The software adds your type to the typing library. Creating multi-element chemical types In contrast to element-rich types, you might like to identify a mixed-element type containing 70% gold and 30% platinum. Later, when you size features, you can set the software to search for multi-element particles first. The software would find the gold-platinum multi-element first, followed by pure-element concentrations. Set up the structure for your type as described above. To create a multi-element type: 1. Select Multi-Element on the Chemical Type tab. 408 NSS Spectral Imaging System Handbook

421 2. Click the drop-down arrow to select your first element from the periodic table. 3. Enter a Minimum Wt.%. An example would be setting gold to a 60% minimum weight. 4. Enter a sigma (variance percentage), such as Click the button to add the element to the list. 6. Repeat to add other elements to your type. An example would be adding platinum with a 40% concentration and 10% sigma. Note Total weight percentages must be less than or equal to 100%. 7. When ready, click the Create Type button. The software adds your new multi-element type to the library. Editing or deleting chemical types To edit an element to change its concentration or sigma, select it under Element in the list, make your changes and then click the button. To delete an element, select it in the list and then click the button. Creating chemical types from spectra NSS can automatically learn chemical types by analyzing a spectrum that you acquire or open from disk. Once chemical types are learned, you can edit or merge them to meet your needs. Follow these steps: 1. Create and name a new project. NSS Spectral Imaging System Handbook 409

422 2. In the navigation pane, under Feature Sizing, click Chem Lib to activate that mode. 3. Click the Start Acquisition button on the Acquisition toolbar to acquire a new spectrum or open a spectrum from which you want to create a chemical type. 4. In Chemical Libraries Explorer, create and name a new library by right-clicking the ChemLib folder and selecting New Library. For example, if you are analyzing steels, create a Steels library. 5. In the chemical library attributes pane, click the Chemical Type tab. 6. Click the Create Type From Spectrum button. The software learns the chemical composition of the spectrum, reports the results, and generates a temporary name, such as Learn Analyze the results and rename the type to a name that represents the spectrum s composition. 8. Click the Save button to save the Chemical Typing library. 9. Repeat these steps, as desired, to create more chemical types. Note Consider marking carbon as absent from the analysis to promote greater accuracy. See Removing carbon from chemical typing later in this chapter. Creating chemical types from unknowns A third way to create chemical types is for NSS to learn from unknown measured particles automatically during a Feature Sizing analysis. 410 NSS Spectral Imaging System Handbook

423 To do so, you need to enable the Learn unknown measured particles option. Select that option using the Chemistry tab under Advanced Particle Processing in Feature Sizing Setup mode. See Feature Sizing with Chemical Typing later in this chapter. Note Learned chemical types are stored under Learn 1, Learn 2 and so on, in the active Chemical Typing library. You can edit, rename or merge the learned chemical types using the Chemical Typing Editor. Working with chemical libraries The location of Chemical Typing libraries is controlled by the path under Library Directory in Instrument Configuration mode under Service. To review this setting, in the navigation pane, click the Service button and then click Instrument Configuration. You can create multiple libraries with different sets of chemical types; for example, asbestos, gold, iron, and so on. You can set up different libraries and apply the one most appropriate for your analysis using Feature Sizing Setup mode. Reclassifying chemical type libraries The Reclassify button (below the particle and frame results pane, gives you the ability to chemically retype a feature sizing data base. You can modify the chemical type library. This is useful, for example, if you wish to add a new chemical type or change the chemistry of an existing chemical type, and then have the software automatically reclassify the particles in the data base based using the modified chemical type library. Merging chemical types As NSS learns chemical types from spectra or unknown particles, and as your typing libraries grow, you can merge and rename chemical types for greater accuracy and efficiency. NSS Spectral Imaging System Handbook 411

424 To merge chemical types: 1. In Feature Sizing Chem Lib mode, in Feature Sizing Chemical Libraries Explorer, right-click the library name containing the chemical types you want to merge, and then choose Merge. The Merge Chemical Types dialog box appears: 2. Check one or more listed chemical types to merge. 3. Enter a new name for the merged chemical type file under And Replaced With. 4. To remove original Chem Type files, select Delete Source Files. 5. When ready, choose OK. The software averages the chemical compositions and merges the types into a new typing file. 6. Click the Save button on the NSS toolbar to save the updated Chemical Typing library. 412 NSS Spectral Imaging System Handbook

425 Using the Feature Sizing periodic table In Feature Sizing Analysis mode, in the periodic table under Element Setup, elements that are identified in the ChemType Library appear in purple and are activated so they are searched for in an analysis. If you have enabled the software to learn unknowns, when the system finds a new element, it will do a peak identification, perform a quantitative analysis, and then add the element as identified in the table. Removing carbon from chemical typing In chemical typing, if your samples are carbon-coated or you observe high levels of carbon polymerizing on the samples in normal operation of the microscope, be sure to mark carbon as Absent in the periodic table under Element Setup. Marking carbon as Absent eliminates the chance that residual carbon would unintentionally be introduced into Chemical Typing quantitative analysis. To remove carbon from chemical typing: 1. In Feature Sizing Analysis mode, on the Element Setup tab, click Carbon in the periodic table to select it. 2. In the Lines Utilized box set Quant to Absent. This is a project-level setting that is saved with the project. You must manually set carbon as Absent in other projects, as needed. Feature Sizing with Analysis Automation If you have purchased and installed the Column Communication and Analysis Automation option, you can conduct unattended Feature Sizing to drive the stage for acquisition of multiple frames. To configure Feature Sizing for automated analysis, review and set up these automation-related features, as desired: Set up a stereological guard region for sample full coverage, as described in Selecting guard regions and filters earlier in this chapter. Set the grid overlap range value to match the guard region coverage. See Using Grid and Circular in the Analysis Automation chapter. NSS Spectral Imaging System Handbook 413

426 Consider setting criteria to generate spectra or images for particles of interest. You can review the graphics once automated analysis is completed. See the Extended Acquisitions tab. When automated analysis identifies particles of interest, you can use the software to review those particles in live-time on your microscope. See Moving the stage to a particle earlier in this chapter. Consider setting termination conditions to turn off analysis when certain conditions are met; for example, when the software acquires 1,000 particles for a statistically sound sample. See Defining processing parameters and setting acquisition criteria earlier in this chapter. Feature Sizing parameters The following illustrations and tables show many of the basic and advanced particle and frame parameters included in Feature Sizing mode. In Feature Sizing Setup mode you set up parameters using the Morphology tab in the Advanced Particle Processing dialog box, available through the Advanced button in the Particle Processing box in the bottom-right pane. Particle and inclusion measured with basic parameters 414 NSS Spectral Imaging System Handbook

427 The following table describes the basic Feature Sizing parameters. Parameter Area Aspect Ratio Circularity Frame # INT_PERM Length MAX_PROJ MEAN_PROJ Orientation Particle # Perimeter Width X_COFM and Y_COM Description Particle area, as the number of pixels in the particle times Pixel_Area, in current units squared. Defined as MAX_PROJ divided by Width. Unitless. Perimeter squared divided by (4π times Area). Number assigned to the frame containing the particle. Internal perimeter, as the sum of distances between centers of adjacent pixels on the perimeters of particle inclusions, times Pixel_Width, in current units. Derived length of particle or fiber, after it is straightened into a rectangle of equal area and perimeter, in current measurement units. Maximum particle projection (maximum caliper dimension), as the largest separation between points on the particle convex perimeter, in current measurement units. Minimum particle projection (minimum caliper dimension), as the shortest altitude of all triangles drawn between pixels on the convex perimeter, in current measurement units. Triangle bases are defined by adjacent pixels and peaks by pixels on the opposite side of the particle. Angle between the positive X-axis and the maximum particle projection, in degrees. Clockwise rotation from the X-axis is a positive orientation angle. Number assigned to the particle, cumulative across multiple frames. Sum of the distances between centers of adjacent pixels on the particle perimeter, times Pixel_Width, in current measurement units. Particle projection perpendicular to the maximum projection, in current measurement units. X or Y center of mass, as the average value of particle pixel X or Y coordinates. NSS Spectral Imaging System Handbook 415

428 Parameter X_FERET and Y_FERET Description X_FERET is the projection of the particle on the X-axis. Y_FERET is the projection on the Y-axis. Particle and inclusion measured with advanced parameters The following table describes the basic Feature Sizing parameters. Parameter X_MAX and Y_MAX X_MIN and Y_MIN X_REF and Y_REF CVX_AREA Description Maximum value of particle pixel X or Y coordinates. Minimum value of particle pixel X or Y coordinates. Used in acquiring an EDS spectrum at only one location on a particle, as close to the center of mass as possible. This might become necessary when a particle has a hole and no part of the particle is present at the true center of mass. The Y_REF is defined as the true center of mass. To define the X_REF, the software searches all horizontal chords along the Y center of mass. The center of the largest horizontal chord is the X_REF. Convex area, as the number of pixels inside the particle convex perimeter, times Pixel_Area, in current measurement units. CVX_CIRC Convex circularity, as CVX_PERIM squared, divided by (4π times CVX_AREA). Unitless. 416 NSS Spectral Imaging System Handbook

429 Parameter CVX_LENGTH CVX_PERIM Description Convex length, derived as the length of a particle or fiber after it is straightened into a rectangle of equal area and perimeter, in current units. Convex perimeter, as the sum of distances between centers of adjacent pixels on the particle convex perimeter, times Pixel_Width, in current units. NSS Spectral Imaging System Handbook 417

430 Reports and Printing NSS provides six methods for creating reports: Printer report generation Microsoft Word file generation Microsoft PowerPoint file presentation Copy and paste reporting JPEG file generation Microsoft Excel data generation Printer reports Printer report generation is automatically set up in NSS. You can customize the items you want to appear in the report and preview the report before printing. NSS uses a Page Setup dialog box (shown below) to control the appearance (and sometimes the contents) of the generated report. When you are finished with setup, use Print Preview to view your report and Print to create a paper or.pdf copy. To access the dialog box, choose Page Setup from the File menu. 418 NSS Spectral Imaging System Handbook

431 This dialog box contains tabs for customizing the report. The tabs vary depending on the model of NSS and the options installed. The following tables describe the options on the tabs. Header tab Manages the appearance of text on each report page, and page numbering (use the Margins tab to change the font). Field User Name, Company Name, Title Logo Logo Position Pagination Description These fields appear on each page of the report. Specify a.bmp file to appear on every page. Enter the position of the logo as a percentage of the page width from the right margin. Select On to print the current page and total page numbers; for example, Page 1 of 3. Margins tab Sets the page margins and other layout parameters used for the report. Field Top, Left, Right and Bottom Label Font Orientation PPT Bk Image PPT Resolution Description Margins for reports. Font for report text. Page orientation for reports. Background image for report slides in PowerPoint. See Generating Microsoft PowerPoint reports later in this chapter. Screen resolution for report slides in PowerPoint. See Generating Microsoft PowerPoint reports later in this chapter. NSS Spectral Imaging System Handbook 419

432 Spectra tab Determines which spectral items appear in the report as well as their layout and color. All modes that display spectra use these settings. Field Type Layout Option s Color Description Select Overlaid to print all displayed spectra overlaid on a single graph. Select Discrete to print each individual spectrum in a separate graph. If you selected Discrete in the Type box, select the desired page layout for the spectra. Select the optional information you want included in the report. Quant results that are printed reflect the options selected on the Quant Results tab of the Properties dialog box (available through Properties in the Edit menu). Select Printer Friendly to print items using colors suited to your printer. Select Screen Colors to print using the same colors that are used to display the items. Select Black & White to print in black and white. Point & Shoot, Images, Compass, Phases and Spectral Imaging tabs Determine which items appear in the report as well as their layout and color. Field Layout Option s Colors Description Select a page layout. Select the items you want included in the report. See the description for Color in the Spectra tab table above. Line Scan and Feature Sizing Results tabs Determine the appearance of the linescan and the acquisition information to include. Field Option s Colors Description Select the items you want included in the report. See the description for Color in the Spectra tab table above. 420 NSS Spectral Imaging System Handbook

433 Generating Microsoft Word reports Microsoft Word file generation is similar to printer report generation, loading the report in Microsoft Word, where you can edit the report and save it as a Word file. Microsoft Word is included with NSS. To generate a report for use in Microsoft Word, click the Export To Word button and then use Microsoft Word to edit, print and save the file. So long as the file is open, subsequent exports append to the report you are generating. Generating Microsoft PowerPoint reports Microsoft PowerPoint file generation is similar to printer report generation, loading the report in Microsoft PowerPoint, where you can edit the report and save it as a PowerPoint file. Microsoft PowerPoint is not included with NSS and must be purchased separately. To generate a report for use in Microsoft PowerPoint, click the Export To PowerPoint button and then use Microsoft PowerPoint to edit, print and save the file. So long as the file is open, subsequent exports append to the report you are generating. Note The paper orientation is automatically set to landscape when you export to PowerPoint. Copying objects to third-party programs NSS can copy any of the analysis and results views to the Windows Clipboard for use in third-party programs. The format of the data depends on the currently selected pane. Images, maps, spectra and linescans are copied as bitmaps. Quant results are copied as.csv files. Generating JPEG files JPEG file generation is also similar to copy and paste reporting, creating a.jpg file from the selected area in NSS. You can the file, publish it on a Web page or manually import it to a report. 1. Click the view you want to copy to a JPEG file. If the currently selected view is a spectrum, map, image or linescan, it is outlined on the NSS screen with a yellow box. 2. Choose Copy To from the Edit menu. The Save As dialog box appears. NSS Spectral Imaging System Handbook 421

434 3. Select the directory in which you want to save the.jpg file. 4. Enter a file name. 5. Choose Save. Directly generating Microsoft Excel data Microsoft Excel-compatible files (.csv) are generated by both Feature Sizing mode and batch quantitative analysis. You can copy these files from a project to another folder for use in Microsoft Excel. (Microsoft Excel is an option for purchase with NSS). Using Feature Sizing data in Microsoft Excel Note When you save data in Feature Sizing mode, the data is saved in two.csv files. One file contains particle results. The other includes frame results. Data is saved as.csv files located in a.siz subfolder of the project. Make a copy of the.csv files that you want to open in Excel. After you start Microsoft Excel, just choose Open from the File menu and select the copy of the appropriate.csv file. If you use Excel to make changes to the original Feature Sizing.csv files, these changes might be incompatible with NSS. In this case, you could be unable to review your Feature Sizing results. Always make a copy of the.csv file to use in Excel. Using quantitative results in Microsoft Excel Quantitative results are stored directly as a.csv file when spectra or Point & Shoot data are analyzed automatically in an analysis sequence or in a batch analysis. You will find these.csv files in the main project directory or in the ~temp directory under the main project. 422 NSS Spectral Imaging System Handbook

435 Software Reference Material Operating system support U.S. versions of Microsoft Windows XP are supported for all functions of the operating systems that pertain to the operation of NSS as an x-ray microanalysis unit. Supported file formats NSS stores data in industry-standard formats whenever possible. For example, images are stored as.tif files. When the software needs to save a logical group of images together, such as for an x-ray map set, the system saves the file names of these images in an ASCII control file. The following table lists the file types (by extension) used by NSS. Note All TIFF files contain both an 8-bit image and a 16-bit image. The 8-bit image is used by third-party programs such as Microsoft Word. The 16-bit image is used within NSS. File Type.apf.chem.clib.csi.em.emsa.fss.fzm,.fzma or.fzme.fzs,.fzsa or.fzse.grid.jpg.lscan.lsctl Description Automation points file. Feature sizing chemical type file. Feature sizing chemical library file. Spectral Imaging control file. Contains the names of files used for the Spectral Imaging acquisition. Element map if phase data came from map input in TIFF format. Spectrum files stored in industry-standard EMSA format. Feature Sizing setup file. Map from optional XPhase processing in TIFF format. Spectrum from optional XPhase processing in EMSA format. Automation grid file. Image file saved in JPEG format (Edit > Copy To). Linescan file. Linescan control file. 423 NSS Spectral Imaging System Handbook

436 File Type.lsmsa.lsref.map _map.tif.mtdb.p_s.pcm or.pcma.pcs or.pcsa.psmsa.psref.ref.si.simcs.siref.sitif.std.stn.tif.tnp.wstd Description Spectrum files for each pixel in a linescan stored in industrystandard EMSA format. Linescan reference image in TIFF format. Element maps control file. X-ray map file in TIFF format. Spectral match database. Point & Shoot control file. Compass image file in TIFF format. Compass spectrum file in EMSA format. Point & Shoot spectral file in EMSA format. Point & Shoot reference image in TIFF format. User-defined standardless reference spectrum file in EMSA format. Spectral Imaging data file. Spectral Imaging concurrent external input map file in TIFF format. Spectral Imaging reference image file in TIFF format. Spectral Imaging concurrent video image file in TIFF format. EDS standards spectral data file stored in EMSA format. Standards reference list file. Image file in TIFF format. NSS project template file. WDS standards spectral data file stored in EMSA format. More about projects and templates All data is stored within projects. Each project can consist of several subprojects. A project includes the elements list, identification configuration, base file name, and acquisition properties from the project s previous use. When you start NSS, Project Explorer appears allowing you to select or create a project. You have the ability to save a project s settings as a project template. Templates store your project information (acquisition parameters, periodic table settings, etc.) so that you can recall and associate them with other 424 NSS Spectral Imaging System Handbook

437 projects. You can also save a project s settings as a project template and apply it to other projects. The template consists of the acquisition properties, periodic table settings, including the history, and the spectrum processing setup. Templates are stored with a.tnp extension. Project folders Each project consists of a main project folder containing all the data for the project. A project includes all setup information and data associated with the project, such as the elements list, identification configuration, base file, and acquisition properties. When you acquire new data, it is saved in the current project s temporary folder and follows the project s settings. When you create a child project under a parent project, the child project inherits all of the parent project s settings. When you close a project or exit the software, you are asked whether to permanently save any unsaved data with the current project. If you choose to save a file with the project, the file is moved from the project s temporary folder to the main project folder. If you are working with data stored in the temporary folder (not yet saved in a project) and experience a power failure, the data will be in the temporary folder when you restart NSS. Creating a new project Follow these steps to create a new project: 1. Click the Project Explorer button or choose Project Explorer from the File menu. NSS Spectral Imaging System Handbook 425

438 Project Explorer appears: Project folders appear in green. Project data is entered in the fields on the Properties tab. Note You must map your network s shared resources to drive letters before you can use those locations to open and save project files or store acquired images. This applies to data, spectra, images and other NSS files. Please see your operating system documentation for information on mapping network drives. 2. Select the folder where you want to create the project folder. 3. Create a new folder by right-clicking the parent folder and choosing New Project from the pop-up menu. A New Project folder is created. 426 NSS Spectral Imaging System Handbook

439 4. Right-click the new folder, choose Rename from the pop-up menu, and enter the appropriate project name. You can also click the folder, press the F2 key and enter the name. 5. Enter the project information. The following table explains how to enter information in the fields. Field Author Key Words Client Due Date Project Template Notes Instructions Select the author s name from the drop-down list box or enter a new author s name. Select or enter any keywords you want associated with the project. Keywords are searchable. Select or enter the client name. Select or enter the due date. Select the project template from those existing in the System SIX Project Templates directory. Enter any relevant notes. 6. Choose OK. The project folder is created under the folder you selected. The name of the active project appears in the title bar. Note You can also use New Folder in the File menu of Project Explorer to create new folders that are not considered projects. Opening a project Follow these steps to open an existing project: 1. Click the Project Explorer button or choose Project Explorer from the File menu. If any other files are open, the software prompts you to save or delete the data. 2. Open the desired project. NSS Spectral Imaging System Handbook 427

440 If you know the project folder s location, navigate to the folder, click it and choose OK. If you do not know the project s location, right-click the parent folder and choose Project Search. Enter a keyword or select one from the drop-down list. Choose OK. The project folders that include that keyword are marked with a red tag. Click the desired folder and choose OK. When the project is opened, its name appears in the title bar. Note In additional to managing your data in projects, you have the ability to assign a base file name for your data before acquisitions. In the file name pane, you can change the default base name to something more specific to your application. Importing a file You can import a file from another project into the project you have open. Import files using Open in the File menu. To import a file using Open in the File menu: 1. Go to the mode that corresponds to the file type. 2. Choose Open from the File menu. The Open dialog box appears. 3. Navigate to the directory that contains the file. 4. Double-click the file, or click the file and then choose Open. The imported data is copied into the current project s temporary folder and inherits the current project s settings. To permanently save the file in the project, click the Save button on the NSS toolbar or choose Save from the File menu. When you close the project or exit the software, you are asked whether to permanently save any unsaved data with the current project. 428 NSS Spectral Imaging System Handbook

441 Creating a new project template Templates store your project information (acquisition parameters, periodic table settings, etc.) so that you can recall and associate them with other projects. To save the current project settings as a new template: 1. Choose Create Template From Project from the File menu. 2. Navigate to the folder where you want to save the new template. Note Only those templates stored in the System SIX Project Templates directory will be visible when you create a new project. 3. Enter the name of the new template. 4. Choose Save. The acquisition properties, periodic table settings with the history, spectrum processing setup, and Feature Sizing parameters are saved in the template. The new template is stored with a.tnp extension. Project and system security Use System Security in the File menu to prevent unauthorized modification of project templates, acquisition properties and service views. This feature lets you protect templates with a password, specify which functions are protected, and remove password protection. By default, all security is turned off. The computer is set up with the user name Thermo Scientific and no password (choose OK with no password). Additional users and passwords may be added at your discretion consult your Windows documentation. To protect projects and system configurations: 1. Choose System Security from the File menu and then choose Lock Systems. 2. When the lock Projects dialog appears, enter the password to lock the system. NSS Spectral Imaging System Handbook 429

442 To change the behavior when the system is locked: 1. Choose System Security from the File menu and then choose Security Setup from the expanded menu. If a password is installed, enter the password when you are prompted. 2. When the System Security Setup dialog appears, select the items you wish to lock. A check next to the item indicates the item will be locked. 3. If you wish to password protect the locked items, enter an administrator password in the New Password text box. 430 NSS Spectral Imaging System Handbook

443 4. Enter the password a second time in the Confirm New Password text box. 5. Choose OK exit the dialog box and lock the items you selected. Choose Cancel to exit the dialog box without changing the security settings. To turn off protection: 1. Point to System Security in the File menu, and then choose Unlock. The Unlock Projects dialog box appears: 2. Enter the administrator password and choose OK. 3. Choose OK. Resetting a project to the original template settings Resetting a project restores the template settings for that project. To reset a project, choose Reset Project from the Edit menu. Any changes to the settings are restored to the settings for the original template used for the project. NSS Spectral Imaging System Handbook 431

444 Note If the template settings have changed in the time between when the project was created and the time the project was reset, the project will be reset to the original template s current settings. Searching for project keywords You can search project folders to find keywords associated with one or more projects containing the keyword. To search for a project keyword: 1. Click the Project Explorer button or choose Project Explorer from the File menu. 2. Right-click a folder. Projects at or below this folder will be searched. 3. Choose Project Search from the pop-up menu. 4. When the dialog box appears, type a full or partial keyword. The highlight moves in Key Words drop-down list box to the word you typed. Choose OK to begin the search. If the word you typed is not a keyword, the nearest similar keyword is highlighted. If it is an appropriate alternative, choose OK to begin the search. If it is not, browse through the list to find an appropriate keyword. Folders containing the keyword are marked with a red tab. Menu commands File menu The availability of menus and the commands they contain may depend on the current mode and view, whether a displayed item is selected, which options are installed, and which NSS model you have. The sections below describe what you can do with each command when it is available. File menu commands include: Command Function 432 NSS Spectral Imaging System Handbook

445 Project Explorer Close Project Create Template From Project System Security Open Close Save Save Map File Export Image As CSV Page Setup Print Preview Print Export To Word Export To PowerPoint Compress SI File Open, create or edit a project. Close the current project. Create a template from the current project to use when creating projects with the same initial parameter settings. Prevent unauthorized modification of project templates or remove the protection. Open a file stored in a location other than the current project folder. Close the current file. Save the current file with its current file name. Save the current elemental maps as a unit. Available only in Spectral Imaging mode. Save an image or a map as a simple text file. Specify how to print information. See how information will appear when printed. Print the specified report. Place the specified report in a new or current Microsoft Word document. Place the specified report in a new or current Microsoft PowerPoint presentation. Greatly reduce the size of a Spectral Imaging data set. Edit menu Exit Close NSS. Edit menu commands include: Command Undo Cut Copy Copy To Paste Erase All Points Function Reverse the effects of the previous action. Delete the selected item and place it on the Windows Clipboard. Copy the selected item to the Windows Clipboard. Saves the currently selected pane to a *.jpg file. Place a copy of the contents of the Windows Clipboard in the specified location. In Point & Shoot mode erase all unacquired points on the displayed image. NSS Spectral Imaging System Handbook 433

446 Acquisition Properties Microscope Parameters Properties Reset Project Language Set parameters affecting data acquisition. Set parameters affecting microscope operation and specify items to display in the status bar. Set parameters affecting specific mode properties. Restore the current project to its template settings. Select the language for use with NSS. View menu View menu commands include: Command Restore Toolbars Status Bar Drift Diagnostics Function Recall all toolbars, including any that you closed. Toggle the display of the status bar at the bottom of the screen. Display information about the progress of Drift Compensation, such as how the sample has drifted through time. Spectrum menu Spectrum menu commands include: Command Scaling commands Remove Escape Peaks Remove Sum Peaks Identify Quantify Match WDS Scan Decrease Z Increase Z Function Scale the displayed spectrum in the same way as performed with the corresponding buttons on the Spectrum toolbar. Removes the escape peaks from the currently selected spectrum. Removes the sum peaks from the currently selected spectrum. Identify the elements in the displayed spectrum and mark them in the periodic table on the Element Setup tab. Quantify the displayed spectrum. Search the displayed spectrum against the specified spectral database. Initiate a WDS wave length scan. Display KLM lines for the next lower element on the periodic table. Display KLM lines for the next higher element on the periodic table. 434 NSS Spectral Imaging System Handbook

447 Command Search Down Search Up Label Peak Unlabel Peak Show/Hide KLMs Show/Hide Cursor Append notes to spectrum label Element X-ray Lines Reference Subtract/Add Function Search for the next lower element with an energy line near the cursor in the spectrum pane. Search for the next higher element with an energy line near the energy cursor. Label the peak at the energy cursor location with its element symbol. Delete the peak label you have clicked. Display or hide KLM markers. Display or hide the energy cursor. Adds the first line of the spectrum notes to the spectrum label whenever it is displayed. Add or adjust x-ray line energies for elements and their relative intensity values for known KLM lines. Allows peaks in an unknown spectrum to be added or removed after performing a quantitative analysis. Used to ensure that all elements have been accounted for in the quantification. Image menu Image menu commands include: Command Extraction commands Intensity Ruler Legend On/Off All Overlays Off Function Specify points or areas for extraction in the same way as performed with the corresponding buttons on the Extract toolbar. Toggle the display of the image intensity cursor and location and intensity readouts. Display a ruler for measuring image features. Toggle the display of the image overlay legend. Remove all map overlays from the image. Batch Processing menu Batch Processing menu commands include: Command Function Create Montage Create a montage of images and maps from adjacent fields in a grid automation sequence acquired using Analysis Automation. NSS Spectral Imaging System Handbook 435

448 Quant Analysis Linescan Analysis Point and Shoot Analysis Automatically quantify a selected series of spectra in the current project. Automatically quantify a selected series of spectra in the current project. Automatically reprocess all of the spectra in the current project using the current processing and analysis setup parameters. Image menu Image menu commands include: Command Extraction commands Intensity Ruler Legend On/Off All Overlays Off Function Specify points or areas for extraction in the same way as performed with the corresponding buttons on the Extract toolbar. Toggle the display of the image intensity cursor and location and intensity readouts. Display a ruler for measuring image features. Toggle the display of the image overlay legend. Remove all map overlays from the image. Linescan menu Linescan menu commands include: Command Export as *.csv Function Export the current linescan plot data into a CSV format file. Help menu Help menu commands include: Command Help Topics What s This? About NSS Function Find information about software features. Display a special pointer that you can use to click features to display information about them. Display the version number and other information about your copy of the software. 436 NSS Spectral Imaging System Handbook

449 Installing the software Note This section explains how to install and uninstall NSS software. If you are reinstalling NSS software, either as an upgrade or if you have purchased new options (new license key), first uninstall the existing NSS software as explained later in this section. To install NSS software: 1. Insert the NSS installation CD. The installation program starts automatically. Note If the installation program does not start automatically, reinsert the installation CD or navigate to the CD-ROM drive and double-click the file named Setup.exe. 2. Follow the on-screen instructions. In the Customer Information screen, enter a user name, company name and your license key. The license key is a 24-digit code shipped with your system. Choose Next and continue with the on-screen instructions. Choose Finish when the installation is complete. To uninstall NSS software: 1. Open the Add Or Remove Programs window. See your Windows documentation if you are unfamiliar with adding and removing programs. 2. Select NSS. 3. Choose Change/Remove. 4. Follow the on-screen instructions. Choose Finish when the uninstall is complete. NSS Spectral Imaging System Handbook 437

450 Enabling roaming user accounts for Spectral Imaging If a network user (roaming user) cannot open or acquire Spectral Imaging data, the user might not have the correct rights. If a user with a network account wants to log on to the NSS computer using his or her network account, the system administrator must make the following changes to the user s network account on the network server (not the local NSS computer). To enable the roaming user to access Spectral Imaging data on the NSS computer: Increase scheduling priority. Lock pages in memory. To give the user the correct rights: 1. In Windows, go to User Rights Assignments. Start > Control Panel > Administrative Tools > Local Security Policy > Local Policies > User Rights Assignments 2. Scroll down the list of rights to Increase Scheduling Priority. 3. Double-click the entry to display the Add Users And Groups dialog box, click the name and then choose Add. 4. Scroll down the list of rights to Lock Pages In Memory. 5. Double-click the entry to display the Add Users And Groups dialog box, click the name and then choose Add. 6. Confirm that the user rights are correct. Scroll through the list of rights for Increase Quota, Increase Scheduling Priority and Lock Pages In Memory. In each case, the user s name should appear in the Grant To box. 438 NSS Spectral Imaging System Handbook

451 Screen appearance NSS allows you to customize the appearance on-screen, window sizes, and toolbar locations for convenience and better viewing. Changing the size of window panes To change the size of window panes, move the cursor to a border. When the arrows appear, drag until the window is sized as you like. Rearranging, removing and restoring toolbars You can dock toolbars on the top or either side of the NSS window for move convenient access or have it float over the panes in a tool palette To move a toolbar, drag the toolbar by its handle or the palette title to the new location. To return a floating toolbar to its previous edge position, double-click the toolbar s title bar. You can remove a floating toolbar from the screen by clicking the button labeled X in the upper-right corner of the toolbar s window. To restore a removed toolbar, choose Restore Toolbars from the View menu. NSS Spectral Imaging System Handbook 439

452 Saving your rearranged screen When you exit NSS, the toolbar positions and window pane sizes are saved. The next time you start the software, the screen is arranged as it was when you last exited. Screen resolution and color NSS is designed for a screen resolution of 1024 x 768 or larger. See the documentation that came with your computer if you are unfamiliar with setting screen resolution and color. For best viewing, maximize the NSS window. Detector status To view the detector status while in Spectrum mode, click the Detector Status tab in the bottom-right pane. This tab displays the current PHA status and times for the detector. These values are constantly updated. The zero histogram centroid is used to keep the spectrum offset correct. The measured distribution of the zero strobe (zero histogram) indicates how well the detector is performing. Detectors for a specified resolution expect a specific zero histogram. If it is too wide, the detector might not be functioning properly. The next section explains how to use the Advanced Status button to view additional detector status information. 440 NSS Spectral Imaging System Handbook

453 Advanced detector status To see more detailed information about the status of the detector, click the Advanced Status button to display the FrontEnd Status dialog box. Here is an example for a single-detector system: You can use the information in this dialog box to monitor detector operation and diagnosis detector problems. If the system has two detectors, two separate sets of values are displayed one for each of the two pulse processor subsystems. On single-detector systems the second set of values is dimmed, as in the example above. The full version string from the embedded software running on the chassis in <Major>.<Minor>.<Build> notation. <Build> corresponds to the Analyzer Build number displayed in the title bar. The version can be useful in tracking known or new problems with a specific version of the embedded software. The features in the FrontEnd Status dialog box are explained in detail in the next sections. NSS Spectral Imaging System Handbook 441

454 Acquisition Parameters/Values The information in the Acquisition Parameters/Values box indicates the status of the detector and digital pulse processor (DPP) as well as the chassis and detector temperatures: Feature(s) Detects/sec, Converts/sec, Stores/sec, % Dead Time Resets/sec Energy Range (kev) Time Constant (µs) Discriminator ev/channel Fine Gain Description These values are averaged and updated simultaneously using a sliding half-second window. They are interrelated and indicate the number of x-ray energy events the detector is presenting to the DPP and how many of those raw events are converted into usable energy events at the output of the DPP. These values are affected by the beam current, the time constant, the sample being scanned and other factors. A sliding sum representing the number of resets per second that the detector is experiencing. An abnormally high reading can indicate that the detector crystal is warm or that the FET (field effect transistor) is bad. (There may also be a large number of resets in a TEM when the grid bar is crossed.) If the reading exceeds a calibrated threshold, the detector bias automatically turns off to protect the crystal. If this occurs, the corresponding Bias On status LED (described below) changes to show that the bias is disabled. The maximum energy range of the spectra being collected for the current acquisition. In conjunction with the ev/channel value (described below), this value indicates the number of channels in the MCA array. For example, if the energy range is from 0 to 10 kev and the ev/channel value is 10, the MCA array contains 1024 bins. The time constant being used by the DPP for the current acquisition. The discriminator value being used by the DPP for the current acquisition. The width of each channel in the MCA array. Together with the Energy Range (kev) value (described above), this value indicates the number of channels in the MCA array. For example, if the energy range is from 0 to 10 kev and the ev/channel value is 10, the MCA array contains 1024 bins. The fine gain calibration value for the current time constant. A separate fine gain value is stored for each available time constant. The fine gain calibration values are stored in the registry on the host (that is, not in the calibration file on the chassis), and the host updates the chassis each time a new time constant is selected. The initial value is This value is modified when EDS Fine Grain Calibration is run from NSS. 442 NSS Spectral Imaging System Handbook

455 Feature(s) Zero FWHM (ev) Chassis Temperature ( C) Detector Temperature (K), Detector Temperature (mv) Detector Bias Voltage(V) Description A filtered and averaged value indicating the current Full Width Half Maximum (FWHM) value of the zero peak. This value reflects baseline noise and ultimately the resolution of the system. The current temperature in degrees Celsius at the thermocouple on the EDS board in the chassis. The reading should be around 30 to 32 degrees Celsius after the chassis has been powered up and running for some time. The first value indicates the approximate detector temperature in kelvins. The chassis has conversion functions to go from mv to K for those detectors with temperature sensors that support it. Note that although the conversion functions are accurate to within roughly ± 5 kelvins within the operating range, some inaccuracies are unaccounted for (such as the coupling of the detector to the stack, manufacturing differences from sensor to sensor, etc.). Consequently, the temperature at the crystal varies somewhat from the temperature displayed here. If the conversion from voltage to temperature results in a negative value, Error appears. This should happen only if the temperature sensor circuit has failed (that is, an open circuit). Note that some detectors do not support direct readout of temperature (such as a liquid nitrogen-cooled detector using the dipstick to monitor the liquid nitrogen level). For these detectors, these features are dimmed and display N/A. This value is the actual bias voltage being generated by the chassis. the bias required for a SiLi detector is printed on the detector serial number label. This reading will be approximately 0 volts for an UltraDry detector since the bias is supplied by the support box. Diagnostic message history The large pane in the FrontEnd Status dialog box displays a scrolling log of the diagnostic error messages emanating from the chassis. Here is an example: NSS Spectral Imaging System Handbook 443

456 To pause the message log (if the messages are streaming too quickly), click the Pause button. Notice While the log is paused, any messages sent by the chassis are lost. To clear the log (to delete extraneous information), click the Clear Log button. To save the log in a file for later review, click the Save Log To File button. In the dialog box that appears, specify a file name and location and then choose Save. From the point that the embedded software on the chassis starts until it is turned off or a fatal error is encountered, the software is constantly monitoring the state of the chassis. These messages are grouped into three different log levels of increasing severity (and decreasing verbosity): 1. Info (Verbose) 2. Warning (default setting) 3. Errors Only Each log level displays its own level of messages as well as those from the lower verbosity settings (for example, in Info mode the chassis also displays both Warning and Errors Only messages). Select the desired level from the Logging Level drop-down list box. Info messages are positioned rather liberally throughout the code to give a more complete picture of the chassis state transitions as well as the message passing between the host application and the chassis. When the chassis is in Info mode, the sheer number of APV messages being sent by the chassis can disrupt the timing of an acquisition running on the chassis. Therefore, you should place the chassis in Info mode only when diagnosing a specific problem. After you collect the desired information, either cycle the chassis power or place the chassis back in Warning mode. Warning messages are typically displayed when the chassis encounters a recoverable error. Also, some messages are logged at the Warning level by the software developers to aid in understanding the state transitions of the chassis and its current operating mode. Receiving a Warning message is not by itself a cause for concern; you must read the message to determine whether it was intended as a true warning or merely a diagnostic aid. 444 NSS Spectral Imaging System Handbook

457 Errors Only messages are considered fatal errors; that is, the chassis is in an unrecoverable state, and the power must be cycled before acquisition can resume. The Echo All Commands option provides the lengthiest output of all. When this option is selected, the chassis echoes every command it receives from host applications including requests sent by the FrontEnd Status utility to update its own display. The commands are echoed immediately upon receipt and before the chassis acts. This can be useful for troubleshooting in situations where even Info mode does not provide sufficient information. However, placing the chassis in this mode consumes a lot of network and processing bandwidth on the chassis and disrupts timing. Therefore, you should select this option only in rare circumstances that require it and should never leave the chassis in this mode after the information is collected. Status LEDs The Status LEDs box displays the EDS status parameters as a series of LEDs whose color indicates the current status: The parameters containing the time-averaged raw voltages of the chassis power supply and the derived voltages on the EDS board are monitored to ensure that they are in range, and their state is displayed by the last two LEDs. These are described in the table at the end of this section. The EDS subsystem in the chassis has a status parameter that is continually monitored by the host software. This status parameter is a bit mask with the bits assigned to two groups of information: Error and Diagnostic Flags, and Acquisition State. The Error and Diagnostic Flags are displayed in red NSS Spectral Imaging System Handbook 445

458 if the respective bit is set, and black if the respective bit is cleared. The Acquisition State bits are displayed in green if set and red if cleared. The Error and Diagnostic Flags parameters are described in the following table: Parameter Low LN High Reset Rate Warm Detector Validation Error Hardware Failure High Dead Time Bias On Diagnostic Description Active only for LN detectors with a dipstick. In this case, the LNSENSE signal on the EDS board is an output, biased with 5 V by the chassis. The chassis continually compares the LNSENSE signal with the High voltage temperature threshold as set during detector calibration. If the measured voltage is above the threshold voltage, this bit is set and the time to off timer is started. If the timeout is reached without the voltage (that is, temperature) returning below the threshold, the Warm Detector bit is set and bias is disabled. The time to off can be zero if the sensor is mounted in close thermal proximity to the crystal (cryogenic detectors). Set if the Resets/sec count exceeds the threshold set during detector calibration (typically 5000/sec). In addition to flagging the High Reset Rate warning, the chassis also simultaneously disables the bias current to avoid detector crystal damage. After Reset Time 2 tenths of a second, the bias is reapplied and the reset rate is measured again. It the Resets/sec count returns to below the threshold, the bias remains applied. If not, the bias is disabled and the cycle starts anew. Active for LN detectors with a dipstick and for LN detectors with a stack sensor. For LN detectors with a dipstick, the bit is set after the voltage rises above the DPPCal threshold and stays there for the time to off period as described above for the Low LN bit. For LN detectors with a stack sensor, the LNSENSE line is an input. The chassis continually compares the LNSENSE signal to the High voltage stack temp threshold as set during detector calibration. If the voltage rises above the threshold (positive slope) or falls below the threshold (negative slope), this bit is set. In addition to setting the bit, the chassis simultaneously and immediately disables the bias voltage to avoid detector crystal damage. The chassis maintains numerous variables that the host sets to constrain an acquisition. Before activating the variables, the chassis error checks the variables to ensure they are within bounds and otherwise contain allowed values. If they do not, the Validation Error bit is set. Since it is normal for this bit to be set during normal operation of the chassis and EDS application, it cannot be used alone to diagnose problems. This is currently unused. Set when high dead time (greater than 95%) is encountered by the DPP. Set when the chassis enables the bias voltage, and cleared when the bias voltage is disabled. This will always be off with an UltraDry detector since the bias is supplied by the support box. This is currently unused. 446 NSS Spectral Imaging System Handbook

459 The Acquisition State parameters are described in the following table: Parameter Active Downloading Starting Stopping Description Set when an acquisition is in progress. Both the Starting and Active bits (described below) are set at the beginning of an acquisition. The Starting bit is cleared to indicate that any setup steps are complete and data is being gathered. Both bits are set at the end of an acquisition (when the termination conditions have been met) and cleared when the acquisition has terminated cleanly. Set to indicate that new parameters (such as Time Constant) have been downloaded to the DSPs that make up the DPP. Set to indicate that an acquisition is starting. Both the Starting bit and Active bit (described above) are set at the beginning of an acquisition. The Starting bit is cleared to indicate that the acquisition setup is complete and data is being gathered. Set to indicate that an acquisition has met its termination conditions and is in the process of stopping. Both the Stopping bit and Active bit (described above) are simultaneously set at the end of a normal acquisition. Both bits are cleared when the acquisition has terminated cleanly. The power supply parameters are described in the following table: Parameter EDS Power Supply Power Supply Description If all EDS power supply values are within their normal ranges, the LED appears green. If any value is outside its normal range, the LED appears red. If all power supply values are within their normal ranges, the LED appears green. If any value is outside its normal range, the LED appears red. Connectivity and control The features at the bottom of the FrontEnd Status dialog box display information about connectivity with the chassis and let you control the application: When the FrontEnd Status utility starts, it attempts to connect to the chassis. The IP address used is the one set by IP Address in the Hardware Communications box in Instrument Configuration mode under Service. This address is stored in the registry on the Windows host. If a registry entry is not present, the default IP address is used: The IP address that FrontEnd Status is attempting to connect to is displayed in the lower-left corner of the dialog box alongside the NSS Spectral Imaging System Handbook 447

460 connectivity LED. When a good connection is established, the connectivity LED appears green. When a connection is not established, the LED appears red. If a connection is dropped (or was never successfully achieved), you must manually reconnect by clicking the Reconnect button after the problem with the chassis or Ethernet cabling has been resolved. When you are troubleshooting, it is often useful to reset the chassis to start from a known quiescent and clean state. As an alternative to cycling the power, you can use the Reboot button to cleanly reboot the chassis. Choosing Reboot sends a reboot message to the chassis, resulting in a hardware reset being asserted internal to the chassis and a complete software reboot. For most purposes this gives the same results as a power cycle. However, the reboot does involve software control. If the embedded software image has become corrupted in RAM or the software is otherwise not responding (that is, if a fatal error is detected), you may need to cycle the power. To cleanly exit the FrontEnd Status utility, click the Close button. EDS Calibration NSS systems are installed and calibrated by a factory trained FSE. Periodically it is recommended that the Fine Gain calibration be performed. 448 NSS Spectral Imaging System Handbook

461 Fine Gain calibration procedure The Fine Gain calibration should be used to make final corrections to the Fine Gain value. There are actually several Time Constants that need to be calibrated. The procedure below runs through one of them. For each pass through the procedure select a different Time Constant in step 4 until the fine gain for all of the Time Constants are calibrated. 1. Click the Auto tab in lower-right corner of the EDS Calibration mode to display the Fine Gain calibration settings. NSS Spectral Imaging System Handbook 449

462 2. Position the stage to a pure standard sample in the microscope. Pure copper is recommended for performing the Fine Gain calibration. Use the following microscope conditions: Optimum working distance per installation documentation. Minimum accelerating voltage of 20 kv. Obtain a store rate of approximately 4000 cps. 3. In the Setup section of the window, select Cu from the element chart, K as the Line, and 30 for Maximum Iterations using the pull-down selections. 4. Select a Time Constant from the drop-down selections. 5. Click the Play button to start the calibration. A spectrum will be acquired. 6. The Automatic Calibration prompt appears. Place the cursor on the centroid of the Cu Ka peak in the display and click the OK button to continue with the calibration. The Calibration program automatically moves the selected peak to the proper energy value for the element that was chosen in step NSS Spectral Imaging System Handbook

463 7. A prompt displays stating that Calibration completed successfully. Click the OK button to finish. The new Fine Gain setting and the Calibration Date will be updated in the status section in the lower right hand corner of the Auto tab. 8. Repeat steps 4-7 to calibrate the Fine Gain for all available Time Constants. NSS Spectral Imaging System Handbook 451