IDRaman mini Installation and Operation Manual

Transcription

1 IDRaman mini Installation and Operation Manual For Products: IDR-MINI, IDR-MINI-KIT, IDR-MINI-ACCY Document: A

2 AMERICAS & WORLD HEADQUARTERS Phone: Fax: Sales: Orders: Support: EUROPE, MIDDLE EAST & AFRICA Phone: Fax: Germany : UK : France : ASIA Phone: Fax: asiasales@oceanoptics.com Japan & Korea: Ocean Optics, Inc. 830 Douglas Ave. Dunedin, FL USA Manufacturing & Logistics 4301 Metric Dr. Winter Park, FL USA Sales & Support Geograaf EW Duiven The Netherlands Manufacturing & Logistics Maybachstrasse Ostfildern Germany Ocean Optics Asia 666 Gubei Road Kirin Tower Suite 601B Changning District Shanghai PRC, Copyright 2013 Ocean Optics, Inc. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, by any means, electronic, mechanical, photocopying, recording, or otherwise, without written permission from Ocean Optics, Inc. This manual is part of an order and subject to the condition that it shall not, by way of trade or otherwise, be lent, re-sold, hired out or otherwise circulated without the prior consent of Ocean Optics, Inc. in any form of binding or cover other than that in which it is published. Trademarks Microsoft, Windows, Windows 95, Windows 98, Windows Me, Windows NT, Windows 2000, Windows XP and Excel are either registered trademarks or trademarks of Microsoft Corporation. Limit of Liability Every effort has been made to make this manual as complete and as accurate as possible, but no warranty or fitness is implied. The information provided is on an as is basis. Ocean Optics, Inc. shall have neither liability nor responsibility to any person or entity with respect to any loss or damages arising from the information contained in this manual.

3 Important Safety Notices The laser described here is safe to operate, provided the user pays attention to all safety warnings: 1. Post warnings in the area of the laser beam to alert those present. 2. Keep all unauthorized personnel out of the area where the laser is operated. 3. Whenever the laser is running and the beam is not in use, it is good operating practice to mechanically block the path. 4. Never look directly into the laser source or scattering laser light from any reflective surface. Never sight down the beam into the source. 5. Maintain experimental setup at low heights to prevent inadvertent beam-eye contact. 6. As a precaution against accidental exposures to the output beam or its reflection, operators should wear laser safety glasses attenuated to the wavelength being generated. For additional information: Laser Institute of America Ingenuity Drive, Suite 128 Orlando, FL Toll Free: Tel: Fax: A

4 Important Safety Notices Laser Safety WARNING This device is intended for use by trained personnel only. Use of controls or adjustments, or performance of procedures other than those described in this manual may result in hazardous laser radiation exposure. This is a class IIIB laser device and up to 100 mw of 785nm (NIR) laser light may be emitted during data acquisition. Only personnel trained in laser safety protocols should be allowed to use this instrument. The aperture warning label indicates where laser radiation may be emitted from the instrument when using the point-and-shoot attachment. The laser safety goggles provided in the unit accessory kit must be worn when using the point-and-shoot attachment. Internal maintenance or repair must be performed at the factory or by authorized personnel only. B

5 Locations of the Warning Labels Remote Interlock The IDRaman mini has remote interlock capability via the ID pin in the Micro USB port. Contact Ocean Optics for more information on the remote interlock connector. Nominal Optical Hazard Distance Calculations The IDRaman mini is a Class IIIB laser device, containing a 785nm, 100mW rated laser diode. These Class IIIB devices are hazardous when intra-beam ocular (eye) exposure occurs, i.e., when one intentionally or unintentionally looks directly into the beam from within the Nominal Optical Hazard Distance (NOHD). Never look directly into any laser beam. The information and calculations below contain details of the intra-beam NOHD calculation for the IDRaman mini (785) in accordance with the recognized international standard, IEC , Safety of Laser Products, 2nd ed., Assumptions Safety interlock(s) failed or bypassed; Raster (motor) stalled or stopped; Laser on continuously at maximum possible component power of 140mW, CW. General Equation C

6 Important Safety Notices Condition 1 Sample door open; Safety interlock defeated or failed; No auxiliary lenses present: N.O.H.D. = 10.3 cm (4.06 in.) Condition 2 Point and Shoot attachment installed: N.O.H.D. = 11.5 cm (4.53 in.) D

7 Table of Contents About This Manual...iii Document Purpose and Intended Audience... iii Document Summary... iii Product-Related Documentation... iii Upgrades...iv Warranty...iv Chapter 1: Introduction... 1 Overview...1 Features...1 Models...2 About Raster Orbital Scanning (ROS)...3 Chapter 2: Set-up and Operation... 5 Overview...5 Point and Shoot Adapter...5 Controls and Indicators...7 Focusing Using the PS Adapter and the F Button...10 Calibrating the IDRaman mini...12 IDRaman mini Start-up with OceanView Software...13 Start-up with Windows 7 and Start-up with Windows XP Using OceanView...16 Acquiring a Spectrum Saving Data Appendix A: IDRaman Software Overview...21 IDRaman Software Set-up...21 Software Overview...22 Creating Library Files i

8 Table of Contents Saving a Library Spectrum Acquiring a Reference Acquiring a Spectrum Acquiring an Average Improving Your Spectrum Control Tab Display Options Saving Spectra Display Features...31 Graph Palette Scale Palette Cursor Home Tab Advanced Tab...33 Analysis Tab...34 Resetting the Time and Date...35 Using the USB Connection for IDRaman mini Library Building...35 Appendix B: Tera Term Software Installing Tera Term Software...39 Changing Pin Codes...40 Turning Baseline Correction On and Off...40 Checking the Serial Number and Firmware Version...41 Appendix C: Specifications Index ii

9 About This Manual Document Purpose and Intended Audience This document provides you with information to get your laser set up and operating. What s New in this Document This version of the IDRaman mini Installation and Operation Manual updates specifications. Document Summary Chapter Chapter 1: Introduction Chapter 2: Set-up and Operation Appendix A: IDRaman Software Appendix B: Tera Term Software Appendix C: Specifications Description Contains a list of product features and the model types available, and offers an explanation of ROS. Provides instructions for setting up and operating the IDRaman mini. Describes how to install and operate the IDRaman software. Describes how to install Tera Term and how to change the PIN, turn baseline correction on an off, and how to check the serial number and firmware version. Provides a list of product specifications. Product-Related Documentation You can access documentation for Ocean Optics products by visiting our website at Select Select Support Technical Documents, then choose the appropriate document from the available drop-down lists. You can also access operating instructions for Ocean Optics products on the Software and Technical Resources CD included with the system. Detailed instructions for OceanView Spectrometer Operating Software are located at: iii

10 About This Manual Upgrades Occasionally, you may find that you need Ocean Optics to make a change or an upgrade to your system. To facilitate these changes, you must first contact Customer Support and obtain a Return Merchandise Authorization (RMA) number. Please contact Ocean Optics for specific instructions when returning a product. Warranty Our 1-Year Warranty covers Ocean Optics IDRaman products regardless of the application from manufacturing defects. The warranty covers parts and labor needed to repair manufacturing defects that occur during the warranty period. We also will cover the costs of shipping warranty-related repairs from our customers to Ocean Optics and from us to our customers. iv

11 Chapter 1 Introduction Overview The IDRaman mini is the smallest, most powerful handheld Raman instrument available today. Designed to make rapid and accurate measurements that identify, authenticate and verify samples, the IDRaman mini is ideal for: Authentication analysis Counterfeit detection Rapid material identification Verification of incoming materials Harsh and demanding environments In-line or at-line testing From rugged field measurements of chemical and explosive agents to quality assurance and quality control in the laboratory, the IDRaman mini is a truly compact choice for fast and accurate measurements. IDRaman uses an internal calibration routine to ensure the most accurate Raman shift data is acquired. Measuring most samples in less than 9 seconds, the IDRaman provides visual confirmation of results and displays both the sample and library spectrum with a confidence factor. You can store a library of thousands of compounds in the IDRaman. Using a proprietary fluorescence rejection algorithm, the IDRaman mini minimizes both false positive and false negative results. With IDRaman s Raster Orbital Scanning technology, the limitation of weak signals from unknown and non-uniform samples is overcome. Features Long battery life - >11 hours from 2 Lithium AA batteries Light weight 330 grams (11 oz.) Compact size x 7.1 x 3.8 cm (3.6 x 2.80 x 1.5 in) Great flexibility measures both liquids (vials) and solid samples (with accessory kit) Rugged design made from solid aluminum

12 1: Introduction High visibility display 7.1 cm (2.8 ) resistive touch display Easy to use intuitive user interface via touch screen High speed acquisition visual confirmation in <9.0 seconds Self-calibration includes onboard software driven calibration Raster Orbital Scanning (ROS) function -- allows detection of inhomogeneous samples without sample degradation Library recognition - use of proprietary data analysis algorithm for high accuracy identification without low false positives and false negatives Models The IDRaman mini (IDR-MINI) is available as a standalone product or packaged with a helpful accessory pack (IDR-MINI-KIT). The accessory pack can also be purchased separately (IDR-MINI-ACCY). IDR-MINI Consists of the handheld Raman spectrometer, a 785 nm excitation source and a micro USB cable for computer connection. A basic component library is provided, as well as software for you to build your own library. This version provides for vial sampling only and contains a box of ml vials. IDR-MINI-ACCY The accessory pack is comprised of a point-and-shoot solid sampling attachment, plus laser safety glasses and a handy storage case. IDR-MINI-KIT For your convenience, the IDR-MINI and the IDR-MINI-ACCY are available as a combined item for a complete solution to your measurement needs

13 About Raster Orbital Scanning (ROS) 1: Introduction The Ocean Optics IDRaman mini uses ROS to rapidly scan a tightly focused beam in an orbital pattern, allowing lower average power to produce high-integrity data from a larger area of the sample without sample ignition or damage. A tightly focused beam may result in noisy signals or missing the Raman active target completely, leading to false negative readings from unidentified samples. Increasing the spot size of the laser dilutes the valuable information about the material, leading to inconclusive matches or false identification of samples. ROS increases the effective size of a tightly focused beam. Information is obtained with complete integrity while sampling the large area needed for complex mixtures or irregularly shaped samples, leading to confident identification

14 1: Introduction

15 Chapter 2 Set-up and Operation Overview This section provides instructions for setting up and operating the IDRaman mini. Read all instructions and warnings carefully before attempting to install and operate your device. IDR-MINI Point and Shoot Adapter The Point and Shoot (PS) adapter (available in the IDR-MINI-ACCY accessory kit) is designed to be used with many different samples. These include materials on surfaces and materials in vials or bottles. With a simple twist of the PS collar it adjusts the position of the sample in relation to the Raman focal point to obtain the best signal to noise. When rotated counterclockwise (viewed from the sample end) it adjusts the sample position further away from the final lens of the PS adapter. When rotated clockwise it adjusts the sample position closer to the final lens of the PS. When the PS collar is placed against the sample the focal point of the system is adjusted to accommodate a container or surface of the sample using these steps. See Focusing Using the PS Adapter and the F Button for more information on focusing using the PS adapter. Be sure to remain at least 11.5 cm from the PS Adapter for safety from the laser

16 2: Set-up and Operation

17 Controls and Indicators 2: Set-up and Operation The IDRaman mini features a user-friendly touch screen display for taking and viewing measurements in autonomous operation. The screen indicators and controls are described below. Screen Description The initial power-up screen. Enter your 4-digit pin (the default is 1234). The system has been activated. The cover has been left open. The door is closed and the calibration standard is in the sample chamber. When prompted, the unit will complete a calibration. A calibration standard is shipped with every unit. Place the standard vial in the sample chamber. Click the Calibration button (under Tools). The button turns red if the calibration is not successful. Tap the vial to settle the calibration sample and retry the calibration. Contact Ocean Optics if you are unable to calibrate the instrument

18 2: Set-up and Operation Screen Description The system is ready for a sample. Press to begin acquisition. The system is ready to fire. This is a safety feature when the pointand-shoot laser attachment is used. The system is acquiring data. If the Point and Shoot (PS) accessory is attached, observe caution as the laser radiation will exit the PS laser attachment

19 2: Set-up and Operation Screen Description This match screen uses the Pearson correlation to calculate and then displays the Hit Quality Index (HQI), a statistical measure of fit indicating the quality of the match. Stored spectrum library is green Sample spectrum is red When is pressed, this screen appears with the time and date, as well as the name for the saved file. The saved file is named with the time, and saved in a folder labeled with the date (for example, File: S10_52_23_am in folder Thu 2 nd Oct 2014). Ready screen. Press the Tools button ( (see below). ) to access the Tools menu

20 2: Set-up and Operation Screen Description Tools menu consists of the following functions: -- Activates the USB connection mode. In this mode, the library can be updated through the USB connection. -- Allows you to set the time. -- Allows you do a manual calibration using an external calibration standard. This tool will turn green if the calibration passes and red if it fails. -- Activates Dynamic Raman Scattering (DRS). The DRS is active if this tool is green and inactive if this tool is red. -- Allows you to view a list of library entries (see below). -- Advances to the Ready screen (see above). Displays the list of library entries. Focusing Using the PS Adapter and the F Button Adjusting the PS (Point and Shoot) collar to the correct position in the autonomous mode is easy with the Focus or F function. The focal length is 8 mm from the front of the lens when using the PS Adapter. Procedure 1. Place a sample in a container representative of the container you will use in your analysis

21 2: Set-up and Operation 2. Arm the system by pressing the button in the home screen. The Armed screen appears. 3. Place the sample container against the tip of the PS collar and press the (F) button. The system will take an initial scan and automatically find the highest peak in the spectrum and report the intensity on the screen. 4. The system will then continually take a spectrum at a set integration and report the peak intensity on the screen. As you adjust the PS collar by twisting it clockwise or counterclockwise, it will move the sample closer or farther away, respectively, from the final lens of the PS attachment and report the peak intensity. Adjust the PS collar until you observe the maximum peak intensity number on the screen. 5. When you are satisfied with the peak intensity PRESS AND HOLD the button until the system returns to the Armed screen. You are now ready to use your PS attachment with the container or surface used to perform the Focus adjustment

22 2: Set-up and Operation Calibrating the IDRaman mini Calibrate the IDRaman mini using the calibration standard that came with the device. Note The calibration standard is made from TiO2 (titanium dioxide) powder inside clear ABS plastic. The combined Raman spectra of these two materials produces a set of distinct peaks at both extremes of the IDRaman mini's wavelength range. This allows the device to be very accurately calibrated across its entire useful range. Check your calibration regularly to ensure the quality of your results. Procedure 1. Turn the power on for the device. 2. Place the calibration standard into the vial compartment. 3. Select the Tools menu

23 2: Set-up and Operation 4. Press Calibrate button ( ).This tool icon will turn green if the calibration passes and red if it fails. If the calibration fails, please contact Ocean Optics tech support for more information. IDRaman mini Start-up with OceanView Software The procedure differs, depending on your operating system version. Start-up with Windows 7 and 8 Procedure 1. Turn on the computer. 2. Ensure that OceanView software is installed. 3. Be sure that power is supplied to the instrument. Turn on the IDRaman mini. 4. Connect the IDRaman mini to the computer via a USB cable. 5. When you first plug in your spectrometer, Windows 7 will attempt (unsuccessfully) to automatically install the driver for your spectrometer due to Windows operating settings. You must manually install the new 64-bit driver for your spectrometer. Click close to close the warning message: 6. Select Start Control Panel Device Manager. 7. Right-click on CBEX (under Other devices) and choose Update Driver Software. 8. Choose the Browse my computer for driver software option. 9. Click Browse and go to C:\Program Files\Ocean Optics\Oceanview\System Files

24 2: Set-up and Operation 10. Click Install. 11. Launch OceanView software. Start-up with Windows XP Procedure 1. When you first plug in your spectrometer, Windows XP displays the following screen. Choose No, not this time

25 2: Set-up and Operation 2. Choose Install from a list or specific location (Advanced). 3. Navigate to C:\Program Files\Ocean Optics\Oceanview\System Files

26 2: Set-up and Operation 4. The Progress window appears. When the installation has completed, the final window appears. Click Finish to complete the installation. Using OceanView OceeanView software is available from Ocean Optics to acquire spectral measurement data from your IDRaman instrument. This section describes how to use the features available for your IDRaman mini. For more information on OceanView software see Product-Related Documentation. Be sure to turn the power on to the IDRaman mini before starting OceanView so that OceanView recognizes the instrument

27 2: Set-up and Operation The Acquisition Group Window provides the following functions for the IDRaman micro: Control Function Take continuous acquisitions. See Acquiring a Spectrum. This control is not recommended for systems such as the IDRaman mini that use a laser due to laser safety issues. Take a single acquisition. Every time this control is activated, the laser fires and a measurement is captured. Pause acquisitions. Select the desired integration time and units (µm, ms, or seconds). The default is 100 ms. Check Auto for auto integration. This setting sets integration automatically by waiting for the peak to hit counts. Maximum auto integration is 8 seconds. Enter the number of scans to average. Click averaging. See Acquiring an Average. to stop

28 2: Set-up and Operation Control Function Select the units for the x-axis, Ramanshifts or Pixels Pixels on the detector (useful for calibration only). Check the box to enable a reference spectrum. See Acquiring a Reference. Check the box to enable the Clean Peaks function. See Peak Cleaning. Select the laser power. This is the power at the sample: High (full power, 70 mw), Medium, or Low). Check the box to enable the laser. Check this box to enable raster orbital scanning (see About Raster Orbital Scanning (ROS)). Acquiring a Spectrum Set your integration time to the desired rate, choose your x-axis units, select the laser power, and then click to acquire a single spectrum. Spectra can be adjusted by averaging scans, enabling reference spectra, and using the Clean Peaks function. Save spectra using OceanView functions (see Product- Related Documentation). Acquiring a Reference OceanView allows you to take a reference measurement for a set integration time. The reference spectrum takes a measurement with the laser off, and then turns laser on and takes the Raman measurement. This lets you exclude ambient light and other environmental background as well as any fixed pattern noise from the CCD. Acquiring an Average Averaging is used when your sample has a high background. Often samples will produce some or even large amounts of fluorescence. The quality of a spectrum is determined by the signal-to-noise ratio. The noise is determined by shot noise which is equal to the square root of signal. This means that samples with large backgrounds will inherently have poor signal-to-noise ratios. Increasing the integration time will improve the signal-to-noise ratio, but with high background samples this may be impossible due to the detector s limited dynamic range

29 2: Set-up and Operation Averaging allows you to take multiple short acquisitions and average them to improve signal to noise. Until the detector becomes dark noise limited, the signal to noise ratio will improve by the square root of the number of averages. Select the number of scans to average using OceanView. Peak Cleaning Clean Peaks is a beta correction algorithm that takes the measured Raman spectra and removes the baseline, removing the effect of fluoresence. This method is not appropriate for every sample, but when spectral backgrounds are a problem it can provide background free spectra. Raw spectra and cleaned spectra can be displayed on the same graph using the Schematic View (Advanced Math Filtering Clean Peaks). Example of Clean Peaks Node Used in the Schematic View

30 2: Set-up and Operation Note Checking the Clean Peaks Enable checkbox produces a single signal on the graph view showing just the clean peak processed spectra. Using this function in the schematic view allows you to view both the original AND the cleaned spectra. Saving Data Use following OceanView controls to save your data to an ASCII text or.spc file: Control Function Save graph to file. Saves your data as an ASCII text file unless you configure a different format using the Configure Graph Saving button described below. Save content over time to one or multiple files (depending on how it is configured). OceanView provides the capability of saving and exporting processed data for each graph view to an ASCII file. When combined with external triggering, this feature can be used to automatically save full spectra timed to one or more external events. After this is selected once, press the spacebar for additional saves. Refer to the OceanView Installation and Operation Manual for more information (see Product-Related Documentation)

31 Appendix A IDRaman Software Overview IDRaman Software is a versatile data acquisition package with built-in baseline and smoothing features for the most difficult samples. This section describes how to use all of the features available and how they can be used to acquire the optimal spectrum for your application. The software provides data storage in the universal ASCII format for spreadsheets or other third-party analysis and display software programs. Also provided is the popular.spc format used with Thermo Scientific s GRAMS spectroscopy software. IDRaman software is an alternative to OceanView and is included with all IDRaman products. IDRaman Software Set-up Procedure 1. Turn on the computer. 2. Copy the device initialization file, IDRamanMini.inf, from the IDRaman Driver folder on the USB memory stick to C:\Windows\inf. 3. Turn on the IDRaman mini instrument (using pushbutton on the front of the unit). Plug the instrument into the computer using the micro USB cable supplied. It will automatically load device drivers. 4. Copy the IDRaman Installer folder from the USB memory stick to the computer. 5. Double-click on Setup.exe in the Volume folder. 6. Follow on-screen instructions to complete installation of the IDRaman Software. 7. Upon completion of installation, restart the computer. 8. Click the IDRaman Software in the Startup Menu. Wait until the system connects to the computer. You are ready to take spectra

32 A: IDRaman Software 9. Install Tera Term open source software from the USB memory stick for later use during library building. Chapter 3: Tera Term Software. Software Overview

33 Creating Library Files A: IDRaman Software The IDRaman mini stores library files on an internal flash drive in a compact format. You can create your own libraries using this software. The Library button enables the library collection routine. In this format the system collects the sample spectrum exactly as it would in the autonomous collection mode. Procedure 1. Select Library from the Acquisition Type menu. 2. Press the Acquire button. The system will collect the library spectrum. Saving a Library Spectrum To save the library spectrum use the SAVE feature described in Display Options. Save the files in the.lib Lib file format. After you save your library spectra you can transfer them to the IDRaman mini. Procedure 1. To initiate the transfer, exit the IDRaman Software (completely close the program). 2. Convert the IDRaman mini to a Mass Storage Device (MSD) by clicking on USB connection button in the Tools menu on the IDRaman mini. --OR-- Open TeraTerm and type reset msd. This converts the IDRaman mini to a Mass Storage Device (MSD). 3. See Using the USB Connection for IDRaman mini Library Building for directions to copy library files to the IDRaman mini. 4. Disconnect the system from USB drive and reconnect. The system will now use the library files that you created

34 A: IDRaman Software Note If you do not disconnect and reconnect, the system will continue to act as an MSD and it will not use your library to match. If you intend to encrypt your files, you will need to use the Secure Library function when you are ready to place them on the IDRaman mini. Acquiring a Reference Spectra can be acquired several different ways depending on your application or the sample s composition. Reference Type This menu allows you to choose how and when a reference is taken for a set integration time. Normally the shutter closes during this period and the reference spectrum is subtracted from the acquisition. This removes any environmental background and it eliminates any fixed pattern noise due to the CCD detector. No Reference -- takes an acquisition without a reference. Reference Once -- takes a reference only once before an acquisition or series of acquisitions in a multi-acquire. Reference Every Acquisition -- takes a reference after each acquisition in a multi-acquire. Block Reference -- takes a set number of references, equal to the number of acquisitions, at the beginning of a multi acquire. This is useful for photo-bleaching

35 Acquiring a Spectrum A: IDRaman Software Procedure 1. Select the Referencing Type. 2. Select the Acquisition Type. 3. Click the Acquire button to begin the acquisition. This button acquires a spectrum for the set parameters and integration time. The shutter opens for a period of time determined by the integration time. The Abort button stops the process and returns to the main menu. Some delays exist to allow for the raster and communication; however, the exposure time is precisely set by the integration time selected. Acquiring an Average Averaging is used when your sample has a high background. Often samples will produce some or even large amounts of fluorescence. The quality of a spectrum is determined by the signal-to-noise. The noise is determined by shot noise which is equal to the square root of signal. This means that samples with large backgrounds will inherently have poor signal-to-noise ratios. Increasing the integration time will improve the signal-to-noise ratio, but with high background samples this may be impossible due to the detector s limited dynamic range. Averaging allows one to take multiple short acquisitions and average them to improve signal to noise. Until the detector becomes dark noise limited the signal to noise ratio will improve by the square root of the number of averages

36 A: IDRaman Software Procedure To average a set of spectra together, 1. Set the # of Multi-Acquisitions to a desired number of spectra to be averaged. 2. Set the Referencing Type to the way you want the reference performed (no reference, reference one or reference every acquisition). 3. Set the Acquisition Type to the type of data to be displayed (calibrated, Calibrated Cleaned, or pixel data). 4. Click on the Multi-Acquire button to start the acquisition. The Abort button stops the process and return to the main menu. Acquiring Spectra Over Time The Multi-Acquire button acquires multiple spectra over a period of time at known intervals. Timed spectral acquisition is a useful method of data acquisition when performing reaction monitoring. For example, information on the kinetics of a reaction can be determined from the Raman spectra as a function of time. Procedure To use the Multi-Acquire function, 1. Set the # of Multi-Acquisitions to the desired number. 2. Set the delay between each start with the Interval Time. 3. Choose a Referencing Type, and then click on the Multi-Acquire button. The delay time is the delay between the start of each acquisition. For example, if the integration time is 10 seconds and the desired delay between each acquisitions is 2 seconds the delay input should be 12 seconds (10 integration-12 sec delay = 2 seconds between each acquisition start)

37 A: IDRaman Software 4. Once the acquisition is complete, click on the File drop down menu and select Save Multi- Spectra, namenthe file and click Save. Note the Multi-file created is an ASCII file. Improving Your Spectrum Cleaning Peaks Peak Clean is a beta correction algorithm to produce spectra that are baseline corrected with powerful detrending algorithms. This method is not appropriate for every sample, but when spectral backgrounds are a problem it can provide background free spectra. Peak Clean can be particularly useful for library matching. Select Calibrated Cleaned under Acquisition Type. Wavenumbers

38 A: IDRaman Software Control Tab Option Raster ON/OFF (see Raster Scan) Shutter OPEN/CLOSE Function Turns the raster on and off: ON: Laser beam rasters in a circular pattern (~ 2mm in diameter). OFF: Laser beam is ~ 25 microns. Allows the user to open the shutter during laser power testing. Caution: this turns the laser on. Use proper safety equipment and precautions. Raster Scan Sometimes your sample is not homogenous. In this case the tightly focused laser beam may miss the particles in the sample and produce false signals. Raster scan enlarges the sampled area and provides a more statistically significant signal for heterogeneous samples. Procedure 1. Select the Control drop down menu. 2. Select Raster ON/OFF. The raster emblem appears indicating the raster is on. Raster ON -- the laser beam will raster in a circular pattern that is ~ 2mm in diameter. Raster OFF -- the laser beam will be a ~ 25 micron beam

39 Display Options A: IDRaman Software After an acquisition there are different display options for viewing the data collected. Option Reference Average Last Acquisition View Multi-Spectra Function View the last reference taken that is associated with the current data set. If a multi-acquisition was performed you can view the averaged data. View the last acquisition. Choose an individual file in a multi-acquisition. The last multi-acquire performed is stored in the temp file until a new multifile is collected. This allows you the ability to take as many single acquisitions but still view the average and individual data sets from the multi-acquire. Saving Spectra You can choose to save spectra in one of three formats: SPC saves the spectrum as displayed on the screen with baseline correction applied in the.spc format used with Thermo GRAMS. The comments will be stored in the metadata in the.spc format. ASCII saves the spectrum as displayed on the screen in the.prn format, ASCII X-Y format. The ASCII format is a column of wavenumbers and a column of intensities

40 A: IDRaman Software LIB saves the file in an encrypted format that can be used on our hand-held devices. Procedure 1. Select the File drop down menu and then Save Current Display. A dialogue box will open with 4 options: ASCII, SPC, and LIB. One or all of these selections can be selected

41 A: IDRaman Software 2. After selecting a save option, click Save a second time. You will be asked to create a comment in the comment line. Click OK when finished. A windows file storage dialogue will open to save the spectrum. Display Features Graph Palette The Graph Palette brings up a menu to expand spectral regions

42 A: IDRaman Software Scale Palette The scale palette is used to lock or unlock the autoscale features. Cursor Home Tab This function allows you to bring the cursor to the center of the display

43 A: IDRaman Software Advanced Tab Option Microscope: Calibrate (Factory Only) Microscope: Level Calibration (Factory Only) Dynmaic Raman Scattering Library Matching Function Allows the system to be calibrated at the factory. Allows the intensity calibration to be performed at the factory. Allows the user to open the shutter during laser power testing. See Dynamic Raman Scattering (DRS). Caution: this turns the laser on. Use proper safety equipment and precautions. Turns the raster on and off: ON: Laser beam rasters in a circular pattern (~ 2mm in diameter). OFF: Laser beam is ~ 25 microns. Dynamic Raman Scattering (DRS) DRS is a spectroscopic technique developed to enhance spectra produced by free floating particles in solution. The feature is available both on the system s firmware and in IDRaman Software. DRS measures the extra noise created when particles move in and out of the laser beam used to create the spectrum. This technique was developed by Scott and Carron * to remove the interfering background from material surrounding the moving particles and the container material. The principle of DRS is that the solvent matrix surrounding small free floating particles is constant and the container material is also constant. However, the spectrum produced by a low concentration of particles will exhibit large fluctuations due to their movement in and out of the laser beam. DRS is performed by selecting Dynamic Raman Scattering (DRS) from the drop down menu in Analysis. When selected, the software acquires according to the integration time and # of multi acquisitions selected. DRS will produce optimal results with short integration times and statistically most significant with a relatively large number of acquisitions. A good starting point is 0.11s integration time with 50 acquisitions. *Scott, B. and Carron, K. Dynamic Surface Enhanced Raman Spectroscopy (SERS): Extracting SERS from Normal Raman Scattering, Anal. Chem., 2012, 84 (20), pp

44 A: IDRaman Software Analysis Tab The Analysis tab allows you to select Denoise or Savitzky-Golay smoothing, that is, to increase the signal-to-noise ratio without greatly distorting the signal. A Savitzky Golay filter is a digital 1 filter that can be applied to a set of digital data points for the purpose of smoothing the data. This is achieved, in a process known as convolution, by fitting successive subsets of adjacent data points with a low-degree polynomial by the method of linear least squares. When the data points are equally spaced an analytical solution to the least-squares equations can be found, in the form of a single set of "convolution coefficients" that can be applied to all data sub-sets, to give estimates of the smoothed signal, (or derivatives of the smoothed signal) at the central point of each sub-set. The method, based on established mathematical procedures, 2,3 was popularized by Abraham Savitzky and Marcel J. E. Golay who published tables of convolution coefficients for various polynomials and sub-set sizes in ,5 Some errors in the tables have been corrected. 6 The method has been extended for the treatment of 2- and 3- dimensional data. The number of smoothing points can be adjusted through the dialog boxes that appear Whittaker, E.T; Robinson,G (1924). The Calculus Of Observations. Blackie And Son Limited. pp "Graduation Formulae obtained by fitting a Polynomial. 3. Guest, P.G. (1961). "Chapter 7, Estimation of Polynomial Coefficients". Numerical Methods of Curve Fitting. Cambridge University Press. 4. Savitzky, A.; Golay, M.J.E. (1964). "Smoothing and Differentiation of Data by Simplified Least Squares Procedures". Analytical Chemistry 36 (8): doi: /ac60214a Savitzky, Abraham (1989). "A Historic Collaboration". Analytical Chemistry 61 (15): 921A 923A. doi: /ac00190a Steinier, Jean; Termonia, Yves; Deltour, Jules (1972). "Smoothing and differentiation of data by simplified least square procedure". Analytical Chemistry 44 (11): doi: /ac60319a

45 A: IDRaman Software Resetting the Time and Date Any time the batteries are removed for more than 30 minutes the time and date stamp will reset to Procedure To reset the time and date stamp, 1. From the Tools menu, select the Time Tool. 2. Set the Day, Month, and Year, and then select the Check Mark. 3. Set the Seconds, Minutes and the Hours then select the Check Mark. Using the USB Connection for IDRaman mini Library Building Procedure 1. Connect the IDRaman mini to the computer using the supplied micro USB cable and turn it on. 2. Go to the Tools menu on the IDRaman mini and select the USB Connect Tool. The computer will recognize the IDRaman mini as a USB storage device. 3. Select Open folder to view files. The Folders on the IDRaman mini will appear in a window

46 A: IDRaman Software There are three folders on the IDRaman mini device: Spectra Contains time and date stamped files saved using the Save function on the IDRaman mini in an ASCII format which can be opened by any spreadsheet software. LibraryTemp Contains the same time and date stamped files saved using the Save function on the IDRaman mini but in the.lib format. These files can be renamed and transferred into the library folder. Library Contains the Library (.lib) files that are used in the library search. The name of these files will be displayed on the IDRaman mini screen when there is a match. 4. If you created library files using the IDRaman Software you can copy and paste those files into the Library folder to add more compounds to the library. 5. If you saved a spectrum of a compound using the Save function on the IDRaman mini, follow these procedures to add the file to the library. A saved spectrum of toluene is used for an example

47 A: IDRaman Software a. Open the LibraryTemp folder and find the file. b. Rename the file. c. Copy the file. d. Paste the file into the Library folder

48 A: IDRaman Software

49 Appendix B Tera Term Software Tera Term is third-party software provided with your IDRaman mini on a USB drive. It is used to administer the settings of the IDRaman mini. This includes functions such as changing the pin, turning the baseline correction on and off, and checking the serial number and firmware version. Installing Tera Term Software Procedure 1. Find the Tera Term folder on the USB drive provided and copy it to your computer. 2. Double-click the installation file in the Tera Term folder. 3. Once the software is installed: a. Turn on the IDRaman mini b. Connect it to the USB port on the computer using the supplied cable. 4. Start the Tera Term software. 5. Select Serial. 6. Select port that you are using to connect to the IDRaman mini

50 A: Tera Term Software 7. Click OK. 8. Select the Setup tab. 9. Select the Terminal option. 10. Select the Local Echo box and click OK. You can now see what you are typing. Changing Pin Codes Procedure To reset the PIN using Tera Term, 1. Type ID Pinset nnnn Where: nnnn is any 4-digit number you choose 2. Select Enter. Turning Baseline Correction On and Off Libraries have been built for baseline-corrected data (also see Peak Cleaning); you will need to rebuild libraries if you switch. By default the IDRaman mini is set to use a baseline correction that removes the effects of fluoresence from your measurement. This generally increases the accuracy of the library matching. However, there

51 A: IDRaman Software may be times where you will prefer to view and save the raw data. The baselining algorithm can be turned on and off using TeraTerm. 1. With the IDRaman mini connected in Teraterm, type the following: "baselining off" to turn off baselining. "baselining on" to turn baselining on. "status" to query the current state of the device, including whether baselining is on or off. Checking the Serial Number and Firmware Version With the IDRaman Mini attached and connected to Teraterm, type "ID. This will return the device serial number (S/N XXXX-XXXX) and the firmware version

52 A: Tera Term Software

53 Appendix C Specifications Specifications Criteria Raman Spectrum Range 400 to 2300 cm -1 Spectral Resolution 18 to 20 cm-1 (FWHM) across spectral range Laser (excitation wavelength) 785nm±0.5 nm, 2 cm -1 line width, stability <0.1 cm -1 Laser Output Power Collection Optics Signal to Noise Ratio (SNR) Exposure Battery External Power Supply Weight Dimensions Operating Temperature Display Enclosure Rating Security Log-in Measurement Accessories 100 mw, 70 mw at the sample NA = 0.50, 8mm working distance; 0.2 to 2.5 mm spot size SNR = 1000; 70 mw toluene 0.1 second integration Automatic modes (10 ms minimum) 2 AA batteries (6 hours w/alkaline, 11 hours w/lithium) Not applicable, replaceable batteries used, USB power available oz. (0.33kg) 3.6 x 2.80 x 1.5 in. (9.1 x 7.1 x 3.8 cm) -20 C to +40 C (continuous) QVGA high visibility, glove compatible, color touch screen IP-40 PIN Code, 4 digit Vial holder, Point and Shoot Compliance CE certification (IEC , EN ) Collection Techniques Safety Raster Orbital Scanning (ROS) to reduce explosive ignition risks and narcotic sample damage. Dynamic Raman Scattering (DRS) technology for low level Raman code detection. Class 1 laser safety with vials Class 3B with Point-and-Shoot accessory

54 C: Specifications

55 Index A acquiring average, 18, 25 reference, 18, 24 spectra over time, 26 spectrum, 25 advanced tab, 28, 33 Advanced Tab, 33 analysis tab, 34 average acquiring, 18, 25 C calibration, 12 Clean Peaks, 19 controls, 7 cursor home, 32 D date resetting, 35 display features, 31 display options, 29 document audience, iii purpose, iii summary, iii Dynamic Raman Scattering (DRS), 33 F F button, 10 features, 1 focusing Point and Shoot Adapter, 10 G graph palette, 31 IDRaman software overview, 22 set-up, 21 indicators, 7 introduction, 1 library, 23 building, 35 models, 2 I L M O Oceanview, 16 OceanView acquiring average, 18 acquiring reference, 18 acquiring spectrum, 18 Clean Peaks, 19 save data, 20 overview, 1 P Peak Clean, 27 PIN changing, 40 Point and Shoot Adapter, 5, 10 focusing, 10 product-related documentation, iii PS Adapter, 5,

56 Index R Raster Orbital Scanning (ROS), 3 raster scan, 28 reference acquiring, 18, 24 resetting time, 35 restting date, 35 S save data, 20 saving spectra, 29 scale palette, 32 set-up IDRaman software, 21 specifications, 43 spectra over time acquiring, 26 spectrum acquiring, 25 saving, 29 start-up with Oceanview, 13 T tab advanced, 28, 33 analysis, 34 Tera Term software baseline correction, 40 changing PIN, 40 creating library files, 23 firmware version, 41 installing, 39 saving a library spectrum, 23 serial number, 41 time resetting, 35 U upgrades, iv USB, 35 warranty, iv what's new, iii W