SkyScan Desktop x-ray Microtomograph

Transcription

1 SkyScan 1072 Desktop x-ray Microtomograph Instruction Manual SkyScan , ver.3 for 1072-scanners 4NT and 5NT Manufactured by Skyscan n.v. Vluchtenburgstraat 3, 2630 Aartselaar Belgium Instruction Manual 1

2 TABLE OF CONTENTS 1 INTRODUCTION IN X-RAY MICROSCOPY AND MICROTOMOGRAPHY Introduction Basis principles of microtomogaphy SKYSCAN 1072 SYSTEM OVERVIEW CONNECTIONS AND FIRST START SYSTEM CONTROL SOFTWARE Tube setting and start Specimen holders MENU AND SUBMENU FUNCTIONS General layout of the main menu The FILE menu Open command (File menu) Save As command (File menu) Print command (File menu) Print Preview command (File menu) Print Setup command (File menu) Page Layout command (File menu) System Configuration command (File menu) Data Directory command (File menu) Serial Visualization command (File menu) Serial to AVI command (File menu) Delete Serial command (File menu) Exit command (File menu) Image menu commands Line command (Image menu) Instruction Manual 2

3 5.3.2 Profile (Free Profile) command (Image menu) Frame command (Image menu) Sharpen command (Image menu) Soften command (Image menu) Median Filter command (Image menu) Inversion command (Image menu) Grayscale conversions (Image menu) Threshold command (Image menu) Erosion command (Image menu) Dilatation command (Image menu) Noise Reduction command (Image menu) Region of Interest command (Image menu) Analysis command (Image menu) Undo command (Image / Context menu) Acquisition & Reconstruction commands Acquire Data (Reconstruction menu) Reconstruct One Cross Section (Reconstruction menu) Reconstruct All Cross Sections (Reconstruction menu) Acquire for Cone and Spiral (Reconstruction menu) External Reconstructions (Reconstruction menu) D-Model Stereo menu commands Stereo Visualization (Stereo menu) Serial Acquisition (Stereo menu) Control menu commands Filters command (Control menu) Source submenu (Control menu) Camera submenu (Control menu) Door submenu (Control menu) Zoom submenu (Control menu) Lift submenu (Control menu) Rotation submenu (Control menu) Optional drive command (Control menu) Options menu commands Acquisition options (Options menu) Reconstruction options (Options menu) Cross-section to Image options (Options menu) Image Tune command (Options menu) Image format command (Options menu) View menu commands (Options menu) Toolbar command (View menu) Control bar command (View menu) Select bar command (View menu)...49 Instruction Manual 3

4 Status Bar command (View menu) Setup menu commands Flat Fields submenu (Setup menu) Acquire command (Setup menu) Save command (Setup menu) Load command (Setup menu) Reset command (Setup menu) Analytical command (Setup menu) Alignment command (Setup menu) Scanner (Setup menu) Positions command (Setup menu) No Aging command (Setup menu) Context menu commands Analysis command (Context menu) Delete command (Context menu) UNDO command (Context menu) Annotation command (Context menu) Histogram command (Context menu) Help menu commands Index command (Help Topics / Help menu) About command (Help menu) Context Help command Workspace Elements Title Bar Scroll bars Size command Move command Minimize command Maximize command Close command Instruction Manual 4

5 1 INTRODUCTION IN X-RAY MICROSCOPY AND MICROTOMOGRAPHY 1.1 Introduction Any conventional optical or electron microscope allows visualising only twodimensional images of a specimen surface or thin slices. But in most cases a final conclusion about original three-dimensional object structures cannot be made on the base of two-dimensional information. One can obtain the three-dimensional information of object structures by cutting them into very thin slices, which can then be visualised in the light microscope and interpolate the two-dimensional information into a three-dimensional structure model. This method however is not only very cumbersome but also not very reliable since the object structure itself can be altered by the preparation technique and the distance between the slices is usually too coarse to avoid loss of 3-D information. An x-ray (radiography) system produces two-dimensional shadow images of complete internal three-dimensional structures, but in a single two-dimensional shadow projection the depth information is completely mixed. Only an x-ray tomography system allows us to visualise and measure complete threedimensional object structures without sample preparation or chemical fixation. Typically the spatial resolution of conventional medical CT-scanners is in the range of mm, which corresponds to 1-10 cubic mm voxel (volume element) size. Computerised x-ray microscopy and microtomography now gives possibilities to improve the spatial resolution by seven to eight orders in the volume terms. The system "SkyScan 1072" allows to reach a spatial resolution of 5 µm corresponding to near 1x10-7 cubic mm voxel size. As in the "macro" CTscanners, the internal structure can be reconstructed and analysed fully nondestructively. Instruction Manual 5

6 1.2 Basis principles of microtomogaphy Any x-ray shadow image is corresponding to a two-dimensional projection from the three-dimensional object. In the simplest case we can describe it as a parallel x-ray illumination. In this approximation each point on the shadow image contains the integration of absorption information inside the three-dimensional object in the corresponding partial x-ray beam. For parallel geometry one can divide the problem of a three-dimensional reconstruction from two-dimensional projections into the serial reconstruction of two-dimensional object slices from one-dimensional shadow lines. Let's show a possibility of this reconstruction on a simple example, an object with only one point with significant absorption in an unknown place. In the one-dimensional shadow line we will have a decreasing of intensity of the shadow of absorption in the object area, see figure on the next page. Now we can initialise in the computer memory an empty array of pixels (picture elements) corresponding to possible object displacement. Of course one must be sure that all parts of the reconstructed object will be inside the field of view. Because we have the position of the shadow from the absorption points of the object, we can mark on the area of reconstruction in the computer memory all possible positions of absorption points inside the object as lines. Instruction Manual 6

7 Now let's rotate our object and repeat this operation. In each new rotation position of the object we will add to the area of reconstruction the lines of possible object positions corresponding to position of shadow. This operation is named "back-projection". After several rotations we can localise the position of the absorption point inside the area of reconstruction. In increasing the number of shadow projections from different views this localisation become more and more defined. In the case of reconstruction from an infinite number of projections one can get an image with a good definition of the absorption area position inside the initial object. At the same time a blur area will accompany the pointer image because it is produced as a superposition of lines with all inclinations. Now we know what image will be produced from the pointer object and we can "pre-correct" the initial information in absorption lines to make the resulting image more corresponding to the real object. This correction ads some "negative absorption" outside the point of the object shadows to eliminate the positive blur in the back projection process (convolution). Instruction Manual 7

8 The same algorithm can produce the cross-section image not only from the single point object. Any real object can be represented as a big number of separate absorption voxels and linear absorption in any x-ray beam is corresponding to the sum of all absorption from all voxels inside this beam. By this way the two-dimensional cross-sections of the object can be reconstructed from the one-dimensional shadow lines in different views. Unfortunately practically all x-ray sources cannot generate parallel beams. In a real case one will use a pointer source and fan x-ray beam in the object area. For tomography reconstruction we can find the solution of this problem by the reordering of the shadow information. New pseudo-parallel beams can be constructed from the parts of several fan beams with different views and the same reconstruction method for fan-beam x-ray sources can be used. Instruction Manual 8

9 In the case of x-ray acquisition the image contains information about the intensity reduction inside the three-dimensional object. Because the x-ray absorption is corresponding to exponential low, we can restore the linear absorption information from the shadow image by logarithmisation. This operation is very non-linear and any noise in the small signal areas can produce significant errors in reconstruction. To eliminate these errors an averaging of initial data and results of logarithmisation can be used. On the another hand we can try to improve a signal to noise ratio in the shadow image to reach the most representative information. One more effective way of noise reduction in the reconstruction process is a special selection of correction function for convolution before back projection. In the simplest case (described above) the correction function produces two "negative absorption" reactions around any signal or noise peak in the shadow line and this behaviour becomes very dangerous for noisy initial information. Special selection of convolution function for correction with spectral limitation by Hamming window allows solving this problem. In x-ray microtomography an information from voxel with very small physical size should be detected and right choice of parameters for noise reduction becomes very important. Instruction Manual 9

10 2 SKYSCAN 1072 SYSTEM OVERVIEW The "SkyScan-1072" is a compact desktop system for x-ray microscopy and microtomography. It consists of the combination of an x-ray shadow microscopic system and a computer with tomographic reconstruction software. This system allows making a non-destructive three-dimensional reconstruction of the object s inner structure from two-dimensional X-ray shadow projections. The equipment contains an x-ray microfocus tube with high-voltage power supply, a specimen stage with precision manipulator, two-dimensional x-ray CCD-camera connected to the frame-grabber and a Dual Pentium computer with colour monitor. Instruction Manual 10

11 For "SkyScan-1072 x-ray microfocus tube with several microns focal spot size operates at kv / 100 ua or kV / 0-250uA or kV / 0-500uA (specification dependent). The special x-ray CCD-camera is based on highresolution (1024x1024 pixels) cooled CCD-sensor with fibre optic coupling (3.7:1 image reduction) to x-ray scintillator or 768x560 pixels CCD-sensor with lens coupling to x-ray scintillator. The X-ray shadow projections digitised as 1024x1024 pixels with 4096 brightness gradations (12 bit) for cooled camera or 256 gradations (8 bit) for analog camera. The reconstructed cross-sections have a 1024x1024 (or 2048x2048, 512x512, 256x256 ) pixels (float point) format. Typical cycle of data collection for reconstruction contains of shadow image acquisitions from 200 to 400 views over 180 or 360 degrees of object rotation. For the reconstruction in complete three-dimensional objects one can use a serial reconstruction of cross sections. It consisting of one acquisition cycle followed by an "off-line" reconstruction of the complete three-dimensional object in a resolution of 1024 x 1024 x max.1024 layers. After the serial reconstruction one can display the cross-sections of the object onto the screen as well as construct a realistic view to the 3D-object with possibilities to "rotate" and "cut" the object model. Instruction Manual 11

12 3 CONNECTIONS AND FIRST START All subsystems of the x-ray microscope-microtomograph are inside a steel desktop case. For models in 4NT-versions scanner contains internal computer. For models in 5NT-version scanner connected to external computer. To start the system one should make the connections shown in the figures below. All interconnections should be made before connection of the main power plug to V AC ( V AC for USA). Interconnections for SkyScan1072, ver.4nt: Interconnections for SkyScan1072 ver.5nt: In the front panel of "SkyScan-1072" case one can find a power switch, the meters for tube acceleration voltage and current and (for ver.4nt only) the status indicators, a 3"1/2 floppy drive and a CD-reader/writer. A key switch for the x-ray source is located on the right side. Instruction Manual 12

13 Normal positions of switches before the first connection of the power plug to a wall socket are "POWER" OFF, X-RAY TUBE ON and no floppy disks or CD in drives. After connection of power cord to the power supply one can start system by power switch in the front panel. Start (ver.5nt) the external computer also. X-ray scanner should be always ON before starting control software in the external computer. The start procedure for computer can take couple of minutes with following start of "Microsoft Windows NT" or Windows Control and reconstruction software for x-ray microscopy and microtomography can be started from corresponding icon in the screen For normal operations of x-ray system the switch "X-RAY TUBE" must be turned ON. If the system will be used only as an X-ray microscope and microtomograph you can keep the ON position of this switch continuously even when switching off and on the main power. In the case of operation for a long time the internal computer as a conventional computer only (without X-ray) this switch must be turned in OFF position before switching system ON to keep long lifetime for x-ray tube (only for ver.4nt with internal computer). All other system control functions are activated through the software. Instruction Manual 13

14 4 SYSTEM CONTROL SOFTWARE The software package for system control and x-ray microscopy / microtomography has the same operation principles as any other Windowsbased programmes. One can select any functions by "mouse" from the menu / submenu in the top line and change modes and parameters by "mouse pressing" to the corresponding control areas or buttons. Start image in the screen contains the main menu bar in the top of the screen and tool bars in the side or top of the screen. 4.1 Tube setting and start. The control bar into the screen allows to pre-set voltage and current for the x-ray tube. There is also a button to switch the tube on or off. Status bar in the bottom indicate present position of these parameters. To start X-ray tube push X-ray button: In the case of first start or interrupt >8 hours after last usage of the x-ray source, a new information dialog will appear into the screen. It will be indication of aging process for the soft start of the x-ray source. The aging allows keeping a very long tube lifetime. Typical time of an ageing process is minutes (for <1 month s pause in tube usage). In the case of big differences of voltage indications on the status bar and in the front panel meter (>20% from maximum values) contact your supplier for service. After the aging tube will be switched off. One can switch it on in any time without extra delay for soft start. After tube start the normal behaviour is an increasing of the acceleration voltage in the screen indicators and in the front panel meter with following increasing the current up to the pre-set positions. For specimen replacement press Specimen Chamber Open/Close buttons in the control bar: Open/Close Specimen Chamber. The HV will be switched off, the specimen will be brought in front of the chamber door and specimen chamber door will be opened automatically. Instruction Manual 14

15 4.2 Specimen holders There are several standard specimen holders supplied with the system. Specimen holder should be selected according to the object size and necessary magnification range. The specimen holder with diameter of 10-15mm can be used for the objects with size of 5 to 22 mm. Height of the specimen holder should be selected according to the height of the object use short specimen holder for the long objects and long one for the short specimen (some systems supplied with adjustable height holder). To avoid damage of the x-ray source the magnification cannot be higher than with this holder. One should check the object position inside the system by visual camera (described below) to avoid any touching of x-ray source during magnification changes. ATTENTION! Avoid any pressure or vibration during changing of the objects or specimen holders! Never put any pressure to the rotation axle! Never touch x-ray camera or filter changing mechanism in the right side of the specimen chamber! The specimen holder 4mm in diameter can be used to reach maximum magnification for small object sizes (<10mm). During operation with this specimen holder one should also check the object position by the visual camera to avoid object touches the x-ray tube or other parts inside the system. For the scanners in 4NT version specimen holder can be installed at the rotation axle by special hex key. For the scanners in 5NT versions the root part of the specimen holder (1/4 inch in diameter) should be puted in the hole of the rotation mechanism and fixed by rotation of the ring in CWdirection against two pins like it shown in the picture. After specimen exchange the specimen chamber door can be closed be pressing the same button again: Open/Close Specimen Chamber. Instruction Manual 15

16 To start X-ray tube push X-ray button: Current and voltage will be increased automatically up to the pre-set positions. Now we can get an x-ray shadow image of the object by selection of X-RAY IMAGE in the toolbar: Image from X-ray camera. System will start continuous acquisition and after each exposure (typically once in few seconds) x-ray image will appear onto the screen. To grab the image and stop acquisition one can press the same button again. Object can be shown also by a normal visual camera: Select the visual camera. The object movements can be done by following buttons: Rotate the specimen to desired angle ( degrees). Set vertical position (0 20mm for ver.4nt, +/- 10mm for ver.5nt). Magnification changes by mechanical movement of the object stage between the source and detector. Take into account that all microtomography reconstruction procedures need the object completely inside the field of view. Increase the magnification. Attention!!! For magnification >X50 check object position by visual camera to avoid object touches the x-ray source. Decrease the magnification. Set the magnification. Be careful in magnification increasing in the range > X50. Other possibilities of image acquisition, processing and reconstruction will be shown in following general description of all menu functions. Instruction Manual 16

17 5 MENU AND SUBMENU FUNCTIONS 5.1 General layout of the main menu The top menu bar in the screen gives access to all system functions. Let's consider all menu / submenu possibilities in more details. Commands File menu Image menu Acquisition & Reconstruction menu 3D-Model Stereo menu Control menu Options menu Setup menu Help menu It is a standard Windows main menu and operates thus in exactly the same way. Selecting items from the menu, running though and opening of the sub-menus and applications is done as any standard Windows program. Instruction Manual 17

18 5.2 The FILE menu The File menu offers the following commands: Open Save As Print Print Preview Print Setup Page Layout System Configuration Data Directory Serial Visualization Serial to AVI Delete Serial Exit Opens an existing image. Saves an opened image to a specified file name. Prints an image / data. Displays the image / data on the screen, as it would appear printed. Selects a printer and printer connection. Sets the image sizes and margins for printing. Save, load or restore all program settings Selects a data directory. Shows the serial bitmap files. Converts serial bitmap files to video file. Displays the delete serial files. Exits Microtomography Application Open command (File menu) Use this command to open an existing document. Shortcuts: Toolbar: Keys: CTRL+O The following options allow you to specify which file to open: File Name: Type or select the filename you want to open. This box lists files with the extension you select in the List Files of Type box. Type: Select the type of file you want to open. Instruction Manual 18

19 5.2.2 Save As command (File menu) Use this command to save and name the active document. Microtomography Application displays the Save As dialog box so you can name your document. The following options allow you to specify the name and location of the file you're about to save: File Name: Type a new filename to save a document with a different name. Microtomography Application adds the extension you specify in the Save File As Type box. Type: Select the type for file you want to save Print command (File menu) Use this command to print a document. This command presents a Print dialog box, where you may specify the range of pages to be printed, the number of copies, the destination printer, and other printer setup options. Shortcuts: Keys: CTRL+P The following options allow you to specify how the document should be printed: Printer: This is the active printer and printer connection. Choose the Setup option to change the printer and printer connection. Setup: Displays a Print Setup dialog box, so you can select a printer and printer connection. Print Range: Specify the pages you want to print: All Pages Prints the entire document. Prints the range of pages you specify in the From and To boxes. Copies: Specify the number of copies you want to print for the above page range. Collate Copies: Prints copies in page number order, instead of separated multiple copies of each page. Instruction Manual 19

20 Print Quality: Select the quality of the printing. Generally, lower quality printing takes less time to produce. The Printing dialog box may be shown during the time that Microtomography Application is sending output to the printer. To abort printing, choose Cancel Print Preview command (File menu) Use this command to display the active document, as it would appear when printed. When you choose this command, the main window will be replaced with a print preview window in which one or two pages will be displayed in their printed format. The print preview toolbar offers you options to view either one or two pages at a time; move back and forth through the document; zoom in and out of pages; and initiate a print job. The print preview toolbar offers you the following options: Print Bring up the print dialog box, to start a print job. Next Page Preview the next printed page. Prev. Page Preview the previous printed page. One Page / Two Page Preview one or two printed pages at a time. Zoom In Take a closer look at the printed page. Zoom Out Take a larger look at the printed page. Close Return from print preview to the editing window Print Setup command (File menu) Use this command to select a printer and a printer connection. This command presents a Print Setup dialog box, where you specify the printer and its connection. The following options allow you to select the destination printer and its connection. Printer: Select the printer you want to use. Choose the Default Printer; or choose the Specific Printer option and select one of the current installed printers shown in Instruction Manual 20

21 the box. You install printers and configure ports using the Windows Control Panel. Orientation: Choose Portrait or Landscape. Paper Size: Select the size of paper that the document is to be printed on. Paper Source: Some printers offer multiple trays for different paper sources. Specify the tray here. Options: Displays a dialog box where you can make additional choices about printing, specific to the type of printer you have selected Page Layout command (File menu) This menu allows you to select follows options for displacing the image on the printing pages: Left Margin: Select the indent of printing image in mm from left side of paper. Top Margin: Select the space of printing image in mm from topside of paper. Image Size: Select the size of printing image in mm. Name: Add the title name of the image (filename) to the printing image. Date: Add the current date to the printing image. Time: Add the current time to the printing image. Instruction Manual 21

22 5.2.7 System Configuration command (File menu) Use this command to save or to load the specific sets of all acquisition and reconstruction parameters using by the program in current moment. One can restore complete program setup for specific task by loading previously saved system configuration. For return to the factory preset you can select restoring of default system configuration Data Directory command (File menu) Use this command to change active data directory. Microtomography Application displays the Data Directory dialog box so you can select your data directory. This dialog box displays the current data directory. To change it use button Browse..., that displays the Browse directory dialog box so you can select new data directory. Browse Directory dialog box: Draws the tree of the present disks and directory. After selection a pathname all data files like *.bmp, *.wts files and configuration set will be load (save) from (to) it Serial Visualization command (File menu) Use this command to show serial bitmap files (*.bmp) from data directory. Microtomography Application displays the Serial Filename Prefix dialog box so you can select your serial files. Shortcut: Toolbar: Instruction Manual 22

23 Serial to AVI command (File menu) Use this command to transform your serial bitmap files (*.bmp) to video file for Windows (*.avi). Microtomography Application displays the Serial Filename Prefix dialog box so you can select your serial files. The dialog box allows you to select existing group of serial files for conversion to one avi-file (noncompressed format) Delete Serial command (File menu) The following options allow you to specify the type of the files you're about to delete: WTS-files BMP-files TIFF-files Delete Serial WTS files command: Use this command to delete serial shadow data files (*.wts) from data directory. Microtomography Application displays the Serial Filename Prefix dialog box (see above) so you can select your serial files. Delete Serial BMP files command: Use this command to delete serial bitmap files (*.bmp) from data directory. Microtomography Application displays the Serial Filename Prefix dialog box (see above) so you can select your serial files. Delete Serial TIFF files command: Use this command to delete serial files in TIFF format (*.tif) from data directory. Microtomography Application displays the Serial Filename Prefix dialog box (see above) so you can select your serial files. Instruction Manual 23

24 Exit command (File menu) Use this command to end your Microtomography Application session. You can also use the Close command on the application Control menu. Microtomography Shortcuts: Mouse: Double-click the application's Control menu button. or Keys: ALT+F4 Instruction Manual 24

25 5.3 Image menu commands The Image menu offers the following commands: Line Profile Frame Sharpen Soften Median Filter Inversion Grayscale Conversions Threshold Erosion Dilatation Noise Reduction Region of Interest Analysis Undo Selects a line for single cross-section acquisition. Measures a distance in the image. Selects a frame for serial cross-section acquisition. Applies a sharpening filter to an image. Applies a smoothing filter to an image. Applies a median filter to an image. Inverts an image. Applies different filters and transformations to the halftone image. Transforms a halftone image to binary image. Applies erosion to the binary image. Applies dilatation to the binary image. Removes a single point noise from the binary image. Selects a limited region of interest from the binary image. Calculates the numerical characteristics of all objects in the binary image. Cancels the last operation in the image-processing mode Line command (Image menu) Use this command to select a line and see the image profile in this line. The red line in the image corresponds to selected position, the green curve displays the signal profile in this line and two blue lines mark the signal range limits. Shortcut Select bar: Profile (Free Profile) command (Image menu) Use this command to measures the distances in the image. Software will also display the brightness profile, average, min and max signal values in this line in the right part of the screen. Shortcut Select bar: Instruction Manual 25

26 5.3.3 Frame command (Image menu) Use this command to select a space for the acquisition with following reconstruction of the set of cross-sections. Shortcut: Select bar: Sharpen command (Image menu) Increases the contrast of small details and the borders. For noisy images the noise may be increased Soften command (Image menu) Reduces the noise by averaging of neighbor pixels. This operation decreases contrast of small details in the image Median Filter command (Image menu) Removes the single point noise from the half-tone image Inversion command (Image menu) Inverts an image to the "negative" one Grayscale conversions (Image menu) Applies different filters and transformations to the halftone images. Particular kind of conversion can be selected from the following dialog. The transformation will be applied to the screen image or to the set of disk files according to selection in the corresponding check box. Some transformations can be adjusted with specific parameters. (Contrast Stretching function will take parameters from the Histogram calculation -> See Context Menu Commands ) Threshold command (Image menu) Use this command to transform a half-tone image to a binary one for following morphological analysis. Microtomography Application displays the Threshold dialog box so you can select the transformation levels. The operation transforms a half-tone image to a binary one with two-brightness gradations only: black and white. Image parts marked as white will take place in all binary operations for corrections and calculation of numerical characteristics. In this transformation one can select what kind of object brightness in the initial gray-scale image will take place in the calculations. The selection can be made Instruction Manual 26

27 by adjustment of two levels in the dialog box. All objects with brightness inside the "window" between those levels will be shown as white into binary image and will take part in analysis Erosion command (Image menu) Removes a single pixel layer from all objects in the binary image. In the case of, for example, fine bridges through the objects, connecting for example different grains in a grain structure, this operation disconnect them. It will also reduce pointer noise in the background area Dilatation command (Image menu) Adds a single pixel layer onto all objects of binary image with filling pointer and thin holes inside the objects and gaps through the objects. A sequence of erosion or dilatation operations can produce more depth corrections. The pair of erosion + dilatation operation gives us possibilities to remove the pointer noise, disconnect the "bridges" through the objects and restore the size of rest object s parts to the initial values. Another pair of operations - dilatation with following erosion will fill small holes and thin gaps with restoration of object sizes Noise Reduction command (Image menu) Removes the single point noise from the binary image Region of Interest command (Image menu) Use this command to limit a calculation / processing part in the binary image. To select the limited region of interest one should mark the corners of polygon for this area of the image. Close a region by pressing the Ok button and program will displays only the objects in the selected region. Instruction Manual 27

28 Analysis command (Image menu) Use this command to calculate the numerical characteristics of all objects in the binary image. During analysis each object tested separately and binary image will be displayed in brightness or color corresponding to object size. The analysis results will be placed in the right part of the screen and contain following parameters: * total area of all objects; * total perimeter of all objects; * area of objects in respect to complete image or to region of interest (ROI) if it was selected; * number of objects in the image; * average area of single object; * average size of object (as diameter of circle with corresponding area);???? size distribution with size scale in the bottom. Results of analysis can be saved as a text file by pressing of mouse s right button in the right field of the screen. If you want to print the results, press left mouse button on the results area with following selection for one of the print-commands in the File menu Undo command (Image / Context menu) Use this command to delete the last processing action and return one step back, if possible. The Undo command is grayed if you cannot reverse your last action. Instruction Manual 28

29 5.4 Acquisition & Reconstruction commands The Acquisition and Reconstruction menu offers the following commands: Acquire Data Reconstruct One Cross Section Reconstruct All Cross Sections Acquire for Cone and Spiral External Reconstructions Acquires a dataset for following reconstruction of the object to WTS files. Reconstructs a single cross-section of the object form an existing WTS file. Reconstructs a group of cross-sections of the object from the existing WTS files. Acquires projection dataset to disk as 16-bit TIFFfiles for using by external reconstruction programs Start reconstruction by external programs (conebeam, spiral scan, etc.) One can use different options to adjust optimal parameters for acquisition and reconstruction processes: To select acquisition parameters use Acquisition Options dialog box : To select reconstruction parameters use settings in Options -> Reconstruction To adjust results of reconstruction use Cross-section to Image dialog box : To tune display look-up tables user Image Tune dialog box : Acquire Data (Reconstruction menu) Use this command to acquire a dataset for reconstruction and save it as WTS files. Microtomography Application displays the Serial Acquisition dialog box so you can name your group cross-section data and after this starts an acquisition. The following options allow you to specify the filename prefix and parameters acquisition of serial bitmap files: Instruction Manual 29

30 Top Line*: Set topside of the reconstruction area. Bottom Line*: Set bottom side of the reconstruction area. *this two parameters initialized according to selection in the shadow image by Frame command Step: Set Z-axle step of the reconstructions inside selected area. Filename Prefix: Select an existing prefix from list or name new prefix for wts-files. Microtomography Application can switch high voltage off after acquisition if selected (door also can be opened) and start the reconstruction if the corresponding options are checked. The information for reconstruction of the different cross-section will be stored in files with the WTS extension. Each file contains all necessary information to reconstruct one cross section. Filename contains selected prefix with followinf 4- digit number corresponding to the position of cross section and.wts extention Reconstruct One Cross Section (Reconstruction menu) Use this command to reconstruct a single cross-section of the object from existing WTS-file. Microtomography Application displays the Open dialog box so you can select your cross-section data and after this starts a reconstruction. This and next command use fastest reconstruction algorithm convolution with back projection like it was explained in the Introduction. After reconstruction we recommend you to use Cross-section to Image function to select necessary density window for right image in the screen Reconstruct All Cross Sections (Reconstruction menu) Use this command to reconstruct a group of cross-sections of the object from existing WTS files and save results of reconstruction as bitmap files. Before starting serial reconstruction the levels for transformation of reconstructed data to the image should be chosen into Cross-section to Image dialog box. Their levels will be applied to all cross sections during serial reconstruction. Microtomography Application displays the Serial Reconstruction dialog box so you can select your serial WTS files and after this starts a reconstruction. Instruction Manual 30

31 The dialog box allows you to select existing serial files and starts the reconstruction. The reconstruction can be started by internal program, by external one (it will be faster by using multiprocessing) or can be done later from the bat-file, which will be created now and contains all necessary parameters. To start reconstruction from the bat-file one should click into the bat-file with filename like in a prefix of selected dataset. Several bat-lines can be combined into one file for reconstruction in several datasets one after another. Bat-lines and bat-files can be placed in any directory because their contain full pathname of the programs and datasets Acquire for Cone and Spiral (Reconstruction menu) Use this command to store projection images through the object during rotation as a set of 16-bit TIFF files for following reconstruction by external programs. Microtomography Application displays the Export Projection Images dialog box so you can select the parameters. The following options allow you to specify the filename prefix and parameters for acquisition of serial projection files: Filename Prefix: Select an exist prefix from list or name new prefix. All projection files will be saved with filenames which contain selected prefix with following 4-digit number of projection and.tif extension. Spiral checkbox and deviation value (%)*: *only if spiral-scan reconstruction available Switch on acquisition mode with special trajectory for spiral movement of the object through the field of view and select vertical deviation as a part (%) from the image size SUGGESTION(s) and do it button: Propose to change acquisition parameter for compatibility to following reconstruction. Press do it button iif you want to apply listed suggestions. Instruction Manual 31

32 X-ray OFF after Acquisition: Shout down the source after the end of acquisition process External Reconstructions (Reconstruction menu) This section allows starting reconstruction by external programs with more complicated algorithms such as Cone-beam reconstruction (Feldkamp algorithm), spiral-scan reconstruction, etc. One or several reconstruction programs can be supplied with software package or uploaded from Internet. Main program check all available reconstruction programs in the start and connect them to corresponding items in menu. In the submenu one can find list of available reconstruction programs. Typically there are cone-beam and spiral scan reconstructions. Detail descriptions for the external reconstruction algorithms can be found in the corresponding publications. Instruction Manual 32

33 5.5 3D-Model Use this command to constructs 3D object from the results of reconstruction (bitmap files) by external program 3D-Creator. All detail of using in this program can be found in the special Manual for 3D-Creator and Format Converter programs. In the case of big number of complicated 1024x1024 cross sections we recommend to reduce image format in dataset till 512x512 or 256x256. It can be done inside the last version of 3D-Creator program or by external program named Format Converter. One should select the original dataset and name for new one with reduced format as well as a reduction ratio (1/2, ¼ ). New dataset with reduced format can be used for the creation of realistic 3D-images by 3D-Creator program. Instruction Manual 33

34 5.6 Stereo menu commands The Stereo menu offers the following commands: Visualization Serial Acquisition Displays a single stereo projection of the object. Acquire group of stereo projection to bitmap files or displays a stereo movie on the screen Stereo Visualization (Stereo menu) Use this command to acquire a single stereo-pair. Microtomography Application displays the Stereo dialog box so you can select the options of stereo acquisition. The dialog box options allow you: -> To select the stereo image presentation. A combination of red and green colors and image inversion to produce "absorption" image with the black background. A predefined adjustment is set corresponding to the observation of the stereo-image by glasses with a red filter for left eye and a green one for right eye. -> To select an image pre-processing before visualization as Sharpening or Smoothing. -> To set a parallax adjustment, which is the Angle difference of images in stereo-pair. -> To acquire a single stereo-pair with selected parameters by a pressing the Acquire button Serial Acquisition (Stereo menu) Use this command to acquire a group of stereo-pairs and save them as bitmaps files. Microtomography Application displays the Serial Stereo dialog box so you can select the options of serial stereo acquisition. The results of Serial Acquisition can be visualized by the Serial Visualization command or transformed to AVI-file by the Serial to AVI command. The following options allow you to specify the filename prefix and parameters acquisition of serial stereo bitmap files: Instruction Manual 34

35 Filename Prefix: Select an existing prefix from the list or name new prefix. If you do not want to save the stereo images, uncheck the Write to disk check box. Angle -> Rotation: Set a total angle range of rotation during acquisition of serial stereo-pairs. Angle -> Difference: Set a parallax value (angle difference between images in stereo-pair). You can also: -> Select the stereo image visualization. A combination of red and green (cyan) colors and image inversion to produce "absorption" image with the black background. A predefined adjustment corresponding to the observation of the stereo-image by glasses with a red filter for left eye and a green (or cyan) one for right eye. -> Select an image pre-processing before visualization as Sharpening or Smoothing. Instruction Manual 35

36 5.7 Control menu commands The Control menu offers the following commands: Filters Source Camera Door Zoom Lift Rotation Optional Stage Selects the filter (if filter changer installed in the system) Displays the high voltage control commands. Displays the camera control commands. Displays the specimen chamber control commands. Displays the magnification control commands. Displays the lift control commands. Displays the rotation control commands. Displays the control commands for optional drive in the specimen stage Filters command (Control menu) This command can be used only in the systems with automatic filter changer. Use this command to select the filter. Microtomography Application displays the Filters dialog box for these adjustments. The dialog box options allow you to select filter. You can also edit the filter name Source submenu (Control menu) The Source submenu offers the following commands: On Off Set at... SpotSize Turns on the high voltage. Turns off the high voltage. Changes the preset values of tube voltage and current. Switching spot size in the source (if available). Instruction Manual 36

37 HV On command : Use this command to switch on the high voltage. The current and voltage will set to preset values. Shortcut: Control bar: HV Off command : Use this command to switch off the high voltage. Shortcut: Control bar: HV Set at... command : Use this command to change the pre-set of the current and voltage. For systems with 130kV and 150kV sources ONLY: Large, Middle, Small spot command switch the source to corresponding modse. Small spot size produce best resolution in the image, but longest acquisition because of limited power. Large spot size corresponding to maximum flux from the source with low resolution. Middle spot size corresponding to compromise power/resolution solution. Exact values of power and spot sizes for available modes can be found in the corresponding manuals from the source supplier Camera submenu (Control menu) The Camera submenu offers the following commands: X-ray Visual Selects the x-ray camera as the active. Selects the visual camera as the active. X-ray Camera command : Use this command to select the x-ray camera as active. Shortcut: Control bar: Visual Camera command : Use this command to select the visual camera as active. Shortcut: Control bar: Instruction Manual 37

38 5.7.4 Door submenu (Control menu) The Door submenu offers the following commands: Open Close Opens the specimen chamber. Close the specimen chamber. Open Door command: Use this command to open specimen chamber. If the high voltage is on it will be turned off. Shortcut: Control bar: Door Close command: Use this command to close specimen chamber. Shortcut: Control bar: Zoom submenu (Control menu) The Zoom submenu offers the following commands: ZoomIn ZoomOut Set at... Increases the magnification. Decreases the magnification. Set the magnification. ZoomIn command : Use this command to increase the magnification. The specimen moves from the camera to the tube. Shortcut: Control bar: ZoomOut command : Use this command to decrease the magnification. The specimen moves from the tube to the camera. Shortcut: Control bar: Zoom Set at... command : Use this command to set the magnification to the desired position. Shortcut: Control bar: Instruction Manual 38

39 5.7.6 Lift submenu (Control menu) The Lift submenu offers the following commands: Up Down Set at... Lifts up the specimen. Lifts down the specimen. Lifts the specimen to the specific position. Lift Up command : Use this command to lift up the specimen by small step (typically mm in 4NT version and 0.08mm in 5NT version). Lift Down command : Use this command to lift down the specimen by small step (typically mm in 4NT version and 0.08mm in 5NT version). Lift Set at... command : Use this command to lift the specimen to the desired height. Shortcut Control bar: Rotation submenu (Control menu) The Rotation submenu offers the following commands: CCW CW Set at... Step by Step Rotates the specimen by one counterclockwise step. Rotates the specimen by one clockwise step. Rotates the specimen to the new angle. Starts or stops the continuous rotation. Rotation CCW command : Use this command to rotate the specimen by one counterclockwise step. Rotation CW command : Use this command to rotate the specimen by one clockwise step. Rotation Set at... command : Use this command to rotate the specimen to desired angle. Shortcut: Control bar: Rotation Step by Step command : Use this command to start or stop the continuous rotation. Instruction Manual 39

40 5.7.8 Optional drive command (Control menu) Use this command to control the optional drive (if it is present in the system). Microtomography Application displays the Optional drive dialog box for these adjustments. The dialog box options allow you to control optional drive (rotation of translation). One can adjust movement or rotation in mm or degrees (positive or negative value for necessary direction) for optional stepper. For object visualization select "Standard Image. Another option Shifted Image allows getting image with horizontal shift of the camera by 50% of the field of view. Both imaging mode use Visualization settings from the Acquisition Options Dialog. Select Close for returning to standard system operation. Instruction Manual 40

41 5.8 Options menu commands The Options menu offers the following commands: Acquisition Reconstruction Cross-section to Image Image Tune Image format View Sets the acquisition parameters. Sets the reconstruction parameters. Selects the transformation of cross-section data to the image. Selects the screen look up table, brightness and contrast. Selects an image resampling or zoom mode Selects to shows or hides the toolbars and statusbar Acquisition options (Options menu) Use this command to select the parameters for acquisition and visualization. Microtomography Application displays the Acquisition Options dialog box so you can select your parameters. The following options allow you to adjust the acquisition parameters: Median filtration: (available not for all types of cameras) remove specific bright spot noise from the images from X- ray cameras Flat field correction: Improves the illumination irregularity on the shadow images on the basis of the correction maps for the CCDsensor and illumination of the x-ray tube. The corresponding reference fields can be acquired, saved or loaded by the functions described below ( Setup -> Flat Fields ). The Microtomography Application loads automatically the saved correction maps during each software start. Correction maps for different filters will be saved separately and restored from the disk during filter exchange. Instruction Manual 41

42 Geometrical correction: Corrects the distortion in fiber optic or lens inside the camera. Frames Averaging: Averages the shadow projection from the several images. Main purpose of this operation is signal to noise improvement. The number determines how many acquisitions of the same shadow image will be made. The final image is the result of averaging from the acquisitions. Random Movement: Sets the depth value (number of pixels) for random synchronous movement of object stage and acquisition area. It allows removing specific reconstruction arc-artifacts produced from local irregularities of sensitivity of the CCD-sensor. Random movement of the object in the vertical direction with synchronous displacement of acquisition area in the CCD-sensor allows eliminating these artifacts. Acquisition time is increase only by the time of the vertical movement. All above options can be selected separately for the acquisition procedure and image visualization. Scan through central area: Image acquisition for reconstruction will be done by the serial mechanical movement of the object through the central area of the image with selected number of lines. This mode allows avoiding distortion from the strongly inclined fan beam in the top and bottom areas of the image, but increase the acquisition time because of projection set may be constructed in the several acquisitions. If cone-beam reconstruction is available in your package, it can produce the same (sometimes even better) quality of results in the shorter time. Dark field correction during acquisition (if available): allows acquiring new reference field for flat-field correction during acquisition in the case of non-stable temperature in camera cooling system (recommended for systems with Photonic Science cameras only). Rotation: Presets the rotation range during the acquisition. 180 rotation is typically recommended. The rotation range of 360 can be used for reduction of the conical X-ray beam distortions during reconstruction in the top and bottom of the object. 360 with camera shift allow one to enhance the field of view near twice in horizontal direction. In the case of selection for camera shift mode a preview button will allows showing the shadow image from the enhanced field of view (preview acquisition can take enough long tome because of mechanical precision camera shift to the side position and return to the central one). Instruction Manual 42

43 Exposure: Adjusts an integration time for x-ray camera to adopt the sensitivity to the object density and x-ray illumination conditions. It determines the time that will be used for one acquisition. Rotation Step Size: Adjusts the value of one step rotation. For a normal reconstruction the rotation step size 0.9 up to 0.68 for 1024x1024 pixels and as 0.9 up to 1.8 for 512x512 pixels in cross section are recommended. For fast reconstruction or for fast object rotation this value can be increased. Decreasing the value of step rotation increases the corresponding number of views during the acquisition for reconstruction and reconstruction time itself. Gain: Adjusts the amplification of the image from the camera (in software). The signal and noise are amplified by the same way. It should be set in coordination with the integration time to avoid camera saturation To improve signal to noise try to set low gain as possible and use longer integration times Reconstruction options (Options menu) Use this command to select the parameters of reconstruction. Microtomography Application displays the Reconstruction Options dialog box so you can select your parameters. The Reconstruction Options dialog box allows you to set reconstruction options: Smoothing can be used to improve signal to noise but reduce the spatial resolution. In the case of a reconstruction from the generally unknown object the Smoothing should be switched off. Visualization function allows showing the reconstruction process onto the screen. Scales switch allows adding the scales in the X and Y direction and the Z position number into the result of the reconstruction. Post Alignment allows one to correct possible disalignment of rotation axle in acquisition during Instruction Manual 43

44 reconstruction. PostAlignment procedure works on the base of comparison in the shadow projections after 180-degree rotation. In the case of ideal alignment, two shadow images (in the central part) after 180 degrees rotation will be identical after horizontal flip for one of them. Mutual displacement of such images allows calculating disalignment and compensates it during reconstruction. This procedure works only in the case of enough amount of information in the central part of the shadow projection. In the case of selection for Post Alignment a dialog box will appear before reconstruction. One can find a suggested value for alignment correction and Ok / Cancel buttons. In the case of pressing Ok button the suggested value will be used for correction during reconstruction. In the case of Cancel answer the reconstruction will be done without correction. One can change the suggested value to correct disalignment manually. Double reconstruction procedure produce improved reconstruction for highdensity particles or wires inside the matrix of light material. First of two reconstructions in this mode will be done to locate high-density parts with following improvement of star effect during second reconstruction of light matrix. Adjustable threshold for second reconstruction (typically 50 90%) allows adopting to real difference in the object materials. Beam hardening correction allows reducing beam-hardening effect for objects, which contains one material. Following adjustment allows selecting the depth of correction from 0 (no correction) to max value. Because this correction reduce signal to noise ratio, we recommend to use it only in the case of visible beam hardening effects in reconstructed cross section (you will see it as an extra density of material in the border of the object) Cross-section to Image options (Options menu) Use this command to select the parameters for transformation of cross-section data to the image on the screen. Microtomography Application displays the Cross-section to Image dialog box so you can select your parameters. The reconstruction results are calculated as an array of float point pixels because of the unknown density range in investigated object. After such calculation one had to show reconstructed crosssection as an image on the screen or include it as a slice into the 3-dimensional reconstructed object. We have to transform the array of radiation intensities (corresponding to differences in material densities) into an image with brightness or color information. There are following modes of doing this: Instruction Manual 44

45 Adaptive Transformation: This mode allows finding the biggest information range of densities after reconstruction. This approach is based on the histogram calculation (shown in the right part of the dialog window) inside the reconstructed float-point cross-section with following a conversion of the representative density range into the gray scale image. In other words, the full range of usable intensities (without noise and negative values) will be transformed in a range of gray scales from black to white. Manual Fixation: This is a manual adjustment/correction of conversion range as a pre-set for typical object styles. There are the four manual adjustments, each of them can be connected to specific objects and stored with a name, a minimum and maximum value of density. For pre-adjustment one can use the Auto button, this is similar to the adaptive transformation, and than adjust the max and min values to the best results. After modifications one can create the image with the new settings by pushing on the Apply button. In the case of any modifications the values and name of specific window will be saved to the disk Image Tune command (Options menu) Use this command to select the look up table of the image. Microtomography Application displays the Image Tune dialog box so you can select your parameters. The Image Tune dialog box allows you to change the image palette (look up table) and adjust brightness and contrast. To return for standard presentation press the Standard Image format command (Options menu) Use this command to select image resampling mode. Microtomography Application displays the Image format dialog box for these adjustments. Instruction Manual 45

46 The dialog box options allow you to select image resampling or zoom mode. By using this option one can change the resolution of image at: 1024->1024 no transformation >512 image averaging in 2x2 blocks to 512x512 format >256 image averaging in 4x4 blocks to 256x256 format >128 image averaging in 8x8 blocks to 128x128 format >64 image averaging in 16x16 blocks to 64x64 format. 64->1024 image zoom x16 from central 64x64 pixels. 128->1024 image zoom x8 from central 128x128 pixels. 256->1024 image zoom x4 from central 256x256 pixels. 512->1024 image zoom x2 from central 512x512 pixels View menu commands (Options menu) The View menu offers the following commands: Toolbar Control Bar Select Bar Status Bar Shows or hides the Toolbar. Shows or hides the Control bar. Shows or hides the Select bar. Shows or hides the Status bar Toolbar command (View menu) Use this command to display and hide the Toolbar, which includes buttons for some of the most common commands in Microtomography Application, such as File Open. A check mark appears next to the menu item when the Toolbar is displayed. Instruction Manual 46

47 The toolbar is displayed across the top or side of the application window, below the menu bar. The toolbar provides quick mouse access to many tools used in Microtomography Application, To hide or display the Toolbar, choose Toolbar from the View menu (ALT, V, T). Click To Open an existing document. Microtomography Application displays the Open dialog box, in which you can locate and open the desired file. Show the serial bitmap files. Obtain help on some portion of Microtomography Application Control bar command (View menu) Use this command to display and hide the Control bar, which includes buttons for some of the most common commands in Microtomography Application. A check mark appears next to the menu item when the Control bar is displayed. The Control bar is displayed across the top or side of the application window, below the menu bar. The Control bar provides quick mouse access to many tools used in Microtomography Application, To hide or display the Control bar, choose Control bar from the View menu (ALT, V, C). Click To Turn ON or OFF the X-ray source. Close or Open the specimen chamber. Set the magnification. Increase the magnification. Decrease the magnification. Instruction Manual 47

48 Set vertical position of the specimen. Rotate the specimen to desired angle Select bar command (View menu) Use this command to display and hide the Select bar, which includes buttons for some of the most common commands in Microtomography Application. A check mark appears next to the menu item when the Select bar is displayed. The Select bar is displayed across the top or side of the application window, below the menu bar. The Select bar provides quick mouse access to many tools used in Microtomography Application. To hide or display the Select bar, choose Select bar from the View menu (ALT, V, B). Click To Select the x-ray camera. Select the visual camera. Select a line for single cross-section acquisition. Measure a distance and intensity profile in the image. Select a space for serial cross-section acquisition. Display the Acquisition Options dialog box. Display the Cross-section to Image dialog box. Display the Image Tune dialog box. Instruction Manual 48

49 Status Bar command (View menu) Use this command to display and hide the Status Bar, which describes the action to be executed by the selected menu item or depressed toolbar button, and hardware status. A check mark appears next to the menu item when the Status Bar is displayed. The status bar is displayed at the bottom of the Microtomography Application window. To display or hide the status bar, use the Status Bar command in the View menu (ALT, V, S). The left area of the status bar describes actions of menu items as you use the arrow keys to navigate through menus. This area similarly shows messages that describe the actions of toolbar buttons as you depress them, before releasing them. If after viewing the description of the toolbar button command you wish not to execute the command, then release the mouse button while the pointer is off the toolbar button. The right areas of the status bar indicate following: Indicator Description Y=... Magn... Vertical specimen position. Image magnification for acquisition.... Angle position of specimen....kv...µa X-ray tube voltage position. X-ray tube current position. Instruction Manual 49

50 5.9 Setup menu commands This group of commands accessible by password Shift + Ctrl + Alt + s. Pressing the password combination again will close access to the SetUp functions. The Setup menu offers the following commands: FlatFields Alignment Scanner Field of View Positions No Aging Displays the controls for flat field correction. Testing and control the alignment. Sets the scanner parameters. Sets the viewing sizes and corrections. Sets some important constants. Set No Aging flag Flat Fields submenu (Setup menu) The FlatField Correction submenu offers the following commands: Acquire Acquires the reference field data map from camera. Save Saves the reference field data map to disk. Load Loads the reference field data map from disk. Reset Resets the reference field data map Analytical Calculates the typical reference data map. Instruction Manual 50

51 Acquire command (Setup menu) Use this command to acquire the illumination irregularities of the x-ray tube and camera sensitivity map. Reference field acquisition should be made without any object but with the same acquisition conditions as typical object scanning. After acquisition of reference fields one can check the quality of correction by acquiring of the image without object but with flat-field correction. Result image shouldn t contain any regular pattern or differences in brightness. In the case of successful testing the reference fields can be saved to disk by next operation in this section of menu. Reference fields will be downloaded automatically in the next start of the program. Take into account that in the case of using of metal filters in the front of camera, the reference fields should be acquired and saved separately for all filters Save command (Setup menu) Use this command to save the reference field data map to disk (for selected in this moment filter). At next start the Microtomography Application will load this data automatically. Save-operation will separate reference fields for all filters and specific reference field will be loaded or changed automatically in the case of selection for another filter in the camera Load command (Setup menu) Use this command to load the reference field data map from disk. In the case of nonsuccessful acquisition of reference field one can reload the stored reference field by this operation Reset command (Setup menu) Use this command to reset the reference field data map (fill white data map by maximum possible brightness and dark data map by 0) Analytical command (Setup menu) Use this command to generate the analytical data of typical illumination irregularity of the x-ray tube. Adjustments include the linear and parabolic coefficients for irregularity corrections in X and Y directions independently. Instruction Manual 51

52 5.9.2 Alignment command (Setup menu) Use this command to correct alignment of camera and X-ray tube. Microtomography Application displays the Alignement dialog box so you can select your parameters. The Alignment dialog box allows you to correct alignment by moving camera or tube. Corresponding shift can be adjusted as a positive value (number of pixels for the camera or tube shift) with following pressing + or - button. Test for scanner alignment contains several steps. Firstly to test the scanner alignments one should place a cylindrical test object (4mm or less in diameter) in the specimen stage, set the magnification of approx. X15- X17 and press Test button in the Alignment dialog. As a result of this test a displacement of the object rotation axle from the ideal position will be shown. You should correct this displacement by camera movement in the alignment dialog. For example, if result of alignment test was +3.5 pixels in central part of the image (there are three values disalignment in central, top and bottom parts) one should set camera value to 3.5 and press - button to compensate it. After correction one can do the same test once more to check the axle displacement. For normal operation this value should be inside ±1 pixel. Afterwards the same test should be done with magnification of X50 X80. If the axle displacement is more than ±1 pixels the x-ray source position should be corrected by the same way. Described procedure for central alignment allows adjusts scanner mechanically. Difference in alignments in the top and bottom and disalignment during vertical movements should be compensated in software as it will be described in the next chapter Scanner (Setup menu) The following options allow you to adjust the scanner parameters: Instruction Manual 52

53 Screen Size Sets the size of visual image in the screen. Field of View Sets the size of camera field of view in the minimum object magnification. Camera Size Sets the physical size of the camera s sensitive area. This parameter will be used for camera shifting for doubling in field of view. Camera shift mode can be applied by corresponding selection in the Acquisition SetUp Max Scanner Position It s a distance from the object position in minimum magnification to the emission point inside the source. This parameter used for magnification calculations. Optical axis Exact vertical position of optical axis in x-ray beam, which will be used in external reconstruction programs for cone-beam and spiral scans. Next set of parameters adjusts a correction of the object rotation axle s position. It allows aligning the visible center of the field of view to the center of rotation at the reconstruction area. Their options include electronic shift and inclination of the image to compensate mechanical disalignment and extension with temperature. Please remember to switch on Geometrical Correction in the Acquisition SetUp submenu for Visualization mode to display corrected image and to take into account these corrections during axle position test. Top<->Bottom Inclination Corrects the camera and/or rotation axle inclination as a difference of the position of the rotation axle in the top and bottom of the image (in the case if different displacement direction in the top and bottom). This correction should compensate difference in the top and bottom values from the central value, obtained in alignment test shown above. For example if (in the case of 0 value of this parameter) results of alignment test central value equal to 0.3 and top value equal to -3.8, one should place 4.1 pixels in the Top<- >Bottom Inclination value to compensate it. Instruction Manual 53

54 Inclination in Lifting Corrects the scanner disalignment during object lifting. To adjust this value compare the values of central displacement in the alignment test for 0- position of the object and after lifting to 10mm. If (in the case of 0 in this parameter) for example central disalignment at 10mm lifting will be found as 5.7 pixels, put 5.7 to this value for compensation. Termoextension Correction (with temperature indication) allows compensating the specimen stage expanding with temperature (if temperature sensor included in the scanner). Temperature increasing extends the arm and shift object rotation mechanism with following shifting of the image to the left (to the negative values of axle position). For compensation, this parameter should be positive with typical value Positions command (Setup menu) Use this command to set new filters and object stage positions. Microtomography Application displays the Positions dialog box so you can select your parameters. The Positions dialog box allows you to adjust the position of filters for filter changer and to set the object stage during specimen exchange. All positions should be defined in mm for translation movements or in degrees for rotation movements (for example for filter wheel) for corresponding motors and can be tested by the Test button. Four positions for filters plus position of the filter changer to cover camera during specimen exchange can be adjusted or corrected in software. Physically available number of filters can be from 0 up to 4. Please contact to supplier for information about possible number of filters in your particular system. Stage- >Specimen exchange position corresponds to the position of the object stage in the front of the door. Stage->Start lift position adjusts the zero position of lifting for the object stage No Aging command (Setup menu) This command will cancel necessary aging. Attention! Any start without normal aging can reduce the lifetime of the source. Instruction Manual 54