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Bruker SkyScan 1272 User Manual
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Bruker SkyScan 1272 User Manual

Bruker SkyScan 1272 User Manual

Desk-top x-ray microtomograph
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SkyScan1272 User Manual
V1.2 09/2018
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  • Page 1 SkyScan1272 User Manual V1.2 09/2018...
  • Page 2 Desk-top X-ray microtomograph SkyScan 1272 User Manual © Bruker microCT 2018 Designed and manufactured by Bruker microCT Kartuizersweg 3B 2550 Kontich Belgium SkyScan1272 User Manual V1.2 09/2018...
  • Page 3 TABLE OF CONTENTS INTRODUCTION IN X-RAY MICROTOMOGRAPHY ............... 4 1.1 Introduction ........................4 1.2 Basic principles of microtomography ................5 SKYSCAN 1272 SYSTEM OVERVIEW ..................9 INSTALLATION PROCEDURE ..................... 11 3.1 Unpacking procedure ..................... 11 3.2 Installation of the scanner ....................15 3.3 Supplied toolkits ......................
  • Page 4 8.1 Installation ........................76 8.2 How to use ........................81 8.3 Changer calibration ......................88 SKYSCAN 1272 WITH SAMPLE CHANGER: SYSTEM CONTROL BY COMMAND FILES ..93 9.1 Overview......................... 93 9.2 Command File Structure....................94 9.3 Status File Structure ....................... 97 SERVICE AND SUPPORT ....................
  • Page 5 1 - 10 cubic mm voxel (volume element) size. Computerized X-ray microscopy and microtomography now gives possibilities to improve the spatial resolution by seven to ten orders in the volume terms. The system “SkyScan 1272” allows reaching a spatial resolution in the level of microns, which corresponding to near 1x10 cubic mm voxel size.
  • Page 6 1.2 Basic principles of microtomography An X-ray shadow image represents a two-dimensional projection from a three-dimensional object. In the simplest case, we can describe the X-ray illumination as parallel. In this approximation, each point on the shadow image contains the integration of absorption information inside the three-dimensional object along the path of the corresponding partial X-ray beam.
  • Page 7 Now we can 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 the position of the shadow. This operation is named "back-projection". After certain number of rotation steps we can localize the position of the absorption point inside the area of reconstruction.
  • Page 8 This correction adds some ``negative absorption'' outside the region of the object shadow to eliminate the positive blur in the back-projection process (convolution) which is shown in the figure above. The same algorithm can produce cross section images not only from a single point object but from any real object.
  • Page 9 prevents noise from increasing during the reconstruction procedure. In X-ray micro -tomography, information from a voxel with a very small physical size should be detected and the right choice of parameters for noise reduction becomes very important. During acquisition the object will rotate over 180 or 360 degrees with a fixed rotation step. At each angular position a shadow (or transmission) image will be acquired.
  • Page 10 SKYSCAN 1272 SYSTEM OVERVIEW The SkyScan 1272 is a compact desk-top micro-CT system for material science, industrial, biomedical and quality control applications. The X-ray scanner contains a microfocus X-ray source, an X-ray detector (camera), an object manipulator for positioning and rotation of the objects during tomographic acquisition and associated electronics to power the X-ray source and camera and for the control of the object manipulator.
  • Page 11 • Scanned samples can be removed / replaced without interrupting scanning process. • Typical sample replacement time is 65 sec. • Powered from SkyScan 1272 scanner. Control computer configuration: • DELL Precision T7920 Workstation, Windows 10/64bit: • Two Intel XEON GOLD 6128, 3.4GHz, 10.4 GT/s processors, •...
  • Page 12 Email: info@bruker-microct.com, Tel: +32 3 877 5705, Fax: +32 3 877 5769 Only people trained by Bruker microCT are authorized for service and reparations on the scanner! The system is not intended to be placed in the public areas. If the equipment is used in a manner not specified by the manufacturer, the protection provided by the equipment may be impaired.
  • Page 13 For lifting and carrying, keep the scanner in the same orientation as in working conditions, and use the side steps on the enclosure plate as handgrips. The weight of the scanner is around 150kg and we recommend to carry or to lift the system with 4 persons. Alternatively, the scanner can be removed from flightcase using forklift and two lifting slings, (available from RS http://uk.rs-online.com, stock number 729-3057).
  • Page 14 Under the scanner you will find toolkit box, cables to connect scanner to workstation, power cable and factory report. Keep the flightcase for possible moving of the scanner to another location or for sending it back for service or repair. If scanner supplied with optional automatic sample changer, you can find it in the second (small) flightcase.
  • Page 15 The changer can be found under separation plate in the bottom compartment of the flightcase. To remove the changer use two round holes in the plastic foam to put your hands under the neck of the changer in the middle of the case. The changer is relatively light and can be handled by one person. SkyScan1272 User Manual V1.2 09/2018...
  • Page 16 3.2 Installation of the scanner Site requirements: The system needs to be connected to a wall socked with earth connection. The power cord can only be replaced by H05VV-F 3G 1.5mm2 Don’t position the system so it is difficult to manipulate the electrical power cable. To remove the electrical power from the system, unplug the power cable from the appliance coupler.
  • Page 17 User Manuals and necessary device drivers. Most recent versions of software can be downloaded from the producer website: www.bruker-microct.com/products/downloads.htm 3.3 Supplied toolkits The toolkit supplied with scanner contains following parts: Two supplied keys (1) for X-Ray keyswitch can be used for protection against unauthorized access to scanning by the instrument.
  • Page 18 The toolkit supplied with automatic sample changer contains following parts: A cable (1) allows connecting power to the changer from the scanner. A USB-cable (mini-USB) connects data socket on the changer to USB2 socket on the back wall of workstation. Supplied landing pad (3) should be attached to the scanner turntable before changer installation using screwdriver supplied in the scanner toolkit.
  • Page 19 3.4 Connection to external interlock If regulations in the user site require additional protection in access to laboratory during scanning with involvement of X-rays, it may be necessary to connect the system to external interlock switch (typically – switch on the laboratory door) using connection to the socket on the side wall of the scanner. The same socket can be used to control illuminated sign “X-RAY”...
  • Page 20 SCANNER’S CONSTRUCTION 4.1 Main parts of the scanner The construction of the SkyScan1272 scanner is shown below: It contains a microfocus X-ray source in the left part of the scanner. The source operates at 20-100kV with maximum power of 10W. It produces X-ray from the very small focal spot to ensure that smallest details inside the objects can be resolve in X-ray image.
  • Page 21 4.2 Automatically variable acquisition geometry The SkyScan-1272 utilizes automatically variable acquisition geometry invented by Bruker microCT to reduce scanning time and increase scanning quality in microtomography systems with large-format cameras. All other micro-CT systems on the market use static acquisition geometry where the X-ray source and X-ray detector are separated by a fixed distance and image magnification is adjusted by object movement between them.
  • Page 22 Using an X-ray source with a big beam opening angle and a large format detector, the maximum distance between the source and the detector, required for maximum and minimum magnifications, can be reduced with a corresponding increase in detected X-ray intensity. At intermediate image magnifications, both object and detector are moved towards the source until they reach the most compressed geometry possible while collecting all X-ray photons emitted from the source.
  • Page 23 energy cut-off selected by numerous filters allows operator to select the most optimal energy window for any particular object. For object containing transparent for X-ray materials energy window can be pushed down to low values for getting enough significant adsorption from object’s smallest details. In the case of objects, which contain materials with high X-ray absorption, X-ray energy window can be pushed up to get enough transmission through the object body.
  • Page 24 “prefixNNNNNNNN.tif”, where “prefix” corresponds to the selected name for the dataset and “NNNNNNNN” indicates the number of angular projection in an 8-digit format. The set of acquired projection images can be opened and shown as a movie by several supplied programs, such as DataViewer.
  • Page 25 SkyScan1272 User Manual V1.2 09/2018...
  • Page 26 GETTING STARTED The software package for system control has the same operational principles as any other Windows- based program. One can select any function from the menu/submenu in the top line, and also change modes and parameters using the corresponding control buttons or sliders. To start the SkyScan1272 control software double click to the corresponding icon on the desktop: After starting the program, the system will be switched on automatically and an initialization window will be shown on the screen.
  • Page 27 Snap single X-ray image The “Grab Image” function will first start the X-ray source (if it is selected in Menu => Options => Preferences) and then begin acquisition of projection images. Clicking the “Grab Image” button once more will stop continuous acquisition. The “Snap Image” function will also turn on the X-ray source first and acquire a single image, keeping the X-rays ON.
  • Page 28 For large objects one can use a supplied steel sample mount. This mount has a chuck with four independently adjusted jaws to hold the objects with complex shape and to adjust their proper centring: To install steel sample mount use supplied screwdriver. Firstly select angular position of the mount to be sure that connector on the turntable targeted towards milled cavity in the bottom of the mount and afterwards put it coaxial to turntable and secure by two supplied screws: Close the specimen chamber using the leftmost button on the toolbar:...
  • Page 29 All three listed movements can be adjusted using numerical values by clicking to numerical indication on the right side of any status bar pane and filling new position(s) in the following dialog. You can click by right mouse button in the imaging area to show a signal intensity profile along the line where the mouse pointer is situated.
  • Page 30 central camera position. You can make selection of scanning parameter in advance by Menu -> Options -> Acquisition. In this case the Scanning Options dialog will contain only OK and Cancel button like it shown on the image above. When the same dialog appears before beginning of the scan, it will contain also Scan button in the bottom.
  • Page 31 also load the full reconstructed 3D space into DataViewer and visualize three orthogonal slices crossing at any selected point inside the object using third button in the toolbar. The next toolbar button opens a “3D Navigator” display to show the spatial position of three selected slices: You can select any position for the crossing point of the three virtual slices by moving the crossbars in the images or the slice planes in the 3D Navigation window by the left mouse button.
  • Page 32 Add a knot to the opacity curve by clicking in the lower left side of the purple curve on transfer function window. Move the knot down to get low-intensity clouds around the object more transparent. Two modes exist for navigating the scene: •...
  • Page 33 (BMP, JPG or PNG). More details on CTvox functions can be found in “Quick Start Guide” available for downloading from Bruker microCT website. 5.5 2D / 3D image analysis and surface rendering The next button in the toolbar of the SkyScan1272 control program and in the toolbar of...
  • Page 34 direction by two sliders to the right of the files list. Double-click on the blue bar between these sliders to enter upper and lower limits numerically. One can reset all regions-of-interests by the button to “start again” with VOI selection. Go to conversion to binary images with the button.
  • Page 35 User Manual or by “Getting Started” guide, which can be found in the “Manuals” subfolder in the program folder of the computer supplied with the scanner. Most recent versions of the User Manuals can be downloaded from http://bruker-microct.com website. The documents available in the moment of writing this Manual are: NRecon User Manual: http://www.bruker-microct.com/next/NReconUserGuide.pdf...
  • Page 36 CTan List of Functions: http://www.bruker-microct.com/next/CTAn02.pdf CTan Description of Measured Parameters: http://www.bruker-microct.com/next/CTAn03.pdf CTan Creating User Plug-Ins: http://www.bruker-microct.com/next/CTanPlugIns.pdf Most recent versions of all application programs can be downloaded from: http://www.bruker-microct.com/products/downloads.htm To close the control program for the SkyScan1272, double click on the icon in the top left corner of the program window or click once on the red box with a cross in the top right corner.
  • Page 37 This paragraph contains explanations of functions, actions and checks that should be done either routinely or before starting a scan with the SkyScan 1272 micro-CT scanner. Remember that the micro- CT scanner is a sensitive high-precision instrument, and treat it accordingly. Insert and remove the sample holders at the stage with the minimum force possible, and never subject the scanner to jolts or strong vibrations.
  • Page 38 Alignment test can be activated by Menu -> Options -> Alignment Test. Appeared dialog will give you choice in one of two possible options: single point test in the current position or two-point test. Single point test at low magnification will detect mainly camera misalignment and will try to correct it. Single point test at high magnification will detect mainly object stage misalignment and will try to correct it.
  • Page 39 accumulated by CCD during selected exposure time. Second reference image, named as a bright reference field, acquired with X-ray illumination to the camera without any object in the field of view. This image reflects intensity distribution, which can vary pixel-by-pixel. The camera contains CCD connected by fiber-optic plate to scintillator, which converts X-ray to visible light.
  • Page 40 requires significant disk space – 1.7GB for scanners with 11Mp cameras and 2.5GB for scanners with 16Mp cameras. Every time when user saves specific configuration, all flat-field references will be duplicated to “configurations” subfolder. Keeping big number of user-specific configurations may require a lot of disk space.
  • Page 41 How to select scanning parameters Scanning Options dialog shown before every scan contains number of parameters, which can influent to quality of acquired information and results of reconstructions. In this paragraph we will explain what particular influence of every parameter selected. Rotation step is mainly dependent on image format.
  • Page 42 The next option allows automatically switching OFF X-ray source in the end of the scan. The source will be also switched off if you will choose to stop scanner and / or shut down computer in the end of the scan.
  • Page 43 execution in batch mode. For every sample in the list all scanning parameters can be adjusted individually. To activate batch/oversize scanning mode go to Menu -> Options -> Oversize and Batch Scanning. It will add vertical narrow view to the left side of the screen and (if selected in Options -> Preferences) will start scout view with collecting overlapped images using vertical stepping starting from the topmost position of the object stage.
  • Page 44 After completing the list of required scans, start execution of in the batch mode by “Start Scan” button. After starting scanning all editing buttons in this dialog will be greyed and “Start Scan” button will be converted to “Abort Scan”, which will allow interrupting scanning sequence. Using shortcuts to simplify scanner control There is number of shortcuts, which can simplify and accelerate scanner control by operator.
  • Page 45 CONTROL PROGRAM FUNCTIONS 7.1 General layout The control program contains a central image area, a main menu at the top, a toolbar for quick access to the most useful functions, and a status bar at the bottom. The main menu gives access to all system functions.
  • Page 46 7.2 Toolbar The toolbar is displayed across the top of the control program window. It provides quick mouse access to most usable function of the control program. Open / Close specimen chamber Start / Stop X-ray source Acquire X-ray image continuously Snap single X-ray image Show / Hide image from visual camera Start scanning...
  • Page 47 7.3 Status bar The status bar is displayed at the bottom of control program window. It contains a slider to adjust magnification, a slider for object rotation, control pane for object elevation, control pane to select image format, control pane for selection of filters in x-ray beam and information pane to display current camera position of CCD sensor temperature.
  • Page 48 7.4 Actions menu SkyScan1272 User Manual V1.2 09/2018...
  • Page 49 Specimen Chamber Open/Close opens or closes specimen chamber door to install or replace the specimens. X-Ray Start/Stop starts or stops X-ray source. Grab Image starts or stops continuous acquisition of X-ray images with displaying on the screen. Snap Image acquires single X-ray image and displays it on the screen. Snap Double Width acquires X-ray image using two camera offset position to double horizontal coverage of the object.
  • Page 50 7.4.1 Open / Close Specimen Chamber Use this command to open or to close specimen chamber's door to install or replace your specimen. There are several sample mounts supplied with the system. To install small and medium size brass sample mounts insert cylindrical core of the mount in the central hole of the sample stage and tight it by turning brass nut clockwise.
  • Page 51 7.4.2 X-Ray ON / OFF This command starts or stops X-ray source. In the case of more than 8 hours after last usage of X-ray source, this command will start preheating process, which takes typically 15 minutes and will keep X-ray OFF afterwards. After opening-closing specimen chamber and after starting the scanner, short preheating may be also executed with keeping X-Ray source in selected position afterwards.
  • Page 52 7.4.5 Snap Image with Double Width Use this command to snap x-ray image with double width with automatic combining of two images in camera offset positions. Double width image allows checking proper fit for imaging large objects in particular magnification for following scanning using two camera offset positions.
  • Page 53 7.4.8 Save Image Ctrl+S Use this command to save image shown on the screen to the file on the disk: You can select a location of the file using left hand side of the "Save Image" dialog, file format - in the bottom part and choose file name, which you want to use by typing in the corresponding editable area.
  • Page 54 The reconstruction program can work on CPU-only mode with multithreading or in GPU- accelerated mode, which can work 5-30 times faster in the case of using high performance graphical card. You can download from bruker-microCT website complete User Manual for NRecon reconstruction program as well as GPU-accelerated reconstruction Installation Guide. 7.4.12...
  • Page 55 SkyScan1272 User Manual V1.2 09/2018...
  • Page 56 To get more details about menu functions and toolbar buttons, use context help button on the right of toolbar with following click to the item, which you want to clarify. Most recent version of DataViewer program can be downloaded from bruker-microct website. 7.4.14 Start 2D / 3D Image Analysis Selection in the menu “Actions”...
  • Page 57 Options Menu Acquisition opens dialog to choose acquisition parameters, which will be applied during scanning. Data Folder allows selecting the folder where results of scanning will be placed. X-Ray Source opens control panel for X-ray source with possibility to adjust accelerating voltage, beam current and get information on source status and parameters.
  • Page 58 MicroPositioning opens dialog with access to object movement by micro-positioning stage integrated to the instrument. Visual Camera ON/OFF opens or hide additional window, which displays visual image of the object inside the specimen chamber. Oversize and Batch Scanning allows selecting several scans to be executed automatically and/or define position of the scanning of the object longer than vertical field of view by multiple partial scans, which will be afterwards automatically connected.
  • Page 59 7.5.1 Acquisition Options The function accessible through "Options" >>> "Acquisition" menu and also called every time before starting scanning (with additional button "Scan" in the bottom of the dialog). This command opens following dialog: Top part of the dialog allows selecting Filenames prefix and Data directory. Button Browse calls dialog for selecting existing data folder or creating new one.
  • Page 60 Next switch selects camera format with indication which pixel size will be used for every format in current magnification. Partial width selection allows saving disk space in the cases when object takes only part of the width of the image. Be sure that object will not run out of this part during rotation in scanning. During adjustment selected part will be marked on the image.
  • Page 61 7.5.3 X-Ray Source This command opens control panel for X-ray source: The control panel has three tabs: control, warm-up and info. All tabs contain voltage and current indication, Stop button and status indicators in the right hand side. The control tab allows changing source's voltage and current. A manual change of spot size is not accessible for used type of the source.
  • Page 62 7.5.5 MicroPositioning Use this command to open dialog for controlling micropositioning stage (not accessible with sample changer): Every mouse click to buttons with left or right arrows will command micropositioning stage to move object by such way, that operator will see it as left or right independent of current angular orientation of object stage.
  • Page 63 For objects with limited length, scout scanning can be interrupted any time by "Cancel" button in progress dialog. Otherwise it will continue up to the end of possible vertical travel. To zoom in / zoom out scout view, one can move the splitter between two views by mouse. Dragging with left mouse button will show dimensions on the scout view.
  • Page 64 Start Scan button starts execution of all scans listed in the batch dialog. During scanning different lines in the batch list will be highlighted by colour with indication of the current status in the right column: Right mouse click to scout view opens scout submenu: This submenu allows repeating scout scan, to close scout view and show or hide Batch Dialog.
  • Page 65 7.5.8 Preferences This command opens dialog for setting your preferences in the program usage: First two checkboxes allows switching flat-field and geometrical correction ON and OFF. Flat-field correction can be also switch ON or OFF by double mouse click to "ff" (if it is already ON) or to the beginning of "flat-field correction OFF"...
  • Page 66 7.5.9 Configurations: Load, Save, Delete, Load from log-file Use Load command to load scanner configuration from the one of previously saved on the disk. The software will allow choosing configuration by name with following loading all scanning parameters and all flat-field reference maps. To load factory preset use "Options"...
  • Page 67 of scanning all samples in the changer. Next setting allows activating e-mail sending in the end of every scan or in the moment when all samples in the changer will be scanned. Next field controls behaviour of the image from the visual camera, which is displaying in the top of Sample Changer dialog.
  • Page 68 Top two sections of this dialog are identical to corresponding parts of the Scanning Options dialog, which appears before every scan. Next drop-down menu adjusts energy filter. Bottom field of the dialog allows selecting magnification by defining Pixel size, choosing Image Format from four available, selecting Partial width for scanning if necessary and defining vertical position at which you want the object to be scanned.
  • Page 69 First line allows defining serial number of the scanner, which will be indicated in the log-files and identify this scanner in e-mails send automatically. Next parameter - Specimen exchange position for object stage counted from home position in the right hand side of travel. In the proper exchange position specimen stage should be in the middle of the hole in the bottom metal plate.
  • Page 70 Top part contains presets for rotation steps, which will be used for four possible camera formats. Next table defines camera exposures, X-ray source voltage and current for six possible filters. In the case of filter's customization, the names of the filters can be edited here. Camera exposures can be set for every filter for every camera format and for three possible camera distances from X-ray source.
  • Page 71 using horizontal mouse dragging (left button) with Ctrl on keyboard, adjust pin position by such way that it will be inside field of view with small gap from the side of the image: Turn object by 180 degrees from previous position (any direction) and check that now the object will be close to opposite side of the image, but still with small gap.
  • Page 72 Calibration curve should be smooth and without sharp jumps or gaps. Any breaks on calibration curve may indicate that calibration procedure has been done with mistakes. 7.5.15 Sample Changer Calibration The command opens following dialog: Init button in the top allows reinitialize all drive in the changer when necessary. Next three fields can be activated by selection in corresponding first line.
  • Page 73 After selecting this group of functions, robotic arm will be moved to the safe position above landing pad. Using up, down, forward or backward movements of robotic arm and left, right movements and cw, ccw rotation of the object stage, one have align landing position of object mount to the landing pad coming from the top to get the mount concentric to the landing pad.
  • Page 74 Help Menu Help Topics opens access to library of help resources with possibility to chose content or search by command name. About SkyScan1272 opens "about box" with indication of current software version, copyright information and links to producer website and e-mail. Shortcuts shows list of keyboard shortcuts for quick access to number of functions.
  • Page 75 The dialog box also displays current CCD temperature in X-ray detector and allows sending e- mail to producer and connecting to producer website by clicking to corresponding links. 7.6.3 Shortcuts This command opens list of shortcuts for quick access to number of functions. Some shortcuts available in the Service Mode will be shown only after entering...
  • Page 76 stability of CCD temperature stabilization inside the camera. This information is shown as a blue curve with dotted marks for acceptable margins. Information line above the plots shows current position and timing, source voltage/current, emission intensity measured from the camera signal and current CCD temperature.
  • Page 77 AUTOMATIC SAMPLE CHANGER Automatic sample changer can be supplied together with the scanner or purchased separately. In first case it will arrive pre-calibrated. In second one it will require calibration at user site. 8.1 Installation All time when changer not installed to the scanner keep it in the transportation box to avoid damaging precise internal manipulator.
  • Page 78 For changers supplied separately, adjust height of the centering pin to get top surface of fully inserted pin in two millimeters under the top surface of the scanner enclosure like it shown on the following picture. Use supplied spacers and washers to adjust the height of the pin. For changers supplied with the scanner, check that this distance is in the range of 1.5 …...
  • Page 79 Afterwards connect landing pad to the object stage. Extend distance between the jaws in the top of the pad to get screws free to move up, center the pad on the object stage of the scanner and secure it on the stage by two screws using screwdriver supplied with the scanner: Now you can install sample changer to your scanner.
  • Page 80 Slide it in parallel to the top surface of the scanner towards the back wall to reach connection of the fork under the changer’s carrousel with centering pin installed to the scanner. In the proper installation the changer should stay exactly in the middle of the opening of the specimen chamber in parallel to the top surface of the scanner with 2-5mm gap between bottom of the changer carrousel and the top surface of the scanner enclosure: SkyScan1272 User Manual...
  • Page 81 Be sure that two round extensions on the bottom plate of the changer column fit round milled cavities on the front plate of the scanner. Shake a little bit the column of the changer to get both legs properly inserted: Afterwards connect the changer to your scanner by two screws using screwdriver supplied with the changer: Be sure that computer and scanner are switched OFF.
  • Page 82 Start control computer. Start scanner control software. The software should recognize the changer and show Sample Changer control dialog on the screen (image and data in this dialog may be different from the shown on the picture): With changer properly recognized by software, the installation procedure is completed. 8.2 How to use In the first start of the changer without any specimen mount installed all bars in the top of the carrousel will not be illuminated.
  • Page 83 Sample mount with long thin (5mm in diameter) neck (left on the picture) should be used for small samples to be scanned with highest magnification. We would recommend using this type of mounts for samples under 5mm in size and under 8mm in length. Next one (with neck 10mm in diameter) can be used for small-medium size of samples up to 10mm in diameter.
  • Page 84 Attention! Never install new sample in the empty position, which is indicated in red because automatic procedure to return sample after scanning to this position will damage the sample changer by collision of the sample mounts. After filling the carrousel by samples on the mounts (you can keep any number of empty positions), close carrousel lid.
  • Page 85 To check removing procedure, click “remove” button in the Sample Changer dialog. The robotic arm will move the fork to the bottom of the tower and forward up to reaching sample mount from the front. It will open jaws on the landing pad to allow free vertical movement of the mount. Afterwards robotic arm will take sample mount up and around the corner of the carrousel to the topmost position.
  • Page 86 Next edited area in every line contains filename prefix for dataset, which will be saved during scanning of corresponding sample. In the first start of control software all “name” fields are populated by combination of current date and position in the changer. You can edit this filename prefix any time for all non-scanned samples.
  • Page 87 The behaviour during scanning with “Auto” protocol selection and number of other parameters can be adjusted in the “Sample Changer Settings” dialog, which can be called by Menu -> Options -> Sample Changer Settings. The top part of the dialog provides control for distribution datasets in subfolder with incremental folder names.
  • Page 88 previously scanned sample. Second option will adjust magnification individually according to diameter of the neck of the sample mount in assumption that sample is equal or smaller than mount neck. Last option will adjust magnification individually according to sample position, size and shape. Before starting the scanning sample will be moved to minimum magnification and control software will measure margins between sides of the sample and left/right edges of the image for number of angular positions.
  • Page 89 8.3 Changer calibration If sample changer purchased separately or installed to the scanner first time after transportation, one particular check should be done before changer calibration. The changer contains sensor for detection of specimen chamber’s door position. It installed under the right wall of the bridge between vertical column and carrousel.
  • Page 90 The distance can be adjusted by releasing the nuts on the sensor body and tighten them on the proper sensor location. Following sample changer calibration can be done using Menu -> Options -> sample Changer Calibration function. This function is one of the Service functions: if corresponding line of menu is grayed, push Ctrl+Alt+Shift+s first to activate Service Mode.
  • Page 91 Top section of the dialog responsible for calibration of lifting object mounts from the carrousel. After selection of this part insert one object mount (without any sample) to the first position of the carrousel. After scanner and sample changer initialization, the carrousel should be in the rotational position with first place for the sample mount oriented towards operator, but not necessary exactly aligned to direction perpendicular to the scanner.
  • Page 92 “forward”, “backward”, “cw” and “ccw” buttons to reach proper position of the fork against sample mount on the carrousel. The fork and the carrousel will move slowly only when corresponding button is pushed. You will see monitoring of all positions in the numerical values on the right side. After reaching proper lifting position for the fork and proper rotational position for carrousel described above, save selected positions to ini-file by pushing to “save lifting positions”.
  • Page 93 If changer was previously calibrated, you can “load landing positions” and “check landing” / “check removing” using corresponding buttons. Keep the mouse on the “STOP” button to interrupt movements if necessary. If one or several positions should be modified you can edit corresponding lines in ini-file, “load landing positions”...
  • Page 94 SKYSCAN 1272 WITH SAMPLE CHANGER: SYSTEM CONTROL BY COMMAND FILES 9.1 Overview Starting from version 1.1.18, 1272 control software allows full control of acquisition and reconstruction processes by text-form command files. It also supports periodically updated status monitoring by text file.
  • Page 95 If control program can find command files for some or all changer positions, this window will be modified as following (in this example, control files are found for positions 1,2,3 and 12): The drop-down lists are replaced to “from file” indications and filename prefix is taken from the command file.
  • Page 96 The command files are text files. Every file contains three sections started from the header in square brackets with following list of keys and parameters. First section should be started from [sample] header, second one – from [scanning] header and third one – from [reconstruction] header. Following table describes all possible keys in every section and default values, which will be used if corresponding key doesn’t exist in the command file: Section / Key...
  • Page 97 Every section of control file contains listed above header with following list of keys. Key name separated from the value by “=” sign, for example: [sample] Sample Name=MySample Sample Number=123456 Sample Description=sample 1 description [scanning] Pixel Size in um=9.5 Vertical Scanning Position in mm=22.2 Rotation Step in degrees=3.0 X-Ray Source Voltage in kV=80 X-Ray Source Current in uA=100...
  • Page 98 9.3 Status File Structure For monitoring activities of control and reconstruction programs, both are periodically updating status file with time marks of last update. The status file name is “SkyScan_status.log”. It located in the folder defined by “Status File Folder” key in [System] section of SkyScan1272.ini file. Generation of status file is not connected to presence or absence of control files.
  • Page 99 projections in [Input] key, full pass to first reconstructed slice in [Output] key and overview of last executed process in [Finish Status] key. SkyScan1272 User Manual V1.2 09/2018...
  • Page 100 (=> Company => User Meetings) If your control computer is connected to internet, you can get access to the Bruker microCT website by simple click to the corresponding underlined web-address in the “About…” box in the Help part of the Main Menu.
  • Page 101 SkyScan1272 User Manual V1.2 09/2018...