XRADIA microXCT Manual
Contents
1. Part 4 TXM 3D Viewer After reconstruction is finished you may view the image in TXM 3D Viewer You will need to create a folder for your labs images for storage since there is no personalized login for the PC Images will eventually be stored on PACS an image database When viewing images in TXM 3D Viewer by default you will have four windows to view and rotate your images Figure 17 There will be arm three windows to view different planes There is XY YZ XZ and then one that will be a 3D reconstruction You can manipulate the image in different ways such as cropping it It can also be exported into other usable file formats such as JPG or DICOM Animation files can also be created and exported as needed Clicking and dragging the 3D model will rotate it in different directions ee Figure 17 The 3D Viewer window 102. in different formats Section 4 1 1 INSTRUMENT PARTS a ae Signal Tower Indicates status of the X ray system Green means power on yellow means the door is closed properly and red means X ray is on 2 Interior Camera Display To view inside the machine when the cabinet is shut and the X ray is ON 3 PC interface For all controls i e activations of x ray source movement of components etc 4 X ray Source 5 Objectives There are five objectives of optical magnification four fine objectives 2x 4x 10x 20x on the left of the detector and a 0 5x on the right 6 Detector CCD 7 Sample Stage Sample to be secured Figure 2 Interior scanner configuration 7 J on here Details in Section 1 3 NOTE Axis orientation marked in Figure 2 1 2 POWERING UP THE SYSTEM The scanner will not usually be turned off and the system will be on when you come in Press the Emergency Off EMO button Figure 3 only in case of emergency The PC will be on and there is no account to login If there is a problem in powering up or resetting the system check that the EMO button is pulled out Figure 3 Emergency off button If the problem continues check the breaker box Figure 4 located near the base of the scanner flip all switches up and switch the main breaker on Figure 5 If there has been a power surge then this will need to be flipped to the ON position Figure 4 Breaker b
3. Biomedical Imaging Division VIRGINIA TECH WAKE FOREST UNIVERSITY 4 J J 4 X N me hool of Biomedical Engineering and Sciences XRADIA microXCT Manual Multiscale CT Lab Table of Contents 1 Introduction and Basics 1 1 Instrument Parts 1 2 Powering up the system 1 3 Preparing your sample 2 TXM Controller 2 1 Starting up 2 2 Finding the Isocenter 2 3 Capturing a Single 2D X ray Image 2 4 Acquisition of Tomographic Projections 3 TXM Reconstructor14 3 1 Doing a 3D reconstruction 4 TXM 3D Viewer 16 Part 1 INTRODUCTION AND BASICS The Xradia microXCT scanner is a system that has many applications for imaging in a variety of fields such as biology geology and materials science This scanner provides resolution up to 500 nm The main components of the cabinet are explained in Section 1 1 This manual is intended as a brief overview how to use the micro CT and its components For further instructions please consult the full 100 page User Manual from Xradia The Appendix is available for extra tips It explains how to use other features and export files There are three different programs that you will be using to do imaging These are explained in detail sections 2 3 and 4 e TXM Controller for acquisition of X ray images from the micro CT Section 2 e TXM Reconstructor for reconstructing an aligned 2D data set Section 3 e TXM 3D Viewer Reconstructed images can be viewed as a 3D volume and exported
4. he hard drive Opens the settings window Starts an image acquisition O Aborts an acquisition Opens or closes the Image Properties Control Panel y Adjusts the X ray source a Begins acquisition Aetna e The voltage and power can be adjusted as needed based on the material or object being iad imaged Figure 8 Vokage 150 kV Pone ssw e Clicking apply will turn the X ray source on If you make any adjustments to these settings you must click apply again Current 66 uA Interlock CLOSED Figure 8 X ray Source window There are three different scan modes primarily used and are selected from the gear menu Each can be adjusted for time of exposure and number of binnings needed Binning is the procedure for grouping data into data classes for later processing Continuous Mode Used for setting up the Acquisition Mode scans and adjusting movement of the sample This mode takes short coarse images continuously Also be accessed by clicking the video camera icon Single Mode Gives you one quality image similar to a regular X ray taken if you broke your arm Clicking the camera icon can also access this Tomography Mode This mode will slice i the sample and produce a 3D image that can be manipulated later Figure 9 Acquisition mode window There are three tabs for the motion Motion Controller Sample controller Figure 10 This moves the detector source and sample during the course
5. is still in the screen If not then adjust Z direction accordingly 5 Repeat rotations until able to rotate to 90 with no movement 6 Zoom to desired optical magnification e g 20x 7 Use a unique aspect UA of the sample edge particle tooth etc and draw a straight vertical line at this site as shown in Figure 12 8 Rotate to 90 and place new line on UA Figure 13 Figure 12 Drawing the initial line at the unique aspect UA Figure 13 Post 90 rotation draw new line at UA Figure 14 Move UA in Z direction halfway between the two lines 9 Move sample Z direction until halfway between two lines Figure 14 10 Remark UA and rotate back to 90 Move sample in Z direction until halfway between two lines and remark UA 11 Repeat process until there is no change The two lines appear as one Figure 15 Final position of object the Figure 15 two lines appear as one 2 3 Capturing a Single 2D X ray Image 1 Load Sample and launch TXM e Note It is important to get the detector Controller as close as possible to the sample Be sure to view with the interior camera IF 2 Adjust optical objective to desired YOU ARE NOT CAREFUL YOU MAY magnification by selecting Microscope CRASH THE SCANNER then Configure systems on the menu and Move the detector back change the select OK objective and then move to the previous position Pausing or stopping all motors 3 Move source and detect
6. of taking an acquisition Figure 10 Motion controller window To manipulate the sample into the path of the source use the joystick to move the sample or motion controller buttons Figure 10 There are three degrees of spatial freedom for X moving the sample in the XYZ directions The angle will zd rotate the sample To move the stage up you must go in the negative Y direction For further axis orientation see Figure 11 Axis Figure 11 orientation Using following icons can move the source Moves toward sample Z at given step size in millimeters Moves away sample Z at given step size in millimeters Pause stops movement use if unsure of how it is moving Return to the home position You can also select the source to move to a certain position on the track in millimeters The minimum step size is 0 1 mm 2 2 Finding the Isocenter of a Sample The isocenter of the sample is the where all the beams intersect each other It is usually a region of interest Medical scanners have a predefined isocenter for the scan while you have to manually define the axis of rotation To define the isocenter of your sample 1 Choose objective with highest magnification at which the entire object is visible 2 Rotate a small angle away from position usually 10 20 3 Move in Z direction to place region of interest in center of screen 4 Rotate to the negative angle of the angle chosen in step 2 to make sure it
7. or to farthest can be used limit from sample by selecting the limit arrow icon under the respective tab for each E 4 Rotate sample to 90 5 Use the joystick or motion controller buttons to move the sample in XYZ directions to the center and zoom in on the monitor 6 Rotate back to 0 and then move the sample in Z direction 7 Close the door and turn on X ray Adjust the power and voltage according to sample being scanned 8 Defining the isocenter Details in Sec 2 2 9 Move the detector and source as close as possible to the sample 10 Select the gear icon select continuous mode example settings exposure time 1 sec binning 4 After make any necessary adjustments to the detector source or sample 11 Select the gear icon and select single mode typical settings exposure 20 60 seconds binning 1 12 Click the disk icon to save image acquired 2 4 Acquisition of Tomographic Projections This section will be used the most by the majority of micro CT users 2 4 ACQUISITION OF TOMOGRAPHIC PROJECTIONS This section will be used the most by the majority of micro CT users 1 Mount prepared sample inside scanner using three point mount 2 Position sample in correct XYZ location With the door open move the sample in the XYZ directions until it is positioned in the X ray beam line 3 Verify the sample will not hit the source or detector during rotation Move the source and detector
8. ox Figure 5 Main breaker 1 3 PREPARING YOUR SAMPLE The sample will be fitted in a sample holder and then placed on a platform within the scanner Figure 6 There are multiple sample holders for different types of samples You may find them in a cabinet directly to the right of the micro CT system Your sample needs to be stable During acquisition the sample is rotated There should not be morphological change of the sample or there is risk of image distortion such as ring artifacts Biological samples are prone to this e g an organ or limb shifting due to gravity Use wax foam or padding to immobilize it Figure 6 Sample holder Another type of image distortion that can occur is beam hardening This can occur if the sample contains or is near metal This occurs since the metal is too dense and reflects the beams Part 2 TXM CONTROLLER 2 1 Starting up When starting TXM Controller an error message will appear asking to recalibrate the axis Select yes and wait for it to finish the process If everything is good a dialog box will appear and all messages will appear in a blue font If there are any problems messages appear in red font If this occurs contact the coordinator There are several icons located at the top of the window abe EA BO de Figure 7 Icon Toolbar The main ones being uses will be the following y Displays available XRM and TXRM files available to open Saves a file onto t
9. to the positions needed Make sure that source or detector wont collide with the sample in a full 90 rotation 4 Close the enclosure door signal tower yellow light on 5 Activate the X ray source Sec 2 1 6 Begin Acquisition example settings Exposure 1 second binning 4x4 Sec 2 1 Move the sample to the desired position in the X and Y directions Sec 2 2 7 Position sample in rotation axis in Z beam line direction Sec 2 3 8 Select the gear icon select Tomography mode Sec 2 1 and set exposure time binning and readout time Typically 60 seconds 1x1 and fast Set starting angle end angle and number of images to be acquired Typically 90 90 and 721 9 Begin acquisition There is a prompt to choose a filename and location for the acquisition file Name the file according to the naming convention This naming convention is for the folder only 10 The status of the acquisition will be updated with how many hours the scan will take and the memory required After a scan begins it will take several hours to complete The X ray will shut off automatically For storing images the naming convention for folders is PI Name_YYYY_MM_DD Initials Example For Mr John Smith working on a project under Dr Bob Prado on June 23 2009 the folder name will be Prado 2009 06 23 JS Part 3 TXM Reconstructor Use the TXM Reconstructor program to assemble your images into a usable format There are
10. various ways to adjust your images for better quality One way is final center shift if your scan is off axis and this will shift the scans Correction to the beam line can also be made if needed Reconstruction time will vary based on number of projections and settings used TXM 3D Viewer can be used to view the volume and cross sectioned slices If the scanned sample was weak absorbing object use phase contrast in reconstruction Phase contrast relies on the refractive properties of the object 3 1 Doing a 3D reconstruction 1 Launch TXM Reconstructor and open the desired tomography data set Output File Name Eha O Z Shift fin um Do 2 Select the Reconstruction Icon to start Z Dimension fn un ET J apes reconstruction M omus UCHR oa 3 Find the rotation center if needed by clicking on the rotation center icon in the tool bar D Figure 16 Reconstruction settings 4 Click on the reconstruction settings icon in window the toolbar a Figure 16 5 Select a file name and path to store the 3D volume in the Output File Name box 6 Click the PreProcess button to perform the preprocessing before starting the reconstruction 7 Select the OK button to begin the reconstruction 8 The program will now reconstruct the data set into a 3D volume data set 9 When the reconstruction is finished a completion message will be displayed with the amount of time required to complete the reconstruction
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