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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. 

Figure 7: Icon toolbar
The main ones being used will be the following:

  • The voltage and power can be adjusted as needed based on the material or object being imaged (Figure 8).

  • Clicking apply will turn the X-ray source on. If you make any adjustments to these settings, you must click apply again.

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 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’ the sample and produce a 3D image that can be manipulated later.

There are three tabs for the motion controller (Figure 9). This moves the detector, source, and sample during the course of taking an acquisition.

To manipulate the sample into the path of the source, use the joystick to move the sample or motion controller buttons (Figure 9). There are three degrees of spatial freedom for moving the sample in the XYZ directions. The angle Ø will rotate the sample. To move the stage up, you must go in the negative Y direction. For further axis orientation, see Figure 10.


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.

1. Choose objective with highest magnification at which the entire object is visible.

2. Rotate a small angle away from position, usually 10-20º.

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 is still in the screen. If not, then adjust Z direction accordingly.

5. Repeat rotations until able to rotate to +/-90º 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 11.

8. Rotate to +90º and place new line on UA (Figure 12).

9. Move sample Z direction until halfway between two lines (Figure 13).

10. Remark UA and rotate back to -90º 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 14).


1. Load Sample and launch TXM Controller

2. Adjust optical objective to desired magnification by selecting Microscope then Configure systems on the menu and select OK.

3. Move source and detector to farthest limit from sample by selecting the limit arrow icon under the respective  tab for each.

4. Rotate sample to -90º.

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 0º 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. 

  • Note: It is important to get the detector as close as possible to the sample. Be sure to view with the interior camera. IF YOU ARE NOT CAREFUL YOU MAY CRASH THE SCANNER!!!

  • Move the detector back, change the objective, and then move to the previous position. Pausing or stopping all motors can be used.


***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 to the positions needed. Make sure that source or detector won’t collide with the sample in a full +/- 90º 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.


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

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Figure 8: X-ray Source window

Figure 9: Motion controller window

Figure 10: Axis orientation

Figure 11: Drawing the initial line at the unique aspect (UA)

Figure 12: Post-90º rotation, draw new line at UA

Figure 13: Move UA in Z direction halfway between the two lines

Figure 14: Final position of object, the two lines appear as one