Editing Scanco User Instructions (section)

===µCT Tomography===
The µCT-Tomography program is used to perform a scan. 

NOTE: Only Authorized Operators are permitted to use uCT or XtremeCT scanners.  For the XtremeCT scanners, this is a formal process.  To inquire about authorization, speak to your supervisor.  The below description is intended to provide general understanding of how scans are acquired.  It is not a substitute for complete training.

To start the program type <code>$ uct_measurement</code> in a DEC terminal on the scanner computer (remote access does not allow this functionality), or use the scanner button. If you use the button, you must specify an operator prior to using the program.

[[File:Xtremect_button_scan.jpg|40px]]
[[File:Uct_measurement_uct35.jpg|40px]]
[[File:Uct_measurement_vivact40.jpg|40px]]
[[File:VivaCT80_scan.jpg|40px]]

[[File:Uct_tomography_pic00.jpg|600px]]


#'''Select Sample'''
#*When the µCT-Tomography program is first started, you will be prompted to enter the sample name or number of the specimen you are about to scan. 
#*If you have not registered your sample, press "Cancel" to close the select sample box, then press "New..." in the measurement sample box to register a new sample (see [[Scanco_User_Instructions#.C2.B5CT_Samples|'''µCT-Samples''']]). 
#*Once you have entered your sample information, the measurement sample box will show details for that sample, including the sample name and scan (measurement) history.
#:[[File:Uct_tomography_pic01.jpg|400px]]
#*After your first scan you will need to press the "Other..." button to open the sample selection box and find your next sample. 
#'''Select a Controlfile'''
#*The controlfile contains scan parameters such as the x-ray energy, current, and more (see [[Scanco_User_Instructions#Scan_Parameters_.28Controlfiles.29 controlfiles |'''Controlfiles''']]). 
#*Once the controlfile is setup, you need only to select it. If there are many controlfiles, you may want to search for yours using the file filter by entering part of the name or number in the white box and pressing enter; if you do this, you still must click on the controlfile so that it is highlighted in black as shown below.
#:[[File:Uct_tomography_pic02.jpg|400px]]
#'''Precalibrate''' 
#*Calibrations are done before loading your patient/animal and scanning for quality control and to reduce the time the patient/animal is under preparation/anaesthesia. Start the calibration by pressing the  "Precalibrate" button.
#:[[File:Uct_tomography_pic03.jpg|400px]]
#*Press "Start Calibration". The calibration will start with an "X-Ray Warmup", followed by "Measuring Dark" and "Measuring I0" and usually takes about 2-3 minutes to complete.
#:[[File:Precalibrate.jpg|300px]]
#*The precalibration is good for 15~20 min.  The time remaining is shown on the "Precalibrate" button.
#:[[File:Uct_tomography_pic5.jpg|400px]]
#*The precalibrate option cannot be used with batch measurements, and it's not available for MicroCT35 which is not intended for invivo/live scan.
#'''Load and Position the Patient/Sample'''
#*Instruct the patient to remove any jewelry in the scan areas (wrist/ankle/knee/elbow ect). With the patient seated, put the wrist/ankle/knee/elbow into the appropriate cast. Different pads with different sizes can be used to fit the patient.
#*For invivo/invitro samples, prepare your sample in terms of orientation, immobilization, hydration ect.
#*After the precalibration is complete, you can now open the bore cover and insert the patient's wrist/ankle/knee/elbow or sample into the scanner. Gently move the wrist/ankle/knee/elbow or sample into the scanner until you can snap in the cast at the gantry. Check that the cast is positioned correctly and the patient/sample is comfortable. 
#*Close the bore cover.
#'''Scout-View'''
#*A scout-view is similar to a 2D x-ray image and allows the user to set where to start and stop the scan. 
#*After loading your sample, press the "Scout-View..." button to bring up the scout-view window. 
#*The start position (top of the scanner) and end position (bottom of the scanner) can be modified to zoom in on the region of interest. 
#*The angle of the scout view can also be changed to see the object in a different orientation. 
#*Once pressed the "Scout-View" button but the scout view is found not in an appropriate position, press "Cancel", modify the start position, end position, or angle and press "Scout-View" again. 
#:[[File:Scout_view_window.jpg|400px]]
#*Scout view image is displayed in the top right hand corner of the program and will start by showing the right half of the image, followed by the left half of the image.
#'''Set Reference Line and Launch a Scan'''
#*A reference line (solid green line) is placed to set the scan region (green block). 
#*Press the "Reference-Line" button to show the reference line and default scan region over the scout view. 
#*To change the number of slices to scan, move the reference line to the top of the scan region, then hold down the shift button while dragging the mouse to extend the scan region and press the left mouse button to set the reference line. 
#*To centre the scan region between two reference lines, move the reference line to the top of the scan region, then hold down the alt key while dragging the mouse until the second green reference line is in place, then press the left mouse button to set while still holding down the alt key!
#:[[File:Uct_tomography_pic06.jpg|700px]]
#*For a single scan, select "OK", "Scan" and "Start Measurement". Record measurement number on your [[Scanco_User_Instructions#Log_Sheets |'''log sheet''']].
#*For a batch scan which is only available on microCTs, select "Batch Measurement" and record the measurement number on your [[Scanco_User_Instructions#Log_Sheets |'''log sheet''']]. You may now setup a new scan (select new sample and controlfile, perform scout, etc). When you have finished setting up all scans, press "Start Batch Scans."  (See [[Scanco_User_Instructions&action=edit&section=48#Perform_Batch_Scans|'''Perform Batch Scans''']] for detailed instructions)
#'''Cancel or Reposition a Scan'''
#*If you need to interrupt a scan, press the cancel button and restart the scan or if you do not want to rescan then "unload" the scanner.  
#*If you have not started a scan and need to reposition the patient, you also must "unload" the scanner.
#'''Remove Patient/Sample from Scanner'''
#*After the scanning is complete, open the bore cover and slide the patient's wrist/ankle/knee/elbow or sample out of the scanner. Release the cast by pushing down the cast release handle.


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