Editing Scanco User Instructions (section)

===µCT Evaluation Program===
The µCT Evaluation Program is used to evaluate a scan. To start the program type <code>$ uct_evaluation</code> in a DEC terminal, or use the graph button. If you use the button, you must specify an operator prior to using the program.

[[File:Uct_evaluation.jpg|40px]]


'''SCREEN SHOT TO BE ADDED SHORTLY'''



#'''Find Your Sample'''
#:Enter the first part of your sample name in the file filter box and press enter.  The samples are shown in the left hand box.  The measurement box on the right shows scans for the selected sample (highlighted in black).  Select a measurement and press "OK."
'''SCREEN SHOT TO BE ADDED SHORTLY'''
#'''Draw Contours (If Applicable)'''
#*Contours, or GOBJ files, are drawn to define regions of interest.  Depending on the analysis required, contours may be drawn to isolate the object from the sample tube or to separate bone compartments (e.g., cortical versus trabecular).  
#*Contours must always be drawn COUNTER-CLOCKWISE!!!   
#*[[Media:Contouring-tools.pdf |'''Contouring tools reference sheet''']]
#*For this sample, we are only interested in viewing the object in 3D and drew contours to isolate the bone and soft tissue from the sample tube.
#:[[File:Uct evaluation pic03.jpg|600px]]
#'''Evaluate'''
#*Scanco Medical provides several standard evaluation scripts. Open the 3D-Evaluation menu either using the "T..." button or from the top menu by going to "Tasks" and "Evaluation 3D...".  If you set a default evaluation script in your scanning controlfile, it will be listed under "Task/Evaluation."
#:[[File:Uct_evaluation_pic04.jpg|400px]]
#*If you want to run a different evaluation press "Select...", highlight the evaluation script of interest, and press "OK".
#:[[File:Uct_evaluation_pic05.jpg|400px]]
#*When the 3D-Evaluation window is activated, a white box will appear on your reconstructed image.  The white box is the region of interest that will be "cut out" of the full scan.  If you have drawn contours, the white box will automatically be adjusted to fit the contours.  Adjust the box if necessary by grabbing one of the white handles; use the left mouse button to move the box and the right mouse button to resize.  The box can also be resized using the "VOI Start" and "Dimensions" in the 3D-Evaluation window.
#*For most evaluation scripts, you will be required to specify parameters for a Gaussian filter, to reduce noise, and a threshold, to isolate your object (e.g., bone) from the background. Check that the parameters used provide a good representation of your scanned sample by flipping back and forth between the segmented and grayscale image using the "Preview" and "Grayscale" buttons.
#:[[File:Uct_evaluation_pic06.jpg|400px]]
#*When you are satisfied with the segmentation parameters, press "Start Evaluation", which will submit the job to the queue.


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