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Relevant buttons in MicroCT program interface are  marked in Figure 9. 

1. Recording or changing operator data  
2. Recording or changing sample data
3. Perform measurements
4. Evaluate measurements through slicewise evaluation, image documentation, 2D- and 3D histomorphometry. 
5. 3D display and documentation
6. Data management through moving data to/from optical disk or tape, deleting data, backing up a copy of the hard disk, and format optical disks, tapes, and diskettes. 
7. Exit the program

2.1: Control file Window

Figure 10 shows the control file window as it appears when setting up a scan protocol. 

1. Control file name – Enter a meaningful name describing the protocol 
2 – 5. Please reference Section 2.2.
6. Choose Energy and Current Settings – Most biological samples will use low power and energy since they are relatively easy to pierce with an X-ray (e.g. 50 kV, 160 µA).
7. Resolution – There are 3 modes of the resolution option but most of the time "standard" will be chosen. 
8. Diameter of the Animal Bed – The number indicated is the size of the reconstruction area that is slightly larger than the animal bed. 
9. Number of Slices – Choose the number of slices desired. (e.g. 40 slices)
10. Increment Range –the range in mm calculated automatically by using number of slices and diameter.
11. Slice Increment – Step size between each slice (automatically calculated).
12. Isotropic Option – This required to be enabled for MicroCT 40. 
13. Relative Position to Scout View – Reference line (see step 2) or the default position 0 mm if Scout disabled. 
14. Integration Time – How long X-rays will be received. For standard measurements, choose value between 100 and 200 ms. Longer integration time will yield better 3D- displays.  The reconstruction time is not affected, but the measurement time is.
If you have set up your measurement protocol, you have to test it before you can use or save it by clicking on the TEST button. If this is successful, the buttons OK, SAVE AS NEW and SAVE are now clickable. The modified protocol can be used for the next measurement only by clicking on OK. It can also be saved by clicking on SAVE and the clicking on OK to return to the main screen.
2.2: Scout View
Figure 11 shows the scout view window. Scout view is used to determine the measurement area and is a single projection of the sample. When scout view is being used, a reference line can be set determining the first slice and final slice of scan.  

When the ‘scout view’ button is selected, Figure 12 will appear. Using this window, you can adjust the start and end positions for the scout view to cover. You can also set the reference line as needed. In general the smaller range of values the better. To see scout view, simply click the scout view button.
Once the scan has been loaded, select the reference line button and position it on the image as needed. The top line will follow the cursor on the screen. To move the bottom line, press the shift key and adjust it as needed. When the mouse button is clicked, the line is set. 
Make the reference lines as tight as possible. Number of slices being taken is also displayed. More slices will result in longer scan and reconstruction time. The smallest scan slice possible is 105. 256 scout view lines are performed at maximum. If a small scout area is chosen, the increment can be chosen smaller and resolution is improved.
The scout view is automatically saved and shown for other images of the same sample. If you would like to print the scout view, select the print scout button. It can be printed to the printer or to a TIFF file for exporting. 
Several scans can be acquired at once through a batch measurement. You can place multiple reference lines into the batch queue after defining each. Each will be scanned sequentially when the previous scan is finished. 
After selecting the scan button, a window will appear and the scan will begin when the start measurement button is selected.

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Figure 9: MicroCT program interface

Figure 10: Control file window

Figure 11: Scout view image

Figure 12: Scout view distance window