mf 3/05 (<dk, Greenberg lab)

Scanning:
Turn on computer.  (password is 'ct')
Be sure GE CMII is on and that the specimen cover is closed.

I.    During X-ray Tube Warmup (Red lights are on):
a.    Right-click eXplore icon in the task bar
    (OR Programs > GE Medical Systems > eXplore Utilities > eXplore Warmup)
    Click "<=3 minutes to scan".
    It will take ~6 minutes to ramp up to full power.  (Do NOT open specimen cover during this time).
b.  Anesthetize mouse during specimen during warmup.

II. Prepare For Scan:
a.  Evolver window will pop up when warmup has completed.  Click "Evolver"
b.  Choose "Scan New Subject" or "Add Scan to Existing Subject". 
    This is your project name and it will determine the name of the folder to which your scan data is added.
c.   For "Subject Name", put in a description, e.g. Date-mouse ID.
d.  Choose a protocol from drop down list in the Evolver window:  
    93μm_10R_10min for low resolution
    45μm_24R_18min for medium resolution  (This is a lethal dose of radiation?)                   
    See User Manual, Appendix A to design new protocols

III. Scan Mouse
a.  Click "Fluoro" to position mouse.  
    Open specimen cover and place anesthetized mouse onto sled.
    Secure with tape at the farther end and close the cover.
    Note: If this is the first scan of the project, be sure to tape the calibratiing square on the sled under the mouse. 
b.    Click "OK" to continue Fluoro.
    When image appears, select File > Position Stage.  
    Use "arrows" and "Apply" to manipulate the sled position.
    Click "OK" and close Fluoro window when desired position is obtained.
c.    Click "Start Scan" in Evolver window to begin scan.
    Click "OK" in pop-up when scanning is complete, then click "Quit"
d.    To scan next image, click the eXplore Evolver icon on the desktop.  Repeat from Step II above.

Reconstruction:
a.    Launch eXplore Reconstruction icon on desktop.
b.    Select the "Load Image" button and choose an image to reconstruct in D: eXplore data.
c.    Click "Correct' to perform image correction.
d.    Choose "Thumbnail" to set 5x5 pixel averaging.  
    Check "Mini Volume" box to name the thumbnail image 'Mini'.
    Click Start.
e.    The Microview window will ask if you would like to view the image.  Click 'yes'.
    Rotate image so all three planes are visible.
    Adjust brightness to until you can see where the 3 planes intersect.  
    Middle click and drag the planes to delimit one side of the mouse.
    Select Control+7 to define the 1st orthogonal corner.
    (The cursor must be somewhere on the image to selecting control+7)
    Find the opposite diagonal corner by scrolling the planes to the opposite side of the mouse.
    Select  Control+8 to define the 2nd orthogonal corner.
    (Type X if you need to clear the corner selections and start over.)
    Select "Save Crop Coordinates" under File menu.
    Close Microview window.
f.   If calibration is necessary then select Calibrate, Advanced > Reconstruction.
    In MicroView select "Bone".  Use "Calibration Tool" to define a small region of bone, as in step e, above.
    Repeat the process for H2O, and air.
g.    In the eXplore Reconstruction window, choose "Load Crop".
    Choose "Full Resolution" and uncheck "Mini Volume".
    Click "Start".  Name the file.  Reconstruction will begin.
    Note: To line up multiple reconstruction jobs, check "Queue" before choosing "Start".  Then choose "Start" under the eXplore Job Manager icon.  Reconstruction will now begin.

mf 2005