Stanford University
Department of Neurobiology
Department of
Structural Biology

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This Human Brain Project/Neuroinformatics research is funded by the
National Institute of Mental Health

Laboratory of U.J. McMahan

Department of Neurobiology

Department of Structural Biology

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Dual axis rotation calculator

(For Windows: If the calculator is not visible, right click the restriction bar and allow content)


Described for FEI Compustage

1. Insert Grid, center it and set eucentric height.
2. Locate two easily recognizable reference points (Reference point 1: and Reference point 2:). Store these x,y coordinates in FEI's Stage position window. Enter these coordinates in the Dual Axis Calibrator windows.
3. Find your original Target(s) coordinates and save them in the Stage position window. Take a lower magnification image of target(s) for reference after rotation to identify the areas of interest precisely.
4. Take the first data set(s).
5. Rotate the grid (remember which direction), insert, center, and set eucentric height.
6. Locate the two orginal reference points from step 2 and enter their new respective coordinates in the Dual Axis Calibrator as New refeerence point 1 and New reference point 2.
7.Select Calculate button to determine the sample's rotation angle. Copy to Clculator.
8. Enter the coordinates for the original target(s) and select Calculate Target. The new coordfinates will appear in the Predicted target window. Enter those coordinates into the Stage>Set, tab as well as the eucentric height and select Go To to move the stage to the Predicted target position.
9. In the Dual Axis Calculator window, enter the original Target(s) point(s). Locate either one of the two original Reference Points (1 or 2) and enter those x,y coordinates in Reference point. Locate the new, rotated position of the Reference point you entered and select Calculate. The Predicted target point coordinates will appear in the coordinates windows. Enter those coordinates in the Stage positioning window and automatically go to that position. If necessary, refer to the low magnification image taken in step 3


Calculator Designed by Robert Marshall
Developed by Xuchen Zhang
EM3D © 2003-2007 Board of Trustees of Leland Stanford Junior University -- Last modified: 6/9/08-- Web Design by Cornelia Koch-Stoschek