Using image shift matrix calibration to refine image shift scale in jeol.cfg on the scope controlling Leginon installation.¶

The image shift matrix is affected by the IMAGE_SHIFT_SCALE in jeol.cfg. Our initial jeol.cfg scale is rough. Therefore, the first round of image shift matrix calibration will likely fail the default 12% tolerance. We will have to perform iteration of scale adjustment in jeol.cfg and image shift matrix calibration until the values are right.

Note that this procedure relies on correct pixel sizes. Make sure the low magnification range is well calibrated before this calibration/refinement.

Follow Image Shift matrix calibration at each magnification with the following change:¶

1. Leginon/Matrix/Matrix Settings> Reduce the calibration shift percentage to ~ 10 % so that the beam does not move away.
2. Leginon/Matrix/Matrix Settings> Increase the calibration tolerance as this is likely failed due to rough value in jeol.cfg SCALE values. 50 % is quite likely the value you need instead of the 12 % set in the default.

   Examine the log message from a successful calibration. Each axis will have an output like this:

Pixel size error: xx.xx% (pre pixel xxxxxx)
Or config scale multiplication = 1.50

Multiple the corresponding IMAGE_SHIFT_SCALE_axis in jeol.cfg by the value.

Close Leginon and Leginon Client and then restart them so that jeol.cfg is reloaded at the scope.¶

Repeat the calibration in Matrix node. The multiplication factor should be much closer.¶

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