Find Tilt Axis Offset

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Name	Find Tilt Axis Offset
Permalink	https://serialemscripts.nexperion.net/script/8
Category	Calibrations
Language	SerialEM Scripting
Description	Finds an optimised value for the TiltAxisOffset property (the lateral displacement between optical axis and tilt axis of the stage). The script measures the offset averaging $Samples values, then image shifts to the new values, measures again, until the change is below $ThresholdOffset.
Author	Guenter Resch

Version History

Version 1.0 (April 08, 2017; 815 download(s); SerialEM version ≥ 3.6)

Version 1.0

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Upload date	April 08, 2017
Download count	815
SerialEM version ≥	3.6

# (C) Nexperion e.U. - Solutions for Electron Microscopy 2017
# https://www.nexperion.net
# Last update April 8, 2017
# Requires SerialEM >= 3.6.0

ScriptName FindTiltAxisOffset
SuppressReports

# Parameters
Samples = 3
ThresholdOffset = 0.15

Success = 0

Pause Activate "Center image shift on tilt axis" in the "Image Alignment & Focus" panel and make sure the sample is close to eucentric height.
SetProperty TiltAxisOffset 0.0
AverageAxisOffset = 0.0
echo
echo Starting at 0.0 um offset ($Samples measurements per position) ...

Loop 10
   j = 0
   Loop $Samples
      Eucentricity 2
      ReportLastAxisOffset 
      j = $j + $ReportedValue1
   EndLoop 
   DeltaAxisOffset = ( $j / $Samples )  - $AverageAxisOffset 
   AverageAxisOffset = ( $j / $Samples )
   if ( ABS ( $DeltaAxisOffset ) <= $ThresholdOffset ) 
      Success = 1
      echo Stopping at $DeltaAxisOffset um change
      break
   endif
   echo
   echo Continuing at $AverageAxisOffset um offset (last change $DeltaAxisOffset um) ...
   SetProperty TiltAxisOffset $AverageAxisOffset
EndLoop

if ( $Success == 1 )
   echo Use "TiltAxisOffset $AverageAxisOffset" in your properties file
 elseif
   echo The routine did not get below $ThresholdOffset um
endif
FlashDisplay 4 0.15

License

This code can be shared and adapted under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) License (https://creativecommons.org/licenses/by-nc-sa/4.0/)