Beam Intensity Calibration Test

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Details

Name	Beam Intensity Calibration Test
Permalink	https://serialemscripts.nexperion.net/script/20
Category	Testing
Language	SerialEM Scripting
Description	Tests the beam intensity calibration at a given spot size, walking from high intensities to low intensities comparing set vs. actual values
Author	Guenter Resch
Website link	https://www.nexperion.net

Version History

Version 1.0.1

Download

Upload date	May 02, 2017
Download count	827
SerialEM version ≥	3.6

# (C) Nexperion e.U. - Solutions for Electron Microscopy 2016 - 2017
# https://www.nexperion.net
# Last update March 15, 2017
# Requires SerialEM >= 3.6.0

ScriptName BeamIntCalTest
SuppressReports 
echo
echo SerialEM beam intensity calibration test script 
echo (C) Nexperion e.U. - Solutions for Electron Microscopy 2016 - 2017

# Settings
BeamIntensityTolerance = .1
MinimumIntensity = 10

Pause Center beam, set up an intense illumination filling the whole field of view and with a valid beam intensity calibration (spot size highlighted in blue). The "Record" parameter set has to be set up not to oversaturate, the condition to stop scripts at low counts has to be switched off (Script > Controls).

# Read current settings
ReportSpotSize 
SpotSize = $ReportedValue1
ReportProbeMode
if ( $ReportedValue1 == 0 )
   ProbeModeText = nP
 else
   ProbeModeText = uP
endif

echo 
echo Testing beam intensity calibration for spot size $SpotSize $ProbeModeText ...
ReportPercentC2
SavePercentC2 = $ReportedValue1
Record
ReportMeanCounts 
NewIntensityForMean = $ReportedValue1
Loop 100
   NewIntensityForMean = ( $NewIntensityForMean * 0.57 )
   if ( $NewIntensityForMean < $MinimumIntensity )
      echo Ending at $NewIntensityForMean counts.
      Break
   endif
   ReportPercentC2 
   PreSetPercentC2 = $ReportedValue1
   SetIntensityForMean $NewIntensityForMean
   ReportPercentC2 
   # Catch "Warning: attempting to set beam strength beyond calibrated range"
   if ( $ReportedValue1 == $PreSetPercentC2 ) 
      echo Quitting at $NewIntensityForMean counts (target counts were not applied) ...
      Break 
   Endif
   Record
   ReportMeanCounts 
   MeanRelTar = $ReportedValue1 / $NewIntensityForMean
   if ( $MeanRelTar > ( 1 - $BeamIntensityTolerance) ) and ( $MeanRelTar < ( 1 + $BeamIntensityTolerance) )
      echo > Beam intensity calibration test OK ($MeanRelTar of target)
    else
      echo > Beam intensity calibration test FAILED ($MeanRelTar of target)
   EndIf
EndLoop

# Restore Illumination
SetPercentC2 $SavePercentC2
Record
CenterBeamFromImage

echo 
FlashDisplay 4 0.15
echo Done,

Documentation

TODO

Check how JEOL/Hitachi microscopes deal with ReportProbeMode

History

Version 1.0.1 uses Windows line endings instead of Linux line endings

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/)