Intensity Zero

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Name	Intensity Zero
Permalink	https://serialemscripts.nexperion.net/script/67
Category	Single Particle
Language	SerialEM Scripting
Description	Determines the intensity at any give navigator item based on the active image in buffer A. Intended to be used on empty hole in Search mode to estimate the reference intensity (REFINT) for "Measure Sample Thickness (ALS)"
Author	Jan Rheinberger

Version History

Version 1.0 (November 27, 2020; 299 download(s); SerialEM version ≥ 3.9)

Version 1.0

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Upload date	November 27, 2020
Download count	299
SerialEM version ≥	3.9

# Optimized data acquisition workflow by sample thickness determination
# Rheinberger, Oostergetel, Resch, and Paulino, submitted for publication
# (C) Nexperion e.U. - Solutions for Electron Microscopy, 2020
# https://www.nexperion.net
# Requires SerialEM >= 3.9.0
# Last update November 20, 2020

ScriptName HFIT-IntensityZero

SubareaRadius = 8

# Get image coordinates for each point, exclude points in the very periphery that CircularSubareaMean can not be run on
MinX = $SubareaRadius
MinY = $SubareaRadius
ImageProperties A
MaxX = ($ReportedValue1 - $SubareaRadius - 1)
MaxY = ($ReportedValue2 - $SubareaRadius - 1)

ReportItemImageCoords
If ( ( $ReportedValue3 == 1 ) AND ( $ReportedValue1 >= $MinX ) AND ( $ReportedValue2 >= $MinY ) AND ( $ReportedValue1 <= $MaxX ) AND ( $ReportedValue2 <= $MaxY ) )
   ImageX = $ReportedValue1
   ImageY = $ReportedValue2
EndIf

# Getting intensities from unfiltered image, invalid coordinates will be detected by CircularSubareaMean
echo Getting intensites from unfiltered image ...

CircularSubareaMean $ImageX $ImageY $SubareaRadius MeanUnfiltered

echo $MeanUnfiltered

Related Scripts

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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/)