ViewTomo_batch

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Name	ViewTomo_batch
Permalink	https://serialemscripts.nexperion.net/script/88
Category	Tomography
Language	SerialEM Scripting
Description	The script enables the collection of low magnification tilt series using View parameters as defined in the "Low Dose Control" menu. This version of the script can run as a single ViewTomo acquisition or be used in batch through the "Acquire at Items" dialogue.
Author	Robert Gebauer

Version History

Version 1.0 (April 21, 2026; 38 download(s); SerialEM version ≥ 4.2)

Version 1.0

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Upload date	April 21, 2026
Download count	38
SerialEM version ≥	4.2

# Name:		ViewTomo_batch
# Author:	Robert Gebauer
# Version:	1.0
# Last update:  19.03.2026
# Support:	gebauer-robert@protonmail.com

### Tilt series parameters

tiltStart	= 0
tiltRangePos	= 51
tiltRangeNeg	= 51
tiltStep	= 3

### Default settings

tiltLimit	= 68
tiltBacklash	= -1
wait		= 3

### Initialization

tiltNum = 0	
currentTiltAngle = 0
ReportStageXYZ
stageX = $ReportedValue1
stageY = $ReportedValue2
stageZ = $ReportedValue3
currentTiltAngle = $tiltStart

GoToLowDoseArea V

### Image acquisition at tiltStart

TiltTo $tiltStart
View
Save

### Image acquisition for positive tilt angles

tiltNum = $tiltRangePos / $tiltStep
loop $tiltNum indexP
   currentTiltAngle = $tiltStart + ( $tiltStep * $indexP )
   if $currentTiltAngle > ( $tiltStart + $tiltRangePos )
      break
    elseif $currentTiltAngle <= $tiltStart
      break
    elseif $currentTiltAngle > $tiltLimit
      break
   endif
   tiltTo $currentTiltAngle
   MoveStageTo $stageX $stageY $stageZ
   delay $wait sec
   View
   Save
endloop

### Image acquisition for negative tilt angles

currentTiltAngle = 0
tiltNum = $tiltRangeNeg / $tiltStep
loop $tiltNum indexR
   currentTiltAngle = $tiltStart - ( $tiltStep * $indexR )
   if $currentTiltAngle < ( $tiltStart - $tiltRangeNeg )
      break
    elseif ( $currentTiltAngle + $tiltLimit ) < 0
      break
    elseif $currentTiltAngle >= $tiltStart
      break
   endif
   tiltTo $currentTiltAngle
   tiltBy $tiltBacklash
   tiltTo $currentTiltAngle
   MoveStageTo $stageX $stageY $stageZ
   delay $wait sec
   View
   Save
endloop

### Finishing up

CloseFile
TiltTo 0

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/)