SPA multiple images Test Radius

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Details

Name	SPA multiple images Test Radius
Permalink	https://serialemscripts.nexperion.net/script/24
Category	Single Particle
Language	SerialEM Scripting
Description	Center a hole and shoot some Preview images around the hole edge to tweak the radius for image shift.
Author	Wim Hagen

Version History

Version 1.0 (June 01, 2017; 723 download(s); SerialEM version ≥ (untested))

Version 1.0

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Upload date	June 01, 2017
Download count	723
SerialEM version ≥	(untested)

MacroName SPAK2fastTestRadius
# Workout radius for multiple images in hole
# Buffer P is expected to have refference hole image from Low Dose View
# Macro takes Preview images around the hole edge to work out radius
# Watch for hole edges and adjust radius
# Wim Hagen, EMBL Heidelberg 20170309
# Credits to Chen Xu & Henning Stahlberg group

maxholeshift        = 100        # max beam/image shift after hole centering in nanometers
NumberShots      = 6	        # Number of shots in one hole
IS_RAD 	            = 0.75      # Radius in micrometer of off-center ImageShift displacement

####### Align to hole #######

Echo ===> Running align to hole ...

V
AlignTo P
ReportAlignShift
Echo hole shift 1 $RepVal5 $RepVal6
holeshift = sqrt $RepVal5 * $RepVal5 + $RepVal6 * $RepVal6

if $holeshift > $maxholeshift
   ResetImageShift
   V
   AlignTo P
   ReportAlignShift
   Echo hole shift 2 $RepVal5 $RepVal6
endif

####### Acquire images #######

GoToLowDoseArea R
ReportImageShift
isux = $RepVal1
isuy = $RepVal2

Loop $NumberShots icount
   IS_ANGLE = ( $icount - 1 ) * 360 / $NumberShots
   IS_X = $IS_RAD * sin ( $IS_ANGLE )
   IS_Y = $IS_RAD * cos ( $IS_ANGLE )
   ImageShiftByMicrons $IS_X $IS_Y
   Delay 1 sec
   L
   SetImageShift  $isux $isuy
endloop

ResetImageShift

Echo ===> Done ...
Echo ====================================================

Related Scripts

The following scripts provide a similar or related functionality, but are not required to run this script:

test hole centering

Documentation

Setup Low Dose.
Buffer P should have a Low Dose View hole image.
Go to a hole.
Run macro.
Tweak Radius as needed.

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/)