LD - SerialEM Script Repository

LD

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Details

Name	LD
Permalink	https://serialemscripts.nexperion.net/script/17
Category	Single Particle
Language	SerialEM Scripting
Description	main macro for single particle data collection in Low Dose Mode
Author	Henning Stahlberg

Version History

Version 1.0 (February 24, 2017; 771 download(s); SerialEM version ≥ 3.7)

Version 1.0

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This script requires additional scripts to be run – please refer to the Required Scripts section below.

Upload date	February 24, 2017
Download count	771
SerialEM version ≥	3.7

####################################################################
# main macro for single particle data collection in Low Dose Mode
####################################################################
#
# Daniel Caujolle-Bert, Henning Stahlberg, C-CINA, Biozentrum, University of Basel
# Feb. 25, 2017
#
# Based on a cocept by Chen Xu
# http://www.bio.brandeis.edu/KeckWeb/emdoc/en_US.ISO8859-1/articles/SerialEM-howto:macro-explain/x248.html
#
MacroName LD

Echo ===================== Starting LD Macro ================================
ReportClock
ticks = $repVal1

Call Parameters

# Echo ---> Checking, if refilling 
Call CheckDewarAutofill

Call CINACronJob

##ReportNavItem
##ReportNumNavAcquire

## position (X,Y)
RealignToNavItem 1
# Do it more precise still:
# Copy A P
# Call AlignToP

## Drift control
# Call Drift

# Take care of focussing
Call CINAAutoFocus

EarlyReturnNextShot $DisplayReturn

# Goto REcord Mode
GoToLowDoseArea R

# Number of shots in one hole is $NumberShots
# Radius of off-center ImageShift displacement is $IS_RAD

if $NumberShots == 1
   Delay 7
   R
 else
   Loop $NumberShots icount
      IS_ANGLE = ( $icount - 1 ) * 360 / $NumberShots
      IS_X = $IS_RAD * sin ( $IS_ANGLE )
      IS_Y = $IS_RAD * cos ( $IS_ANGLE )
      Echo Taking image at angle $IS_ANGLE : X = $IS_X , Y = $IS_Y
      ImageShiftByMicrons $IS_X $IS_Y
      Delay 5
      R
   endloop
   ImageShiftByMicrons 0 0 
   if $NumberShots > 6
      Delay 5
      R
   endif
endif

ReportClock
eticks = ($repVal1 - $ticks)
Echo ===> Leaving LD Macro (took $eticks s).
Echo .

Required Scripts

The following scripts are required to run this script, either because the are called directly or they provide functions:

Parameters

Related Scripts

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

Documentation

Based on a cocept by Chen Xu
http://www.bio.brandeis.edu/KeckWeb/emdoc/en_US.ISO8859-1/articles/SerialEM-howto:macro-explain/x248.html
#

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/)