Make Grid Alas JEOL CryoARM300

Edit Delete

Details

Name	Make Grid Alas JEOL CryoARM300
Permalink	https://serialemscripts.nexperion.net/script/62
Category	High-Level Functions
Language	SerialEM Scripting
Description	Script for automated grid atlas collection
Author	Marcus Fislage
Literature reference	https://journals.iucr.org/m/issues/2020/04/00/pw5013/index.html
Website link	http://www.becm.be

Version History

Version 2

Download

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

Upload date	November 26, 2020
Download count	270
SerialEM version ≥	3.8

MacroName MakeGridAtlas
###################################
#
# Script to collect a grid atlas
#
# M.Fislage & R. Efremov Nov 2020
#   
# STATUS: functional
#
###################################

# Make a 50x LowMag Grid Atlas of a grid already in the microscope
# SerialEM needs to be in MSD mode before calling the script

# Ensure that tanks are not refilling
CallFunction MyFunctions::WaitForRefillingJ

#Controls if a navigator file is open
ReportIfNavOpen 
if $reportedValue1 == 0
   OKBox You need to have a navigator file open. Program will close.
   Exit
endif

#Prepare LowMagMode
GoToLowDoseArea R
RemoveAperture 0
SetLowDoseMode 0
Delay 2 sec
SetBeamBlank 1
SetMag 50
SetPercentC2 100
SetEucentricFocus 
SetSlitIn 0
ScreenUp

#defines directory for new GridMap based on a K3 detector
UserSetDirectory
OpenNewMontage 7 12 Atlas
SetMontageParams 1 950 950 2748 2024 0 2

#Performs Montage
MoveStageTo 0 0 
SetColumnOrGunValve 1
SetBeamBlank 0
M
NewMap

#Return to LowDoseMode
SetLowDoseMode 1
GoToLowDoseArea R
ReInsertAperture 0
CloseFile 
SaveNavigator

Required Scripts

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

Functions for JEOL CryoARM300

Documentation

Before starting you have to load one old atlas file in which you have already once defined the map parameters.
Open a new navigator file
Have a cartridge loaded on the stage
Run this script

Requires Function script

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/)