Check grid

Edit Delete

Details

Name	Check grid
Permalink	https://serialemscripts.nexperion.net/script/28
Category	Other Data Acquisition
Language	SerialEM Scripting
Description	Quick survey of TEM grid.
Author	Jason de la Cruz

Version History

Version 1.0 (June 30, 2017; 642 download(s); SerialEM version ≥ 3.7)

Version 1.0

Download

Upload date	June 30, 2017
Download count	642
SerialEM version ≥	3.7

ScriptName chkGrid
#20170629 chkGrid M. Jason de la Cruz

# Copyright (c) 2017, Howard Hughes Medical Institute
#
# License ISC: Internet Software Consortium license,
# http://opensource.org/licenses/ISC
#
# This is free software: you are free to change and redistribute it.
# There is NO WARRANTY, to the extent permitted by law.

# INSTRUCTIONS: Modify settings in section below.  Set "setIntensityCmd" to
#               either "SetIlluminatedArea" for FEI Titan series or 
#               "SetPercentC2" for all other microscopes.  Decide on condenser
#               beam illumination (aperture, spot size); enter desired spot
#               size below.  Then set "lowMag" to lowest mag with unobstructed
#               view of TEM grid (i.e., the mag you use for whole-grid atlas),
#               adjust intensity for optimum signal, center beam shift, then
#               record intensity value in "lowMagIntensity".
#               When ready to start, open file to save autodoc metadata (with
#               .mdoc or .idoc) then run the script.  Close the file when done.

# Please check that beam is centered in low mag before continuing.
# Ensure all checkboxes in "Script > Controls..." dialog are unchecked to avoid
# "low counts" errors.
#================================== SETTINGS ===================================
setIntensityCmd = SetPercentC2
spotSize = 10
lowMag = 120
lowMagIntensity = 102.345
#===============================================================================

echo ===> Running chkGrid ...
echo ===> Setting up scope
StopContinuous
SetExposure R 1
SetBinning R 1
SetContinuous R 0
ScreenUp
SetColumnOrGunValve 1
SetSpotSize $spotSize
reportspotsize
SetMag $lowMag
echo Waiting for lens stabilization
Delay 2 sec
SetPercentC2 $lowMagIntensity

echo ===> Imaging Quadrant 1
MoveStageTo 400 400 0
ReportStageXYZ
Delay 1 sec
R
Delay 1 sec
S
Delay 1 sec

echo ===> Imaging Quadrant 2
MoveStageTo 400 -400 0
ReportStageXYZ
Delay 1 sec
R
Delay 1 sec
S
Delay 1 sec

echo ===> Imaging Quadrant 3
MoveStageTo -400 -400 0
ReportStageXYZ
Delay 1 sec
R
Delay 1 sec
S
Delay 1 sec

echo ===> Imaging Quadrant 4
MoveStageTo -400 400 0
ReportStageXYZ
Delay 1 sec
R
Delay 1 sec
S
Delay 1 sec

echo ===> Imaging Center
MoveStageTo 0 0 0
ReportStageXYZ
Delay 1 sec
R
Delay 1 sec
S
Delay 1 sec

echo ===> Scope standby
SetColumnOrGunValve 0

Documentation

Modify settings in section below. Set "setIntensityCmd" to either "SetIlluminatedArea" for FEI Titan series or "SetPercentC2" for all other microscopes. Decide on condenser beam illumination (aperture, spot size); enter desired spot size in settings section. Then set "lowMag" to lowest mag with unobstructed view of TEM grid (i.e., the mag you use for whole-grid atlas), adjust intensity for optimum signal, center beam shift, then record intensity value in "lowMagIntensity".

When ready to start, open file to save autodoc metadata (with .mdoc or .idoc) then run the script. Close the file when done.

Please check that beam is centered in low mag before continuing.
Ensure all checkboxes in "Script > Controls..." dialog are unchecked to avoid "low counts" errors.

License

Copyright (c) 2017, Howard Hughes Medical Institute. License ISC: Internet Software Consortium license, http://opensource.org/licenses/ISC. This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law.