Prepare gridsquare (set eucentric height)

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Name	Prepare gridsquare (set eucentric height)
Permalink	https://serialemscripts.nexperion.net/script/27
Category	Other Data Acquisition
Language	SerialEM Scripting
Description	Operating on points saved in the Navigator, this script automatically sets the eucentric height of each gridsquare by using the Rough Eucentricity routine in SerialEM at two different magnifications.
Author	Jason de la Cruz

Version History

Version 1.0 (June 30, 2017; 460 download(s); SerialEM version ≥ 3.7)

Version 1.0

Download

Upload date	June 30, 2017
Download count	460
SerialEM version ≥	3.7

ScriptName prepSq
#20170629 prepSq 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 "highMag" to a mag that maximizes area
#               of single gridsquare on detector.  Adjust intensity for
#               optimum signal, center beam shift, then record intensity value
#               in "highMagIntensity".
#               Then drop the mag to lowest mag with unobstructed view of TEM
#               grid (i.e., the mag you use for whole-grid atlas), center beam
#               shift, adjust intensity, and enter appropriate values in
#               "lowMag" and "lowMagIntensity".
#               Open Navigator and collect whole-grid atlas.  Add a point at
#               the center of each gridsquare you wish to set at eucentric
#               height.
#               If necessary, go to each XY coordinate to center the point in
#               "highMag" using the Navigator "Move Item" button.  For those
#               points you want to run the script on, set to "Acquire".
#               When ready to start, open file to save autodoc metadata (with
#               .mdoc or .idoc).  Run the script using the SerialEM menu option
#               "Navigator > Acquire at Points".  Close the file when done.

# Please check that beam is centered in both low and high mags 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
highMag = 550
highMagIntensity = 55.965
#===============================================================================

echo ===> Running prepSq ...
echo ===> Setting up scope
ScreenUp
SetColumnOrGunValve 1
SetExposure R 1
SetBinning R 1
SetContinuous R 0

ReportNavItem

echo ===> Doing rough eucentricity
SetSpotSize $spotSize
reportspotsize
SetMag $lowMag
echo Waiting for lens stabilzation
Delay 2 sec
$setIntensityCmd $lowMagIntensity
Eucentricity 1
UpdateItemZ
Delay 1 sec
R
Delay 1 sec
S
Delay 1 sec

echo ===> Refining eucentricity
SetSpotSize $spotSize
reportspotsize
SetMag $highMag
echo Waiting for lens stabilization
Delay 2 sec
$setIntensityCmd $highmagIntensity
Eucentricity 1
UpdateItemZ
Delay 1 sec
R
Delay 1 sec
S
Delay 1 sec

RestoreCameraSet

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 the settings section. Then set "highMag" to a mag that maximizes area of single gridsquare on detector. Adjust intensity for optimum signal, center beam shift, then record intensity value in "highMagIntensity".

Then drop the mag to lowest mag with unobstructed view of TEM grid (i.e., the mag you use for whole-grid atlas), center beam shift, adjust intensity, and enter appropriate values in "lowMag" and "lowMagIntensity".

Open Navigator and collect whole-grid atlas. Add a point at the center of each gridsquare you wish to set at eucentric height.

If necessary, go to each XY coordinate to center the point in "highMag" using the Navigator "Move Item" button. For those points you want to run the script on, set to "Acquire".

When ready to start, open file to save autodoc metadata (with .mdoc or .idoc). Run the script using the SerialEM menu option "Navigator > Acquire at Points". Close the file when done.

Please check that beam is centered in both low and high mags 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.