Continuous image acquisition

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Details

Name	Continuous image acquisition
Permalink	https://serialemscripts.nexperion.net/script/26
Category	Other Data Acquisition
Language	SerialEM Scripting
Description	This script coordinates TEM and imaging detector to collect and save a sequential set of images to disk by operating the detector in continuous imaging mode. Metadata pertinent to MicroED (https://cryoem.janelia.org/pages/MicroED) post-processing is saved in the autodoc file.
Author	Jason de la Cruz

Version History

Version 1.0 (June 08, 2017; 704 download(s); SerialEM version ≥ 3.7)

Version 1.0

Download

Upload date	June 08, 2017
Download count	704
SerialEM version ≥	3.7

ScriptName recMov
#20170608 recMov M. Jason de la Cruz

# Copyright (c) 2017, Howard Hughes Medical Institute
#
# Copying and distribution of this file, with or without modification,
# are permitted in any medium without royalty provided the copyright
# notice and this notice are preserved.  This file is offered as-is,
# without any warranty.

# INSTRUCTIONS: Open file to save autodoc metadata (with .mdoc or .idoc).
#               Modify settings in section below.  Start goniometer rotation
#               (outside of SerialEM) at a few degrees past intended start
#               angle, then start this script to initiate continuous recording.
#               When done, close file.
#
# recordMode options: V (View mode), F (Focus mode), R (Record mode)
# frameExposureTime is in seconds

#================================== SETTINGS ===================================
recordMode = R
frameExposureTime = 4
numberFrames = 20
#===============================================================================
echo ===> Running recMov ...

ScreenUp
SetColumnOrGunValve 1
SetBinning $recordMode 1
CameraProperties
AddToAutodoc PhysicalPixel $reportedValue4
ReportCameraLength
AddToAutodoc CameraLength $reportedValue1
SetContinuous $recordMode 1
WriteAutodoc
SetExposure $recordMode $frameExposureTime 0

UseContinuousFrames 1

Loop $numberFrames index
   echo === START PROCESS FOR EXPOSURE $index of $numberFrames ===
   echo --- Resetting clock
   resetclock
   echo --- Recording $frameExposureTime -second exposure
   $recordMode
   WaitForNextFrame
   echo --- Saving exposure $index with initial angle
   S
   reportclock
   echo ===
EndLoop

StopContinuous
echo Acquisition complete
RestoreCameraSet $recordMode
echo ===> Scope standby
SetColumnOrGunValve 0

Documentation

Open file to save autodoc metadata (with .mdoc or .idoc). Modify recordMode, frameExposureTime, and numberFrames settings in script. Start goniometer rotation (outside of SerialEM) at a few degrees past intended start angle, then start the script to initiate continuous recording. When done, close file.

recordMode options: V (View mode), F (Focus mode), R (Record mode)
frameExposureTime is in seconds
numberFrames is the total number of frames comprising the movie

License

Copyright (c) 2017, Howard Hughes Medical Institute. Copying and distribution of this file, with or without modification, are permitted in any medium without royalty provided the copyright notice and this notice are preserved. This file is offered as-is, without any warranty.