CRmov

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Details

Name	CRmov
Permalink	https://serialemscripts.nexperion.net/script/44
Category	Other Data Acquisition
Language	SerialEM Scripting
Description	Continuous rotation movie acquisition for MicroED. Refer to the references below for documentation.
Author	Jason de la Cruz
Literature reference	https://doi.org/10.1016/j.ultramic.2019.03.009
Website link	https://doi.org/10.1101/446658

Version History

Version 1.1 (March 23, 2019; 1687 download(s); SerialEM version ≥ 3.7)

Version 1.1

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Upload date	March 23, 2019
Download count	1687
SerialEM version ≥	3.7

ScriptName CRmov
#20190302 M. Jason de la Cruz, MSKCC. For SerialEM-controlled continuous
#stage rotation and simultaneous mode movie recording for MicroED.
#Currently works only on Thermo Fisher (FEI) microscopes.

# Copyright (c) 2019, M. Jason de la Cruz, Memorial Sloan Kettering Cancer Center
# License ISC: Internet Software Consortium license,
# http://opensource.org/licenses/ISC

# CHANGEABLE SETTINGS
fullPath = E:\Jason\20180719\20180720_ProtK_1B
rotationSpeed = 0.0032
angleStart = 30
angleEnd = -30
# Direction: For rotation in positive direction, enter 1; For rotation
#                     in negative direction, enter 0
Direction = 0
# plusMinusRange: This is the buffer range for end angle, due to
#                                     goniometer imprecision
plusMinusRange = 0.2
frameExposureTime = 4
frameBinning = 1
#imagingMag: This is generally set to mag setting when exiting out of
#                           diffraction mode, for scopes that require stage
#                           calibration in imaging mode
imagingMag = 1250

# ADVANCED SETTINGS
# cameras are numbered from 1
currentCamera = 1
recordMode = R
#numberFrames: This is the maximum setting; set to last past
#                                 tilt range, otherwise data saving will stop
#                                 before rotation completion; default 400
numberFrames = 400
delayTime = $frameExposureTime / 2
#darkgain: 0 = unprocessed, 1 = dark-subtracted, 2 = gain-normalized
darkgain = 2

echo ========================================
echo ===> Running CRmov ...
echo ========================================
ProgramTimeStamps

SetDirectory $fullPath
MakeDateTimeDir
ReportNavItem
SetNewFileType 1
ReportDirectory
echo $navLabel
OpenNewFile $navLabel.idoc

ScreenUp
SetLowDoseMode 1
GoToLowDoseArea $recordMode
SetColumnOrGunValve 1

SelectCamera $currentCamera
CameraProperties
AddToAutodoc PhysicalPixel $reportedValue4
ReportCameraLength
AddToAutodoc CameraLength $reportedValue1
AddToAutodoc RotationRate $rotationSpeed
WriteAutodoc
SetExposure $recordMode $frameExposureTime 0
SetBinning $recordMode $frameBinning
SetCameraArea $recordMode F
SetProcessing $recordMode $darkgain

echo ===> Tilting to $angleStart degrees
TiltTo $angleStart
echo ===> Preparing beam and settling...
StopContinuous
GoToLowDoseArea $recordMode
echo Waiting for $delayTime seconds
Delay $delayTime sec

UseContinuousFrames 1
echo angleEnd is $angleEnd
echo rotationSpeed is $rotationSpeed
BackgroundTilt $angleEnd $rotationSpeed

StartFrameWaitTimer 0

Loop $numberFrames index
   echo === START PROCESS FOR EXPOSURE $index of $numberFrames max frames ===
   echo --- Resetting clock
   resetclock
   echo Recording $frameExposureTime -second exposure
   $recordMode
   WaitForNextFrame
   echo --- Saving exposure $index with initial angle
   S
   reportclock
   
   ReportTiltAngle
   CurrentAngle = $ReportedValue1
   echo Current Tilt Angle is: $CurrentAngle
   if $Direction == 0
      negLimit = $angleEnd + $plusMinusRange
      echo Specified tilt direction is negative with end angle stop at $negLimit degrees
      if $CurrentAngle < $negLimit
         break
       else
         continue
      endif
    else
      posLimit = $angleEnd - $plusMinusRange
      echo Specified tilt direction is positive with end angle stop at $posLimit degrees
      if $CurrentAngle > $posLimit
         break
       else
         continue
      endif
   endif
   
EndLoop

echo Acquisition complete
CloseFile
SetDirectory $fullPath
ReportDirectory
StopContinuous
UseContinuousFrames 0
RestoreCameraSet $recordMode
GoToLowDoseArea R
SetColumnOrGunValve 0
SetLowDoseMode 0
Delay 1
TiltTo 0
SetMag $imagingMag
ProgramTimeStamps
echo ===> Scope standby

License

Copyright (c) 2019, M. Jason de la Cruz, Memorial Sloan Kettering Cancer Center. 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.