Dose-symmetric tomography

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This script is considered obsolete, as the functionality has largely been integrated into the SerialEM graphical user interface. As even obsolete scripts can be useful for learning scripting or serve as the basis for new developments, it will continue to be available on this site.

Details

Name	Dose-symmetric tomography
Permalink	https://serialemscripts.nexperion.net/script/12
Category	Tomography
Language	SerialEM Scripting
Description	The script will tilt the stage back and forth to give a tilt series with perfect dose distribution.
Author	Wim Hagen
Literature reference	http://www.ncbi.nlm.nih.gov/pubmed/27313000
Website link	http://www.embl.de/research/units/scb/briggs/dose-symmetric-tilt-series-macro/

Version History

Version 1.0 (February 01, 2017; 961 download(s); SerialEM version ≥ 3.6)

Version 1.0

Download

Upload date	February 01, 2017
Download count	961
SerialEM version ≥	3.6

MacroName DoseSymmetricTomo
# EMBL Heidelberg 2015 Wim J. H. Hagen
# Roll Buffers A-> H.
# Uses LowDose
# Run eucentric rough and fine
# Track plus	K
# Track min 	L
# Record plus M
# Record min 	N

########## SETTINGS ##########

step		= 3	# stage tilt step in degrees
tilttimes	= 10	# multiply by 4 images + 1 image
Tiltbacklash	= -3	# negative tilts will be backlashed, must be negative value!

Driftcrit	= 3	# Angstrom/second
Driftinterval	= 10	# wait time between drift measurements in seconds
Drifttimes	= 10	# maximum number of drift measurements before skipping

########## END SETTINGS ##########

tiltangle = 0

CallFunction DoseSymmetricTomo::TiltZero

# prevent runaway focus
AbsoluteFocusLimits -10 10
FocusChangeLimits -2 2

Loop $tilttimes
   # tilt plus1
   tiltangle = $tiltangle + $step	
   CallFunction DoseSymmetricTomo::TiltPlus
   # tilt min1
   tiltangle = -1 * $tiltangle	
   CallFunction DoseSymmetricTomo::TiltMinus
   # tilt min2
   tiltangle = $tiltangle - $step
   CallFunction DoseSymmetricTomo::TiltMinus
   # tilt plus2
   tiltangle = -1 * $tiltangle	
   CallFunction DoseSymmetricTomo::TiltPlus
EndLoop

TiltTo 0
ResetImageShift
SetDefocus 0

function TiltZero
   # store stage position
   ReportStageXYZ	
   StageX = $ReportedValue1
   StageY = $ReportedValue2
   
   # drift and tracking
   T
   Copy A K
   Copy A L
   Delay $driftinterval
   Loop $drifttimes index
      T
      AlignTo K
      ReportAlignShift
      dx = $reportedValue3
      dy = $reportedValue4
      dist = sqrt $dx * $dx + $dy * $dy
      rate = $dist / $driftinterval * 10
      echo Rate = $rate A/sec
      If $rate < $driftcrit
         echo Drift is low enough after shot $index      
         break
       Elseif  $index < $drifttimes
         Delay $driftinterval 
       Else
         echo Drift never got below $driftcrit: Skipping ...
         break  
      Endif
   EndLoop
   
   # autofocus
   G
   G
   G
   
   # store defocus
   ReportDefocus
   focusplus = $RepVal1
   focusmin = $RepVal1
   
   # acquire tilt image
   R
   S
   Copy A M
   Copy A N
   
   # store image shifts
   ReportImageShift
   ISxplus = $RepVal1
   ISyplus = $RepVal2
   ISxminus = $RepVal1
   ISyminus = $RepVal2
   
   # tracking after just to be sure                     
   T
   Copy A K
   Copy A L
endfunction

function TiltPlus
   # tilt stage
   TiltTo $tiltangle
   
   # reset stage XY
   MoveStageTo $StageX $StageY
   
   # set defocus and image shift
   GoToLowDoseArea R
   SetDefocus $focusplus
   SetImageShift $ISxplus $ISyplus
   
   # drift and tracking             
   T
   AlignTo K
   Delay $driftinterval
   Loop $drifttimes index
      T
      AlignTo K
      ReportAlignShift
      dx = $reportedValue3
      dy = $reportedValue4
      dist = sqrt $dx * $dx + $dy * $dy
      rate = $dist / $driftinterval  * 10	
      echo Rate = $rate A/sec
      If $rate < $driftcrit
         echo Drift is low enough after shot $index      
         break
       Elseif  $index < $drifttimes
         Delay $driftinterval 
       Else
         echo Drift never got below $driftcrit: Skipping ...
         break  
      Endif
   EndLoop
   
   # autofocus. Two rounds. Remove one G for single focus round.
   G
   G
   
   # store defocus
   ReportDefocus
   focusplus =  $RepVal1
   
   # acquire tilt image
   R
   S
   
   # tracking after
   AlignTo M
   Copy A M
   
   # store image shifts
   ReportImageShift
   ISxplus = $RepVal1
   ISyplus = $RepVal2
   
   # new track reference
   T
   Copy A K
endfunction

Function TiltMinus
   # tilt stage with backlash
   TiltTo $tiltangle
   TiltBy $Tiltbacklash
   TiltTo $tiltangle
   
   # reset stage XY
   MoveStageTo $StageX $StageY
   
   # set defocus and image shift
   GoToLowDoseArea R
   SetDefocus $focusmin
   SetImageShift  $ISxminus $ISyminus
   
   # drift and tracking 
   T
   AlignTo L
   Delay $driftinterval
   Loop $drifttimes index
      T
      AlignTo L
      ReportAlignShift
      dx = $reportedValue3
      dy = $reportedValue4
      dist = sqrt $dx * $dx + $dy * $dy
      rate = $dist / $driftinterval  * 10
      echo Rate = $rate A/sec
      If $rate < $driftcrit
         echo Drift is low enough after shot $index      
         break
       Elseif  $index < $drifttimes
         Delay $driftinterval 
       Else
         echo Drift never got below $driftcrit: Skipping ...
         break  
      Endif
   EndLoop
   
   # autofocus. Two rounds. Remove one G for single focus round.
   G
   G
   
   # store defocus        
   ReportDefocus
   focusmin =  $RepVal1
   
   # acquire tilt image
   R
   S
   
   # tracking after
   AlignTo N
   Copy A N
   
   # store image shifts
   ReportImageShift
   ISxminus = $RepVal1
   ISyminus = $RepVal2
   
   # new track reference
   T
   Copy A L
endfunction

Documentation

Setup Low Dose.

Set eucentric height.

Start 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/)