Fast-Incremental Single-Exposure tomography

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Name	Fast-Incremental Single-Exposure tomography
Permalink	https://serialemscripts.nexperion.net/script/48
Category	Tomography
Language	SerialEM Scripting
Description	Acquires tilt series in single long exposure without any tracking or auto-focussing. Can use precalibrated image shifts to compensate specimen shifts.
Author	Fabian Eisenstein
Literature reference	https://doi.org/10.1016/j.jsb.2019.08.006
Website link	https://github.com/feisenstein/FISE

Version History

Version 1 (August 16, 2019; 411 download(s); SerialEM version ≥ 3.7)

Version 1

Download

Upload date	August 16, 2019
Download count	411
SerialEM version ≥	3.7

ScriptName FISETomo

# ETH Zurich 2018/10/10, Fabian Eisenstein
# Last change: 	2019/03/06: added alignToP and group scaling
#		2018/12/02: added focus adjustment
# 		2018/11/19: added IScal

###### TO DO BEFORE USE ######
# - check Frame folder and naming
# - check Target defocus
# - activate Trial in LD for fine euc
# - find and set tilt axis offset
# - test base time
# - run CalFISE with same settings (needs to be run after every SerialEM restart!)
# - check buffer P for view of hole in case you activated centerHole

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

TStype 		= 3		# 1: unidirectional, (2: bidirectional), 3: dose-symmetrical
increment 	= 3		# tilt angle increment
maxtilt 	= 60		# maximum +/- tilt angle

maxtiltG1	= 60		# NOT TESTED # maximum tilt for 2 steps per group (set to maxtilt to disable group scaling)
maxtiltG2	= 60		# NOT TESTED # maximum tilt for 4 steps per group (set to maxtilt to disable group scaling)

expTime 	= 1		# exposure time per tilt in seconds
delay 		= 0		# delay after tilting in seconds
useCal 		= 0		# use global cal variables (run CalFISE script on carbon with gold before; only for dose-sym TS)
frameTime 	= 0.2		# K3 allows only <0.1 (DM plugin limited)
frameThreshold 	= 1		# threshold for saving frames (depends on dose rate and frameTime; default of 1 seems to work well)

minDefocus 	= -3		# minimum defocus of defocus cycle
maxDefocus 	= -5		# maximum defocus of defocus cycle
defocusStep 	= 0.5		# defocus increase between targets

centerHole	= 0		# align to buffer P (1: center on holes; view image of hole needs to be in buffer P)
maxHoleShift 	= 100   	# max beam/image shift after hole centering in nanometers to not iterate

dryRun 		= 0		# dryRun without saving Frames to get estimate for baseTime
# baseTime should be > ([time after frames saved] - [time before frames saved] - [tilt angles] * [exposure time])

baseTimeType3 	= 150		# Time needed for tilting during whole tilt scheme. Needs to be tested on each system and each increment.
# Example values:
# dose-sym ST/K3 increment 3: 	89
# dose-sym DT/K2 increment 3: 	148
# dose-sym ST/K3 increment 2: 	124
# dose-sym DT/K2 increment 2: 	208

baseTimeType1 	= 50		# uni-dir ST/K3 increment 3: 	50
# uni-dir DT/K2 increment 3: 	76
# uni-dir ST/K3 increment 2: 	65
# uni-dir DT/K2 increment 2: 	95

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

ResetClock

######## CALIBRATIONS ########
defocusSlope = 0
IScal = {0 0 0 0 0 0 0 0 0 0}			#default image shift calibration values
IScal = {$IScal 0 0 0 0 0 0 0 0 0 0}
IScal = {$IScal 0 0 0 0 0 0 0 0 0 0}
IScal = {$IScal 0 0 0 0 0 0 0 0 0 0}
IScal = {$IScal 0 0 0 0 0 0 0 0 0 0}
IScal = {$IScal 0 0 0 0 0 0 0 0 0 0}
IScal = {$IScal 0 0 0 0 0 0 0 0 0 0}
IScal = {$IScal 0 0 0 0 0 0 0 0 0 0}

IScal = {$IScal 0 0 0 0 0 0 0 0 0 0}		#extra entries incase of 2 deg increments
IScal = {$IScal 0 0 0 0 0 0 0 0 0 0}
IScal = {$IScal 0 0 0 0 0 0 0 0 0 0}
IScal = {$IScal 0 0 0 0 0 0 0 0 0 0}

if $useCal == 1
   IScal = $IScalGlobal
   defocusSlope = $defocusSlopeGlobal
endif

######## END CALIBRATIONS ########

echo ##### New Tilt Series #####
echo TS scheme: $TStype with increment $increment 
echo Exposure time: $expTime s ($frameTime s frames)
echo Delay: $delay s
echo useCal: $useCal

### DETERMINE TARGET DEFOCUS ###

ReportTargetDefocus
targetDefocus = $RepVal1

targetDefocus = $targetDefocus - $defocusStep
If $targetDefocus < $maxDefocus
   targetDefocus = $minDefocus
Endif  
echo Target defocus: $targetDefocus
SetTargetDefocus $targetDefocus

echo #####

### PREPARE TS ###

Eucentricity 6
echo Target eucentricity confirmed...
ReportClock

if $centerHole == 1
   V
   AlignTo P
   
   ReportAlignShift
   holeshift = sqrt $RepVal5 * $RepVal5 + $RepVal6 * $RepVal6
   echo Hole shift 1: $holeshift (x: $RepVal5; y: $RepVal6)
   if $holeshift > $maxHoleShift
      ResetImageShift
      V
      AlignTo P
      ReportAlignShift
      holeshift = sqrt $RepVal5 * $RepVal5 + $RepVal6 * $RepVal6
      echo Hole shift 2: $holeshift (x: $RepVal5; y: $RepVal6)
   endif
   echo Target centered...
endif

G
echo Target defocussed...
ReportClock

FrameThresholdNextShot $frameThreshold

If $TStype == 3
   
   baseTime = $baseTimeType3
   
   angleplus = 0
   angleminus = 0
   Tilts = {$angleplus $expTime $delay 0 0 0}
   calx = -1
   caly = 0
   
   loopno = ($maxtiltG1 / 2 / $increment) + (($maxtiltG2 - $maxtiltG1) / 4 / $increment) + (($maxtilt - $maxtiltG2) / 6 / $increment)
   loop $loopno
      group = 2
      if $angleplus > $maxtiltG2
         group = 6
       elseif $angleplus > $maxtiltG1
         group = 4
      endif
      
      if $angleplus + $group * $increment > $maxtilt		#make sure TS does not go beyond maxtilt
         group = $maxtilt - $angleplus * $increment
      endif
      
      loop $group
         angleplus = $angleplus + $increment
         calx = $calx + 2
         caly = $caly + 2
         foc = $defocusSlope * $angleplus
         Tilts = {$Tilts $angleplus $expTime $delay $foc $IScal[$calx] $IScal[$caly]}
      endloop
      
      loop $group
         angleminus = $angleminus - $increment
         calx = $calx + 2
         caly = $caly + 2
         foc = $defocusSlope * $angleminus
         Tilts = {$Tilts $angleminus $expTime $delay $foc $IScal[$calx] $IScal[$caly]}
      endloop
   endloop
   
   FrameSeriesFromVar Tilts 31
   
 Elseif $TStype == 2
   
   Tilts = {-18 $expTime -15 $expTime -12 $expTime -9 $expTime -6 $expTime -3 $expTime 0 $expTime 3 $expTime 6 $expTime 9 $expTime}
   Tilts = {$Tilts 12 $expTime 15 $expTime 18 $expTime 21 $expTime 24 $expTime 27 $expTime 30 $expTime 33 $expTime 36 $expTime}
   Tilts = {$Tilts 39 $expTime 42 $expTime 45 $expTime 48 $expTime 51 $expTime 54 $expTime 57 $expTime 60 $expTime -21 $expTime}
   Tilts = {$Tilts -24 $expTime -27 $expTime -30 $expTime -33 $expTime -36 $expTime -39 $expTime -42 $expTime -45 $expTime -48 $expTime}
   Tilts = {$Tilts -51 $expTime -54 $expTime -57 $expTime -60 $expTime}
   
   FrameSeriesFromVar $Tilts 3
   
 Elseif $TStype == 1
   
   baseTime = $baseTimeType1
   
   tiltNumber = (60 * 2 / $increment) + 1
   QueueFrameTiltSeries -60 $increment $tiltNumber 0 $expTime $delay
   
 Else
   echo This tilt scheme is currently not supported!
Endif

totalExpTime = $baseTime + (120 / $increment + 1) * ($exptime + $delay)

echo Set total exposure to $totalExpTime s with $frameTime s fractionation.
SetExposure R $totalExpTime
SetFrameTime R $frameTime

If $dryRun == 1
   echo It's just a drill!
   SetExposure R 10
   SetFrameTime R 0.1
   EarlyReturnNextShot 1
Endif

echo Fire!
ReportClock
R
echo Target eliminated!
ReportClock
#S
#ReportClock
WriteFrameSeriesAngles FISE_tilts.txt
TiltTo 0
SetDefocus 0
ResetImageShift
CloseFile

echo Mission complete!
ReportClock

Related Scripts

The following scripts provide a similar or related functionality, but are not required to run this script:

Pre-calibrations for FISE tomography

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/)