Jensen lab FISE

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Name	Jensen lab FISE
Permalink	https://serialemscripts.nexperion.net/script/52
Category	Tomography
Language	SerialEM Scripting
Description	Acquire a tilt-series using the FISE method
Author	Georges Chreifi
Website link	https://github.com/chreifi/FISE

Version History

Version 1 (May 19, 2020; 298 download(s); SerialEM version ≥ 3.8)

Version 1

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This script requires additional scripts to be run – please refer to the Required Scripts section below.

Upload date	May 19, 2020
Download count	298
SerialEM version ≥	3.8

# Remember to UserSetDirectory before starting
ScriptName FISE

###### USER INPUTS ####
TotalRecordTime := 150 # Total Record Time for entire FISE tilt-series
ExpTime := 0.9 # Exposure time per tilt
MaxAngle := 60 # Max tilt angle to collect (positive direction)
TiltIncr := 3 # Tilt increment (degrees)
Settling := 0.75 # Delay time to allow the stage to settle before unblanking beam
FrameThreshold := 0.005 # Frames with a mean value below this threshold will not be saved
useCDS := 1 # Set to 1 to acquire data in CDS mode.
useNewEucentricHeight := 1 # set to 1 to use the separate eucentric height method (or 0 to use SerialEM’s)
##################

SetUserSetting UseK3CDS 0
If $useNewEucentricHeight == 0
   Eucentricity 6
Endif
If $useNewEucentricHeight == 1
   Call GetEucentricHeight
Endif
AutocenterBeam
Autofocus

Echo Checking if calibration is needed...
ReportNavItem 
CurrentItem = $reportedValue1
NavIndexItemDrawnOn $CurrentItem
NextMap = $reportedValue1

IsVariableDefined CurrentMap
If $reportedValue1 == 0
   CurrentMap := 0
 Else
   Echo Current map is $CurrentMap
Endif

If $NextMap != $CurrentMap
   CurrentMap := $NextMap
   Echo Current map is updated to $CurrentMap
   Echo RUNNING CALIBRATION
   Call GetCalibrations
 Else
   Echo Item $CurrentItem is in map $CurrentMap. Proceeding with the same calibration.
   If $useCDS ==1
      SetUserSetting UseK3CDS 1
      UpdateHWDarkRef 0
   Endif
Endif

IniDelay = 0.5 # Initial Delay Before starting FISE acquisition (seconds)
SetExposure 3 $TotalRecordTime
Echo Total Record Time is set to $TotalRecordTime s
Echo Working on Nav# $CurrentItem 
FrameThresholdNextShot $FrameThreshold
FrameSeriesFromVar ArrayTilt 31 $IniDelay
ResetClock 
R
ReportLastFrameFile 
WriteFrameSeriesAngles $reportedValue1.angles
ReportClock 
TiltTo 0
Echo Done!

Required Scripts

The following scripts are required to run this script, either because the are called directly or they provide functions:

Jensen lab FISE Calibrations

Related Scripts

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

Measure Eucentric Height Alternative

Documentation

1) Insert all 3 related/required scripts into serialEM.
2) Add targets to the Navigator. The first target picked in each map will be a calibration tilt-series.
3) In the FISE script, adjust user inputs according to your project.
4) Enable dose fractionation and set the correct frame rate for the Record parameter.
5) Choose a working directory and file name to save the frames.
6) Adjust file properties. Recommended file properties: unnormalized TIF with LZW compression.
7) Run FISE script. To batch collect, acquire nav items and run FISE script as primary task.

Note: Working directory must contain the ArrayTilt_angles.txt and ArrayTilt_defoci.txt for the script to work correctly!

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/)