Dual-Axis Tomography

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Name	Dual-Axis Tomography
Permalink	https://serialemscripts.nexperion.net/script/81
Category	Tomography
Language	SerialEM Scripting
Description	...
Author	Peter Kirchweger

Version History

Version 1.0 (October 08, 2024; 190 download(s); SerialEM version ≥ 4.2)

Version 1.0

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Upload date	October 08, 2024
Download count	190
SerialEM version ≥	4.2

ScriptName DualAxis
#
# Written by Guenter Resch, adapted by Peter Kirchweger
#
SuppressReports
SaveLogOpenNew secondaxis.log
echo #################
echo ### I am running ###
Echo # $ScriptName # 
Echo #################

# Microscope specific parameters
RotationTarget = 98     # Depends on the microscope
RotationCenterX = 0
RotationCenterY = 0
TempFile @= X:\Path\to\your\file.mrc

# Check prerequisites
ReportIfNavOpen
If ( $ReportedValue1 == 0 )
   Echo ERROR: Navigator not open, exiting
   Exit
EndIf
Echo
echo #################
ReportColumnOrGunValve 
If $repVal1 == 0
   SetColumnOrGunValve 1
   Echo I have opened the Valves
 Else
   Echo Valves are still open
Endif
echo #################

# SIM OpenOldFile T:\series4.mrc
Echo
echo #################
Echo I will record the center image
echo #################
# Acquire reference map at original rotation and store in P
SetNavRegistration 1
MoveStageTo $RotationCenterX $RotationCenterY
Delay 5
#SIM Search # TODO or acquisition with other LD area set up for LM images; TEM: remove aperture?
Record
# SIM ReadFile 0 A # SIM
NewMap
Copy A P

Echo
echo #################
Echo I rotate the grid
echo #################
# Rotate stage by 90 degrees, incl backlash correction - TODO required?
SetStageBAxis ( $RotationTarget + 3 )
Delay 5
SetStageBAxis $RotationTarget
Delay 5
SetNavRegistration 3

Echo
echo #################
Echo I record the 90 deg center image
echo #################
# Recenter on rotation center and acquire new image
MoveStageTo $RotationCenterX $RotationCenterY
Delay 5
# SIMSearch # TODO or acquisition with other LD area set up for LM images; TEM: remove aperture?
Record
# NewMap rRequired or not?
NewMap 
# SIM ReadFile 1 A # SIM
# A = 90 deg center image
# P = 0 deg center image

Echo
echo #################
Echo Now I will AlignWithRotation and transform items
echo #################
Copy P E
AlignAndTransformItems -90 6
ListVars

# Close all open files
Loop 8
   CloseFile
EndLoop

Echo

# Let user specify the MRC file with all maps
Pause Select the MRC file containing all the maps
UserOpenOldFile
ReportCurrentFilename
MapFile = $reportedvalue1
ReportFileZSize
MapFileZSize = $reportedValue1

# Open temporary file
AllowFileOverwrite 1
OpenNewFile $TempFile

Echo 
echo #################
Echo Now I rotate the Navigatoritems
echo #################
# Rotate all images in map file and save to temporary file
Loop $MapFileZSize i
   j = $i - 1
   echo Rotating section $j
   SwitchToFile 1
   ReadFile $j N
   Rotate90CCW N
   Save A 2
EndLoop

# Close map file and temporary file and replace map file with temporary file
CloseFile
CloseFile
RemoveFile $MapFile
RunInShell copy "$TempFile" "$MapFile" & pause
RemoveFile $TempFile

Echo
echo #################
echo Script execution complete
echo #################
SaveLogOpenNew

Documentation

How to run the script:
1. Before running the script save the navigator as a new file
2. Remove the objective aperture and return to the smallest magnification in LowMag-
STEM mode
3. Change the TempFile name and location in the script
4. Open a new .mrc file (different from the TempFile)
5. Start the script and watch it run:
5.1 The stage moves to the coordinates defined in the script (Variables: Rotation-
centerX and RotationcenterY)
5.2 It takes a Record image, saves it in the open file, and makes it a new map in
the Navigator
5.3 It rotates the grid inside the microscope by 90◦ (set by the RotationTarget
Variable in the script) and takes a new Record image at the coordinates defined
in the script
5.4 The script calls the Align-with-rotation procedure with a search settings of
90◦and plus-minus 6◦ (can be adjusted in the script)
5.5 All the items in the Navigator are then rotated by the amount calculated
5.6 The Record images are then saved in a new file
6. The new Navigator is now rotated at around 90◦ and when the position of the
tomogram is not too close to the edge of the grid square automated continuation of
the data collection including the ’realign-to-items’ procedure works very well.

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/)