PACE-tomo target selection

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Name	PACE-tomo target selection
Permalink	https://serialemscripts.nexperion.net/script/76
Category	Tomography
Language	SerialEM Scripting
Description	Selects targets, saves maps and writes text file with coordinates for PACE-tomo.
Author	Fabian Eisenstein
Literature reference	https://www.biorxiv.org/content/10.1101/2022.04.07.487557v1

Version History

Version 1.2 (April 09, 2022; 187 download(s); SerialEM version ≥ 3.9)

Version 1.2

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Upload date	April 09, 2022
Download count	187
SerialEM version ≥	3.9

#!Python
# ===================================================================
# Name:		PACEtomo_selectTargets
# Purpose:	Selects targets, saves maps and writes text file with coords for PACEtomo.
#		More information at http://github.com/eisfabian/PACEtomo
# Author:	Fabian Eisenstein
# Created:	2021/04/19
# Revision:	v1.2
# Last Change:	2022/03/31
# ===================================================================

import serialem as sem

# Please set the appropiate tilt axis offset to improve performance!

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

delaytime = 10		# time in seconds to apply image shift before next image is taken
targetByShift = False	# ask to enter image shifts instead of dragging manually
targetPattern = False	# regular pattern of targets (holey support film)
alignToP = False	# refine vectors by aligning to hole reference in buffer P
size = 1 		# size of collection pattern (1: 3x3, 2: 5x5, 3: 7x7, ...)

vecA = (2.4, 1.1)	# specimen shift in microns to neighbouring hole
vecB = (-vecA[1], vecA[0])

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

sem.Pause("Please make sure that 'Move stage for big mouse shifts' is unchecked!")

sem.UserSetDirectory("Please choose a directory for saving targets and tilt series!")

sem.EnterString("userName","Please provide a rootname for the PACE-tomo collection area!")
userName = sem.GetVariable("userName")

sem.OpenTextFile("1", "W", 0, userName + "_tgts.txt")
#align center
sem.ResetImageShift()
if alignToP:			#center hole for center of tgtPattern
   sem.V()
   sem.AlignTo("P")
   
   userInput = 0
   while userInput == 0:
   sem.V()
   sem.OKBox("Please center your target by dragging the image using the right mouse button! (Delay: " + str(delaytime) + " s)")
   sem.Delay(delaytime)
   userConfirm = sem.YesNoBox("Do you want to take a preview image here?")
   if userConfirm == 1:
      sem.L()
      userInput = sem.YesNoBox("Do you want to use the current image and coordinates as target 1 (tracking target)? If you choose no, a view image is taken and you have several seconds to apply shifts, before another preview image is taken!")
      
      #save map
      sem.OpenNewFile(userName + "_tgt_001.mrc")
      sem.S("A")
      mapIndex = sem.NewMap(0, userName + "_tgts.txt")
      sem.SetItemAcquire(int(mapIndex))
      
      #save coords
      (SSX0, SSY0) = sem.ReportSpecimenShift()
      (stageX, stageY, stageZ) = sem.ReportStageXYZ()
      (RepVal1, RepVal2, RepVal3, RepVal4, ISX, ISY) = sem.ReportImageShift()
      stageX += ISX
      stageY += ISY
      
      sem.WriteLineToFile("1", "_tgt = 001")
      sem.WriteLineToFile("1", "tgtfile = " + userName + "_tgt_001.mrc")
      sem.WriteLineToFile("1", "tsfile = " + userName + "_ts_001.mrc")
      sem.WriteLineToFile("1", "map = " + str(mapIndex))
      sem.WriteLineToFile("1", "stageX = " + str(stageX))
      sem.WriteLineToFile("1", "stageY = " + str(stageY))
      sem.WriteLineToFile("1", "SSX = 0")
      sem.WriteLineToFile("1", "SSY = 0")
      sem.WriteLineToFile("1", "")
      
      sem.CloseFile()
      
      sem.Echo("Target 001 (" + userName + "_tgt_001.mrc) with image shifts 0, 0 was added.")
      
      #make view map tor realign to item
      sem.V()
      sem.OpenNewFile(userName + "_tgt_001_view.mrc")
      sem.S("A")
      sem.NewMap()
      sem.CloseFile()
      
      if targetPattern:
         if alignToP:			#refine grid vectors by aligning to hole reference in P
            sem.GoToLowDoseArea("R")
            sem.Echo("Vector A: " + str(vecA))
            
            shiftx = size * vecA[0]
            shifty = size * vecA[1]
            sem.ImageShiftByMicrons(shiftx, shifty)
            
            sem.V()
            sem.AlignTo("P")
            sem.GoToLowDoseArea("R")
            
            (SSX, SSY) = sem.ReportSpecimenShift()
            SSX -= SSX0
            SSY -= SSY0		
            
            vecA = (round(SSX / size, 4), round(SSY / size, 4))
            
            sem.Echo("Refined vector A: " + str(vecA))
            
            sem.ImageShiftByMicrons(-SSX, -SSY)		# reset IS to center position
            
            sem.Echo("Vector B: " + str(vecB))
            
            shiftx = size * vecB[0]
            shifty = size * vecB[1]
            sem.ImageShiftByMicrons(shiftx, shifty)
            
            sem.V()
            sem.AlignTo("P")
            sem.GoToLowDoseArea("R")
            
            (SSX, SSY) = sem.ReportSpecimenShift()
            SSX -= SSX0
            SSY -= SSY0		
            
            vecB = (round(SSX / size, 4), round(SSY / size, 4))
            
            sem.Echo("Refined vector B: " + str(vecB))
            
            
            targetNo = 1
            for i in range(-size,size+1):
            for j in range(-size,size+1):
            if i == j == 0: continue
               
               targetNo += 1
               
               SSX = i * vecA[0] + j * vecB[0]
               SSY = i * vecA[1] + j * vecB[1]
               
               sem.WriteLineToFile("1", "_tgt = " + str(targetNo).zfill(3))
               sem.WriteLineToFile("1", "tsfile = " + userName + "_ts_" + str(targetNo).zfill(3) + ".mrc")
               sem.WriteLineToFile("1", "SSX = " + str(SSX))
               sem.WriteLineToFile("1", "SSY = " + str(SSY))
               sem.WriteLineToFile("1", "")
               
               sem.CloseFile()
               
               sem.Echo("Target " + str(targetNo).zfill(3) + " (" + userName + "_tgt_" + str(targetNo).zfill(3) + ".mrc) with image shifts " + str(SSX) + ", " + str(SSY) + " was added.")
               
             else:					#loop over other targets
               targetNo = 1
               addTargets = 1
               while addTargets == 1:
               userInput = 0
               while userInput == 0:
               if targetByShift:
                  sem.GoToLowDoseArea("R")
                  shiftx = sem.EnterDefaultedNumber(0, 1, "Enter X shift:")
                  shifty = sem.EnterDefaultedNumber(0, 1, "Enter Y shift:")
                  sem.ImageShiftByMicrons(shiftx, shifty)
                  sem.V()
                  sem.OKBox("Please center your target by dragging the image using the right mouse button! (Delay: " + str(delaytime) + " s)")
                  sem.Delay(delaytime)
                  userConfirm = sem.YesNoBox("Do you want to take a preview image here?")
                  if userConfirm == 1:
                     sem.L()
                     userRefine = sem.YesNoBox("Do you want to refine the position at this mag?")
                     if userRefine == 1:
                        sem.OKBox("Please center your target by dragging the image using the right mouse button! (Delay: " + str(delaytime) + " s)")
                        sem.Delay(delaytime)
                        sem.L()
                        userInput = sem.YesNoBox("Do you want to use the current image and coordinates as target position? If you choose no, a view image is taken and you have several seconds to apply shifts, before another preview image is taken!")
                        targetNo += 1
                        #save map
                        sem.OpenNewFile(userName + "_tgt_" + str(targetNo).zfill(3) + ".mrc")
                        sem.S("A")
                        mapIndex = sem.NewMap()
                        
                        #save coords
                        (SSX, SSY) = sem.ReportSpecimenShift()
                        SSX -= SSX0
                        SSY -= SSY0
                        
                        sem.WriteLineToFile("1", "_tgt = " + str(targetNo).zfill(3))
                        sem.WriteLineToFile("1", "tgtfile = " + userName + "_tgt_" + str(targetNo).zfill(3) + ".mrc")
                        sem.WriteLineToFile("1", "tsfile = " + userName + "_ts_" + str(targetNo).zfill(3) + ".mrc")
                        sem.WriteLineToFile("1", "stageX = " + str(stageX))
                        sem.WriteLineToFile("1", "stageY = " + str(stageY))
                        sem.WriteLineToFile("1", "SSX = " + str(SSX))
                        sem.WriteLineToFile("1", "SSY = " + str(SSY))
                        sem.WriteLineToFile("1", "")
                        
                        sem.CloseFile()
                        
                        sem.Echo("Target " + str(targetNo).zfill(3) + " (" + userName + "_tgt_" + str(targetNo).zfill(3) + ".mrc) with image shifts " + str(SSX) + ", " + str(SSY) + " was added.")
                        
                        addTargets = sem.YesNoBox("Do you want to add another target?")
                        
                        
                        sem.SetImageShift(0,0)
                        sem.OKBox("Target selection completed! " + str(targetNo) + " targets were selected.")

Related Scripts

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

Parallel cryo electron tomography (PACE-tomo)

Documentation

https://github.com/eisfabian/PACEtomo

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/)