STEM data collection on the Panther detector

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Name	STEM data collection on the Panther detector
Permalink	https://serialemscripts.nexperion.net/script/85
Category	Other Data Acquisition
Language	Python
Description	Runs a Record procedure through connecting to AutoScript TEM, and saves the individual segment images to the data folder
Author	Peter Kirchweger
Literature reference	https://doi.org/10.1101/2025.11.26.690630

Version History

Version 1.0 (December 07, 2025; 92 download(s); SerialEM version ≥ 4.2)

Version 1.0

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Upload date	December 07, 2025
Download count	92
SerialEM version ≥	4.2

#!Python
#=============================
#ScriptName CollectSTEMSegments
#Author: Peter Kirchweger
#=============================

import serialem as sem
from autoscript_tem_microscope_client import TemMicroscopeClient
from autoscript_tem_microscope_client.enumerations import *
from autoscript_tem_microscope_client.structures import *
import math
import mrcfile
import pathlib, os, sys
######################################################################
#Make Sure to change the pixelsize to 4096, 2048, 1024, 512; and the Dwell time to 3 (units of microseconds) 
#Before the tilt seires you must run a preliminary record with dynamic focus on, at the same magnification you intend to use here
Pixels = 4096
DwellTime = 5
Binning = int(4096/Pixels)
##################################################################

parentdir = pathlib.Path(sem.ReportCurrentFilename()).parent
os.chdir(parentdir)
print(parentdir)
File_name = pathlib.Path(sem.ReportCurrentFilename()).stem
workdir = os.path.join(pathlib.Path(sem.ReportCurrentFilename()).parent, File_name)
print(workdir)
if not os.path.exists(File_name):
   os.mkdir(File_name)
   print("I save the files to workdir: " + workdir)
   File_name = str(File_name)
   print(f"The dwell time is: {DwellTime} usec!")
   #Retrieve the PixelSize at binning 1
   sem.ReportLowDose()
   sem.GoToLowDoseArea("R")
   sem.ReportMag()
   sem.ReportBinning("3")
   
   ##### SET BINNING TO THE NUMBERS OF PIXELS YOU RECORD IN THE TILT SERIES
   ##### SetBinning takes two argments, the first (in "") is the LowDoseArea (3 for Record)
   sem.SetBinning("3",Binning)
   
   sem.ReportBinning("3")
   ########
   for i in str(sem.ReportCurrentPixelSize(str(3))).split(): 
   try:
   float(i.replace(',', '.'))
   PixelSize = str(round(float(i), 4)*10)
   except ValueError:
   pass
   
   sem.Echo("The PixelSze is: " + PixelSize)
   sem.SetBinning("3",8)
   sem.ReportBinning("3")
   
   # Connect to AutoScript server
   sem.Echo("I'm connecting to the AutoScriptTEM Server")
   microscope = TemMicroscopeClient()
   microscope.connect("192.168.0.1", 7521)
   
   # Change optical mode to STEM
   #microscope.optics.optical_mode = OpticalMode.STEM
   
   # Read out microscope type and software version
   #system_info = microscope.service.system.name + ", version " + microscope.service.system.version
   #print("System info: " + system_info)
   
   # Read out available detectors and cameras
   #scanning_detectors = microscope.detectors.scanning_detectors
   #print("Scanning detectors: ", scanning_detectors)
   
   bf_s = microscope.detectors.get_scanning_detector(DetectorType.BF_S)
   bf_s.set_enabled_segments(DetectorSegmentType.INNER_RING)
   df_s = microscope.detectors.get_scanning_detector(DetectorType.DF_S)
   df_s.set_enabled_segments(DetectorSegmentType.ALL)
   
   segments = bf_s.get_enabled_segments() + df_s.get_enabled_segments()
   print("Activated segments: ", segments)
   
   ExpTime = Pixels * Pixels * DwellTime * 1E-6
   reportedValues=sem.SetupDynamicFocus(ExpTime,Pixels,Pixels,Binning)
   print(reportedValues)
   
   if reportedValues[0]!=-1:
      sem.StartFocusRamper()
      print('Dynamic Focus ramp is on')
      
      #########################################################################
      images = microscope.acquisition.acquire_stem_segment_images(segments, int(Pixels), float(DwellTime)*1E-6)
      #########################################################################
      sem.FinishFocusRamp()
      
      n = len(images)
      columns = min(4, n)
      rows = math.ceil(n/columns)
      
      TiltAngle = str("{0:0=3d}".format(round(sem.ReportTiltAngle())))
      
      for row in range(rows):
      for column in range(columns):
      i = column + row * columns 
      if i < n:
         with mrcfile.new(os.path.join(File_name, File_name + "_" + segments[i].detector_name + "_" + segments[i].name + "_tilt" + TiltAngle + ".mrc"), overwrite=True) as mrc:
         mrc.set_data(images[i].data)
         mrc.voxel_size = PixelSize
         print("Twelve segment script finished successfully for tilt " + TiltAngle)
         sem.SetDirectory(workdir)
         print(os.getcwd())

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/)