PreAquireAtItems

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Name	PreAquireAtItems
Permalink	https://serialemscripts.nexperion.net/script/87
Category	Tomography
Language	Python
Description	Pre Aquire At Item script for parallax corrected STEM data collection
Author	Peter Kirchweger

Version History

Version 1.0 (December 08, 2025; 100 download(s); SerialEM version ≥ 4.2)

Version 1.0

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

Upload date	December 08, 2025
Download count	100
SerialEM version ≥	4.2

#!Python
#=============================
#ScriptName PreTiltSeries
#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 *

############################################
#Set the wanted defocus here
defoc = -0.5
############################################
# Connect to AutoScript server
sem.Echo("I'm connecting to the AutoScriptTEM Server")
microscope = TemMicroscopeClient()
microscope.connect("192.168.0.1", 7521)

# 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)
print("#################################################")
print(f"Camera length is: {microscope.optics.camera_length.value.label}")
print(f"This is the detection angle {bf_s.collection_angle_limits} (rad) of the inner ring")
print(f"This is the detection angle {df_s.collection_angle_limits} (rad) of the two outer rings (DF-I + DF-O)")
print(f"This is the gain {df_s.gain} and offset {df_s.offset}")
print("#################################################")
#sem.ReportDefocus()
sem.SetDefocus(defoc)
print(f"This is the Defocus: {sem.ReportDefocus()}")
#Now go to the LowDose Area Focus and set to a very high magnification
sem.GoToLowDoseArea('F')
sem.ReportLowDose()
sem.SetMag(650000) 
sem.ReportMag()
print("Switching to high mag")
#include CenterDisk

#Now make sure to go back to LowDose
sem.SetLowDoseMode(1)
sem.GoToLowDoseArea('R')
sem.ReportMag()
sem.ReportDiffractionShift()

Required Scripts

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

Center Diffraction Disk

Related Scripts

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

STEM data collection on the Panther detector

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/)