AutoLEI

AutoLEI: Automated Real-time and Offline Batch 3D ED/MicroED Data Processing Graphic User Interface is an XDS-based GUI designed for real-time and batch processing of MicroED/3DED datasets. It provides a user-friendly platform for rapid, automated data processing and merging of multiple MicroED datasets, with well-designed and significantly streamlining structure determination workflows.

Key Features

• User-Friendly Interface: Simplifies MicroED data processing, requiring minimal manual input.
• Batch Processing: Handles large numbers of datasets with automated workflows.
• Real-Time Data Processing: Provides live feedback during data collection.
• Versatility: Supports diverse samples, including small molecules and proteins workflow.

Installation

Requirements

• Operating Systems: Linux or Windows via WSL (versions 1/2).
• Software Dependencies:
  • Python 3.9+ with libraries specified in pyproject.toml.
  • XDS and XDSGUI.
  • Optional tools: xprep for advanced features and LibreOffice for .xlsx files in Linux.

Steps

1. Install via pip:

   pip install autolei
   

   For a specific historical version, use:

   pip install "autolei==<version>"
   

2. For a managed Linux/WSL installation including required XDS and optional XDSGUI tooling, use the reviewed installer from a source checkout:

   bash install_script/linux.sh
   

3. Manual installation: Follow the steps in the Tutorial for AutoLEI and our Wiki.

Usage

Command-line Usage

• Launch the GUI:

  autolei
  

  The equivalent module command is python -m autolei.

  Note: The first launch may take slightly longer as dependencies initialize.

• Configure Settings:

  autolei-setting
  

  Use autolei-setting --path to print the writable per-user settings path.

• Import Instrument:

  autolei-add-instrument instrument_setting_file
  

Custom profiles are stored in the user data directory and survive package upgrades.

• Restore an XDS cleanup backup:

  autolei-restore-cleanup project/.autolei-trash/xds-<timestamp>-<id>
  

• Check External Tools:

  autolei-doctor
  

  Reports the resolved locations of required and optional XDS/SHELX tools.

• Run without the GUI:

  autolei-process xds-generate PROJECT --settings PROJECT/Input_parameters.txt
  autolei-process xds-run PROJECT
  autolei-process --json convert PROJECT mrc
  

  The command also provides cluster, merge, geometry, and shelx workflows. See Headless workflows for validation, cancellation, and Python API examples.

Configuration and provenance

AutoLEI creates setting.ini in the platform-specific user configuration directory when it first starts. Packaged settings and instrument profiles remain read-only defaults. To run with a separate configuration, set AUTOLEI_SETTINGS to another INI file. AUTOLEI_CONFIG_HOME and AUTOLEI_DATA_HOME can override the user directories for managed installations and tests. Missing options retain documented defaults, while invalid values produce a setting-specific error.

AutoLEI 1.0.x supports Python 3.9 through 3.14 and tests every supported minor version. Python 3.9 is retained only for compatibility in the 1.0 release line; the next minor release is planned to require Python 3.11 or newer.

When upgrading from AutoLEI 1.0.5 or older, the managed installer copies a package-local setting.ini and custom-named profiles before pip replaces the old installation. Users upgrading directly with pip should back up any files they previously edited inside site-packages/autolei first.

Batch and refinement runs write xdsrunner.provenance.json or xdsrunner2.provenance.json next to the Excel result. The manifest records the AutoLEI and Python versions, effective configuration and its SHA-256 fingerprint, XDS executable location, run parameters, and SHA-256 hashes of all XDS.INP files used by the run.

GUI pages

AutoLEI is organised into multiple working pages:

• Input: Configure experiment parameters and generate input files.
• XDSRunner: Automate initial processing and data quality inspection.
• CellCorr: Update unit cell information and refine settings.
• XDSRefine: Fine-tune processing parameters, including rotation axis and scaling.
• DataMerge: Filter and merge datasets for downstream analysis.
• Cluster&Output: Perform clustering and generate outputs for structure determination.
• Expert: Miscellaneous tools for data reduction and PETS related function.
• RealTime: Live data processing with real-time feedback and automatic merging.

Package layout

• autolei/app/: PyQt application entry point, pages, realtime processing, and expert tools.
• autolei/core/: Validated settings, package version handling, and run provenance.
• autolei/src/: Scientific processing and file-format implementation modules.
• autolei/workflows/: Headless XDS, image, geometry, clustering, merging, and SHELX services shared by the GUI, CLI, and tests.
• autolei/autolei.py: Small compatibility launcher for existing direct-file commands.

Documentation

Detailed guides and examples can be found in:

• Tutorial for AutoLEI
• Development roadmap
• Our Wiki

Authors and Acknowledgments

Developed by Lei Wang and Yinlin Chen. Contributions from Gerhard Hofer, Hongyi Xu, and Xiaodong Zou at Stockholm University. The project integrates valuable resources from edtools. Special thanks to the XDS team for their support and resources.

Licence

The software is licensed under the BSD 3-Clause Licence.