AutoLEI: An XDS-based Graphical User Interface for Automated Real-time and Offline Batch 3D ED/MicroED Data Processing

AutoLEI 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 streamlined structure determination workflows.

Version selection:

AutoLEI v-1.0.0: version demonstrated in the paper (https://doi.org/10.1101/2025.04.12.648515). Data available: https://zenodo.org/records/14536385

AutoLEI v-1.0.2: latest beta version 

1. 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.

2. Installation

Operating Systems: Linux or Windows via [WSL](https://en.wikipedia.org/wiki/Windows_Subsystem_for_Linux) (versions 1/2).
Software Dependencies:
Python 3.8+ with libraries specified in `pyproject.toml`.
[XDS](https://xds.mr.mpg.de/) and [XDSGUI](https://wiki.uni-konstanz.de/xds/index.php/XDSGUI).
Optional tools: `xprep` for advanced features and LibreOffice for `.xlsx` files in Linux.

Steps:
a) Install via pip:
   bash
   pip install autolei

   For historical versions, use:
   bash
   pip install autolei-[version_name].zip
  
b) Manual installation:
   Follow the steps in the AutoLEI_Tutorial.pdf and https://gitlab.com/395736627tristone/automicroedgui/-/wikis/home.

3.  Usage
Command-line Usage

Launch the GUI
   bash
   autolei

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

Configure Settings:
   bash
   autolei_setting
   
  The opened .ini file includes settings on screen scaling, multi-thread and report format.

Import Instrument:
   bash
   autolei_add_instrument [instrument_setting_file]

4. 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.
- MergeData: Filter and merge datasets for downstream analysis.
- Cluster&Output: Perform clustering and generate outputs for structure determination.
- Expert: Miscellaneous tools for data reduction and PETS2-related function.
- RealTime: Live data processing with real-time feedback and automatic merging.

5. Documentation and other sources
Detailed guides and examples can be found in:

- Tutorial for AutoLEI
- PyPI: https://pypi.org/project/autolei/ 
- Gitlab (our Wiki): https://gitlab.com/395736627tristone/automicroedgui/-/wikis/home

6. 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](https://github.com/instamatic-dev/edtools).

7. License
The software is licensed under the BSD 3-Clause License.