AutoLEI is an XDS-based pipeline with graphical user interface for automated real-time and offline batch 3D ED/microED data processing. 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.
\nIf you use AutoLEI in your work, please cite the following publication:
\n1. Wang, L., Chen, Y., Hutchinson, E. S., Stenmark, P., Hofer, G., Xu, H., & Zou, X. (2026). IUCrJ, 13. https://doi.org/10.1107/S2052252525010784
\n2. Kabsch, W. (2010). Acta Crystallogr D Biol Crystallogr 66, 125–132. https://doi.org/10.1107/S0907444909047337
\nIf you encounter any issues, please report them to:
lei.wang@su.se
yinlin.chen@su.se
Version selection:
\nAutoLEI 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
\nAutoLEI v-1.0.2.250711: latest beta version
\n1. 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 protein workflows.
2. Installation
\nOperating 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/tristonewang/autolei/-/wikis/home
3. Usage
Command-line Usage
Launch the GUI
bash
autolei
Note: The first launch may take slightly longer as dependencies initialize.
\nConfigure 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/tristonewang/autolei/-/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.
The main purpose of this community is the collection of data created within the NanED project. Uploads from participants in the NanED project will be accepted. Uploads from people who are not part of the NanED project will also be considered, as long as they are related to the project, e.g. reusing NanED data.
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\nThe community is managed by CERN on behalf of the European Commission.
\nZenodo’s general policies and Terms of Use apply to all content.
\nThe EU Open Research Repository accepts all digital research objects which is a research output stemming from one of EU’s research and innovation funding programmes. The funding programmes currently include:
\nHorizon Europe (including ERC, MSCA), earlier Framework Programmes (eg Horizon 2020) as well as Euratom.
\nIn line with the principle as open as possible, as closed as necessary both public and restricted content is accepted. See note on how Zenodo handles restricted content.
\nEU programme beneficiaries are eligible to submit content to the community. The community supports three types of content submissions:
\nSubmission via an EU Project Community (through user interface or programmatic APIs).
\nSubmission directly to the EU Open Research Repository.
\nAutomated harvesting from existing Zenodo content.
\nA representative of an EU project may request an EU Project Community and invite other project participants as members of the community. The project community is linked to one or more European Commission grants. All records in the project community are automatically integrated into the EU Open Research Repository immediately upon acceptance into the project community.
\nAny user may submit a record directly to the EU Open Research Repository. The submission will be moderated by Zenodo staff for compliance with the minimal required metadata requirements and its correctness.
\nRecords found among Zenodo’s existing content will on a regular basis automatically be integrated if they are found to comply with the requirements. The submissions through this method are integrated into the EU Open Research Repository with delay in a fully automated way.
\nRecords in the EU Open Research Repository are required to comply with the following minimal metadata requirements:
\nVisibility: Both public and restricted (with or without embargo and/or access request)
\nResource types: All resource types.
\nLicenses: Public and embargoed records MUST specify a license. The chosen license SHOULD be compliant with the Horizon Europe open science requirements (see Open Science in Horizon Europe)
\nFunding information: Records MUST specify at least one grant from the European Commission.
\nCreators: Creators SHOULD be identified with a persistent identifier (e.g. ORCID, GND, …), and affiliations SHOULD be identified with a persistent identifier (e.g. ROR, ISNI, …)
\nSubjects: Records SHOULD specify one or more fields of science from the European Science Vocabulary.
\nThese metadata requirements comes from the related open science requirements in Horizon Europe which are detailed in each project's grant agreement.
\nAll submissions undergo automated curation checks for compliance with the policy. Submissions through project communities are in addition reviewed by the project community. Submission directly to the EU Open Research Repository is in addiotn reviewed by Zenodo staff.
\nCommunity curators may at any point edit metadata of the records in the community without notice through human or automated processing. The curators may at their sole discretion remove records from the community that are deemed not to comply with the content and curation policy or which are deemed of insufficient quality.
\nThe content and curation policy is subject to change by the community owner at any time and without notice, other than through updating this page.
", "description": "Open repository for EU-funded research outputs from Horizon Europe, Euratom, and earlier Framework Programmes.", "funding": [ { "funder": { "id": "00k4n6c32" } } ], "organizations": [ { "id": "00k4n6c32" } ], "page": "The EU Open Research Repository is a Zenodo-community dedicated to fostering open science and enhancing the visibility and accessibility of research outputs funded by the European Union. The community is managed by CERN on behalf of the European Commission.
\nThe mission of the repository is to support the implementation of the EU's open science policy, providing a trusted and comprehensive space for researchers to share their research outputs such as data, software, reports, presentations, posters and more. The EU Open Research Repository simplifies the process of complying with open science requirements, ensuring that research outputs from Horizon Europe, Euratom, and earlier Framework Programmes are freely accessible, thereby accelerating scientific discovery and innovation.
\nThe EU Open Research Repository serves as a complementary platform to the Open Research Europe (ORE) publishing platform. Open Research Europe focuses on providing a publishing venue for peer-reviewed articles, ensuring that research meets rigorous academic standards. The EU Open Research Repository provides a space for all the other research outputs including data sets, software, posters, and presentations that are out of scope for ORE. This holistic approach enables researchers to not only publish their findings but also share the underlying data and materials that support their work, fostering transparency and reproducibility in the scientific process.
\nThe EU Open Research Repository is funded by the European Union under grant agreement no. 101256740 (HORIZON-ZEN Plus). For more information about the project see https://about.zenodo.org/projects/horizon-zen/.
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\nThe community is managed by CERN on behalf of the European Commission.
\nZenodo’s general policies and Terms of Use apply to all content.
\nThe EU Open Research Repository accepts all digital research objects which is a research output stemming from one of EU’s research and innovation funding programmes. The funding programmes currently include:
\nHorizon Europe (including ERC, MSCA), earlier Framework Programmes (eg Horizon 2020) as well as Euratom.
\nIn line with the principle as open as possible, as closed as necessary both public and restricted content is accepted. See note on how Zenodo handles restricted content.
\nEU programme beneficiaries are eligible to submit content to the community. The community supports three types of content submissions:
\nSubmission via an EU Project Community (through user interface or programmatic APIs).
\nSubmission directly to the EU Open Research Repository.
\nAutomated harvesting from existing Zenodo content.
\nA representative of an EU project may request an EU Project Community and invite other project participants as members of the community. The project community is linked to one or more European Commission grants. All records in the project community are automatically integrated into the EU Open Research Repository immediately upon acceptance into the project community.
\nAny user may submit a record directly to the EU Open Research Repository. The submission will be moderated by Zenodo staff for compliance with the minimal required metadata requirements and its correctness.
\nRecords found among Zenodo’s existing content will on a regular basis automatically be integrated if they are found to comply with the requirements. The submissions through this method are integrated into the EU Open Research Repository with delay in a fully automated way.
\nRecords in the EU Open Research Repository are required to comply with the following minimal metadata requirements:
\nVisibility: Both public and restricted (with or without embargo and/or access request)
\nResource types: All resource types.
\nLicenses: Public and embargoed records MUST specify a license. The chosen license SHOULD be compliant with the Horizon Europe open science requirements (see Open Science in Horizon Europe)
\nFunding information: Records MUST specify at least one grant from the European Commission.
\nCreators: Creators SHOULD be identified with a persistent identifier (e.g. ORCID, GND, …), and affiliations SHOULD be identified with a persistent identifier (e.g. ROR, ISNI, …)
\nSubjects: Records SHOULD specify one or more fields of science from the European Science Vocabulary.
\nThese metadata requirements comes from the related open science requirements in Horizon Europe which are detailed in each project's grant agreement.
\nAll submissions undergo automated curation checks for compliance with the policy. Submissions through project communities are in addition reviewed by the project community. Submission directly to the EU Open Research Repository is in addiotn reviewed by Zenodo staff.
\nCommunity curators may at any point edit metadata of the records in the community without notice through human or automated processing. The curators may at their sole discretion remove records from the community that are deemed not to comply with the content and curation policy or which are deemed of insufficient quality.
\nThe content and curation policy is subject to change by the community owner at any time and without notice, other than through updating this page.
", "description": "Open repository for EU-funded research outputs from Horizon Europe, Euratom, and earlier Framework Programmes.", "funding": [ { "funder": { "id": "00k4n6c32" } } ], "organizations": [ { "id": "00k4n6c32" } ], "page": "The EU Open Research Repository is a Zenodo-community dedicated to fostering open science and enhancing the visibility and accessibility of research outputs funded by the European Union. The community is managed by CERN on behalf of the European Commission.
\nThe mission of the repository is to support the implementation of the EU's open science policy, providing a trusted and comprehensive space for researchers to share their research outputs such as data, software, reports, presentations, posters and more. The EU Open Research Repository simplifies the process of complying with open science requirements, ensuring that research outputs from Horizon Europe, Euratom, and earlier Framework Programmes are freely accessible, thereby accelerating scientific discovery and innovation.
\nThe EU Open Research Repository serves as a complementary platform to the Open Research Europe (ORE) publishing platform. Open Research Europe focuses on providing a publishing venue for peer-reviewed articles, ensuring that research meets rigorous academic standards. The EU Open Research Repository provides a space for all the other research outputs including data sets, software, posters, and presentations that are out of scope for ORE. This holistic approach enables researchers to not only publish their findings but also share the underlying data and materials that support their work, fostering transparency and reproducibility in the scientific process.
\nThe EU Open Research Repository is funded by the European Union under grant agreement no. 101256740 (HORIZON-ZEN Plus). For more information about the project see https://about.zenodo.org/projects/horizon-zen/.
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