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Welcome to the

Community call

August 21, 2025

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LinkML Updates

UV migration:

linkml-runtime main is using UV

many pytest conversions, formatting, and reducing of vendoring - thanks Vlad!

linkml v1.9.4-rc2 is out for testing with uv-migration - thanks Carlo!

Expect a new LinkML Project Template using uv, ruff, just, copier - Thanks David L!

preview here: https://github.com/dalito/linkml-project-copier

linkml-runtime - released v1.9.5

linkml - v1.9.4-rc2 - out for testing, release Friday

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Contact us!

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If you aren’t sure who to contact for questions or help, feel free to reach out to the LinkML Community Outreach Manager for guidance: Sarah Gehrke sarah@tislab.org

LinkML is community driven!

Developers and users are available by email, LinkML channels in OBO Slack, and Github.

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Today’s presentation:

“A LinkML-based metadata framework for the Open Microscopy Metadata model to enable easy extension, data exchange with instrument manufacturers, and integration with related models.”

Caterina Strambio De Castillia

Assistant Professor at UMass Chan Medical School (https://profiles.umassmed.edu/display/132167)

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Caterina Strambio-De-Castillia is an internationally recognized cell biologist and imaging scientist who specializes in developing easy-to-use, openly accessible strategies for image data management and sharing to promote scientific discovery in health and disease. As a pioneer in bioimage informatics, she bridges the gap between cutting-edge technology and biomedical research by creating tools that empower scientists to extract deeper insights from complex imaging data.

Leading an interdisciplinary team, Dr. Strambio-De-Castillia drives innovation in facilitating metadata curation, integration of imaging and omics multi-modal, and FAIR (Findable, Accessible, Interoperable, and Reusable) data standards. Her work ensures that large-scale bioimage datasets are not only reproducible and AI-ready but also broadly accessible to accelerate collaborative research. A strong advocate for open science, Dr. Strambio-De-Castillia spearheads community initiatives to establish best practices in bioimaging, engaging global stakeholders from academia and industry to advance data quality and reuse.

Dr. Strambio-De-Castillia is a leading member of the NIH-funded 4D Nucleome research consortia, BioImaging North America and QUAREP-LiMi (quarep.org) and her work has been recognized through the prestigious CZI Imaging Scientist Award. Her standards and tools have been widely adopted (QUAREP-LiMi, RIKEN institute, HuBMAP, SenNet etc.) and she is deeply committed to training the next generation of scientists, fostering a lab culture that values rigor, collaboration, and translational impact.

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Today’s presentation:

“Updates on LinkML Rust Generator”

Frank Dekervel

Partner

Senior Software Engineer

https://kapernikov.com/

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Today’s presentation:

“LinkML-Map”

Corey Cox

Scientific Software Engineer with the Translational & Integrative Sciences Lab (https://tislab.org/)

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