AI4Life & BioImage Archive FAIR AI Workshop

Published: 2023-01-29

On January 24-25, 2023, the BioImage Archive (BIA) in collaboration with the AI4Life project, hosted a virtual workshop with 46 experts from various backgrounds. The objective of the workshop was to bring representatives from the image analysis community together to improve the BIA’s support for image annotations as part of AI-ready datasets and to develop annotation standards for the community. Several members of Euro-BioImaging Nodes participated in this workshop. Learn more about what was discussed and what the expected outcomes are.

Artificial Intelligence (AI) and deep learning (DL) are transforming the way we analyse biological images, benefitting particularly the processing of large and heterogenous image datasets. The development of these AI models relies on high-quality annotated images, which will determine the model’s performance, robustness, and scalability. Therefore, providing open access to useful, annotated datasets adhering to the FAIR principles (Findability, Accessibility, Interoperability and Reusability), is essential for the development, reproducibility, and reuse of AI models. However, sharing biological image AI datasets is challenging due to the lack of standards for representing annotation data widely adopted across the community.

The BioImage Archive (BIA), EMBL-EBI’s data resource for open life sciences image data, provides general purpose deposition services for any imaging dataset accompanying a publication, as well as reference image data. Within the AI4Life project, the idea is to improve the BIA’s support for image annotations as part of AI-ready datasets and to develop annotation standards for the community.

A community workshop

“It was really interesting to attend this workshop to exchange with other data generators, curators, AI researchers and software developers. It's important to be able to discuss together annotations and metadata that would be the most useful for AI in order to define what could be standards for our community,” says Perrine Paul-Gilloteaux, CNRS, France-BioImaging Node (Nantes, France).

Four main topics were discussed:

Each topic was first discussed in breakout rooms and afterwards each group presented their conclusions to the rest of the participants. This approach resulted in lively and insightful discussions and a series of recommendations.

Expected outcomes

The immediate output from the workshop will be a white paper, co-authored by the workshop participants, summarizing community recommendations. Furthermore, the BIA team is now working on transforming the workshop outcomes into metadata standards for AI datasets, and into software and tools to facilitate the deposition and sharing of AI images and annotations.

Beyond these outputs, the workshop recommendations should help annotation generators and consumers work together more effectively, facilitating the construction of benchmark collections of datasets to test model generalization and reuse. Thank you to all the participants for their valuable contributions!

This article was adapted from an article written by Matthew Hartley and Teresa Zulueta-Coarasa. To read the original text:

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