AI4Life & BioImage Archive FAIR AI Workshop

January 29, 2023
AI4Life FAIR Training Opportunities

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:

  • What are the important types of annotation to record, and what extra information/metadata should accompany them?

  • What are the useful ways (formats, metadata) to share and present annotation data?

  • How should we support/allow/encourage sharing and archival of annotations?

  • What are our community recommendations to accelerate AI methods development through sharing AI image annotations, what are the missing pieces?

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 generalisation 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:

More news from Euro-BioImaging

July 12, 2024

Latest developments in cryo-EM and a goodbye to iNEXT-Discovery

The final consortium meeting of the iNEXT-Discovery project took place in Brno in June 2024, alongside the Symposium on Recent Advances in Cryo-EM. This…

July 10, 2024

Contribute to the "Inner Cosmos" art project

Inner Cosmos is an art project by Euro-BioImaging aimed at reaching the general public. The video has been designed as part of an installation…

Overview of the Node-to-Node exchanges from the 12 selected applications to the first round of the Job Shadowing program

July 10, 2024

Participants selected for the first Euro-BioImaging Cross-Node Job Shadowing program!

Open to all Euro-BioImaging Node Staff, the Cross-Node Job Shadowing program is a unique and exciting initiative implemented through…