BIIF Newsletter

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Dear All,

welcome to our latest BIIF newsletter! Many exciting events happened in the end of 2024 and we started 2025 with many new ideas and projects.

Hackathons & Conferences

OME-NGFF Workflows Hackathon 2024

Recent advancements in bioimaging technology led to an increase in computational storage and analysis requirements for bioimaging data. To meet those needs, the bioimage analysis community is currently working on OME-Zarr, a next-generation file format for storing bioimaging image data in the cloud. At the “OME-NGFF Workflows Hackathon” 2024 hosted by the BioVisionCenter Zurich, Switzerland, bioimage analysists from Europe and Northern America came together to work on four main topics: OME-Zarr specification improvements, OME-Zarr for reusable workflows, OME-Zarr Java tooling, OME-Zarr Python tooling. Together with other bioimage analysts, Jonas from the BIIF started to work on adapting the OME-Zarr specification for the storage of “conventional” small bioimaging data in single image files. The work is still ongoing and we expect a summary of the hackathon (preprint) to be released soon. In the meantime, if you would like to learn more about OME-Zarr, check out our webinar about next-generation bioimage file formats in spatial biology from last year.

Towards Composable Nextflow Modules Standardized Analysis Pipelines in Nextflow

Nextflow is a workflow system for creating scalable, portable, and reproducible workflows. Over recent years, Nextflow has gained traction in the field of bioimage analysis, particularly for large data. At the hackathon “Towards Composable Nextflow Modules Standardized Analysis Pipelines in Nextflow”, bioimage analysts from SciLifelab, EMBL, Sanger, Euro-BioImaging, Human Technopole and VIB came together at the VIB in Leuven, Belgium, to work on implementing composable modules for bioimage analysis pipelines in Nextflow. From the event, Jonas from the BIIF brought home some important learnings, which we are looking forward to apply in our upcoming support projects.

European Society for Spatial Biology - Inaugural Conference

The European Society for Spatial Biology had their inaugural conference in Berlin with over 500 participants and 2 days of exciting talks, posters, and industry presenations on the technical advancements and applications in the field. Carolina gave a keynote lecture on spatial biology image analysis in her reserach group, the TissUUmaps team, and BIIF.

Resources & Online Content

LCI course

The LCI course From sample preparation to image analysis is running at the moment. All lectures are broadcasted live and accessbile to anyone. Find the full schedule here. Agus’ lecture “Introduction to Bioimage analysis” will take place Feb 13, 9:10.

GloBIAS YouTube channel

GloBIAS - the Global BioImage Analysts’ Society - has uploaded many relevant videos on its’ YouTube channel. You will find recordings of the first workshop that was hold last year in November in Göteborg, e.g. the video of Agus on his view on navigating new knowledge in a multidisciplinary field. Also uploaded are recordings of the GloBIAS seminar series - e.g. an introduction to Large Language Models for BioImage Analysis.

AI4Life - Artificial Intelligence for Image Data Analysis in The Life Sciences

In 2024, BIIF became a partner within the Ai4Life project. The project is Horizon Europe funded and aims to empower life science researchers to harness the full potential of AI and Machine Learning methods for bioimage analysis. Kristína and Agus are working on several projects, providing image analysis solutions to the researchers. You can join 4 webinars, jointly organized by Ai4Life and GloBIAS, showcasing the AI4Life services. More information here.

Publication Highlights with BIIF support

The study Liver X receptor unlinks intestinal regeneration and tumorigenesis led by Eduardo Villablanca, was published in Nature, November 2024. BIIF-support by Christophe enabled the segmentation of ducts in histological images using Deep Learning. Read more about the project on our project website and explore the code on our public GitHub repo of the project.
Example of the segmentation result:
segmentation_gif

Anna,
in behalf of BIIF

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