The BioImage Archive

A fluorescent embryo on black text, with the words Halfway to I2K: Virtual Tutorials on Image Analysis November 17-19, 2025 Virtual Conference for beginners to developers i2kconference.org Image Credit - "Sweet Embryo",Travis D. Carney, BINA Image Contest 2024

Just 4 days until the start of I2K and its 33 totally free image analysis tutorials and events! Please share with your "home networks", especially early career researchers - the videos will be amazing and high-impact no matter how many people attend live, BUT (1/x)

Bioimaging Bioinformatician About the Team The revolution in imaging technologies has led to the need to share, integrate and reuse image data in a comprehensive way. EMBL-EBI’s imaging databases, EMPIAR and the BioImage Archive...

We’re looking for a Bioinformatician to join our talented team!
If you’re passionate about making bioimaging data FAIR, we’d love to hear from you.
Apply before November 23rd!
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

🔬 We’re also releasing a massive new dataset — over 600,000 annotated nucleus images — now freely available on the BioImage Archive.

www.ebi.ac.uk/biostudies/b...

Reactive microglia looking particularly angry. Iba1 showing cell shape in magenta, large amounts of CD68 in green, nuclei in blue. The cells are outlined in brown and the nuclei are outlined in cyan. There are lines connecting the nuclear centroids from Delaunay triangulation.

All of the segmentation and morphometric analysis was done with the open-source platform QuPath. The scripts I wrote are on Github and the raw images are on the BioImage Archive, because open-source is the way to go!

But seriously, look at these cells! They are so angry.

We recently had the pleasure of chatting about the newly published MIFA guidelines, which aim to improve how we share AI-ready datasets for bioimage analysis.
Huge thanks to Joshua Talks and @rodrigofg.bsky.social for sharing the user perspective — check out the interview below!

Thanks for highlighting the MIFA guidelines! We’re excited to see how they’ll help advance AI in bioimage analysis.

Halfway to I2K is BACK, friends of all kinds! Last year, 650 people attended 30+ TOTALLY FREE image analysis workshops of all kinds, across many timezones.

If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.

@florianjug.bsky.social, @joshmoore.bsky.social, @arratemunoz.bsky.social, @perrinegil.bsky.social, @gnodar.bsky.social, @martinjones.bsky.social, @aybukey.bsky.social, @lucamarconato.bsky.social, @nilsnorlin.bsky.social, @astitchyscientist.bsky.social, @normanrz.com, @virginieuhlmann.bsky.social

MIFA rests on 4 key pillars:
- Clear metadata for annotations
- Incentivise the production of annotated datasets
- Reduce the number of formats used for annotations
- Make data accessible to all

Huge thanks to all collaborators—can’t wait to see MIFA in action!

🎉 Our paper “MIFA: Metadata, Incentives, Formats and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis” is out in @natmethods.nature.com!
Community-driven standards to make bioimage data AI-ready & reusable.
👉 www.nature.com/articles/s41... #AI #Bioimaging #FAIRdata

Virtual course Microscopy data analysis: machine learning and the BioImage Archive 2026. 16 - 20 March 2026. EMBL's European Bioinformatics Institute.

'Microscopy data analysis: machine learning and the BioImage Archive' is back.

Join teams from across @ebi.embl.org to analyse your microscopy data using the latest machine learning and image analysis techniques.

Virtual course, UK time zone | 16 – 20 March 2026

www.ebi.ac.uk/training/eve...

🧬🔬

Honoured to be featured - and even prouder of what the @bioimagearchive.bsky.social team is building together for the life sciences community.

Our group @ebi.embl.org‬ is a host for the ARISE2 MSCA-funded post-doc fellowship, in collab with @bioimagearchive.bsky.social‬ and ‪@scilifelab.se (esp. A Mezger and S. Giacomello) to support the development of next-gen spatial data infrastructures. Apply by 30/09
www.embl.org/training/ari...

We are at #mmc2025! Come to our booth to say hi and learn about the Data Steward Training Program 👋

Ever wished your AI model could test itself before you download it? Now it can.

AI4Life has a new model evaluation platform that connects models from the BioImage Model Zoo to real data in the @bioimagearchive.bsky.social.

Details here 👉 ai4life.eurobioimaging.eu/the-ai4life-...

📣 We are pleased that @natureportfolio.nature.com recommends The BioImage Archive for depositing bioimaging data, as part of their cross-journal microscopy reporting pilot.
www.nature.com/articles/s41...
Here is to improving transparency and reproducibility in light and fluorescence microscopy 🔬!

Graphics image showing webinar at EMBL-EBI about Open FAIR data: the role of public data archives. The webinar will run on 25 June 2025 at 14:30 BST. The speakers are Jeena Rajan and Aybuke Kupku Yoldas. Image credit: Karen Arnott and Rebecca Nicholl, EMBL-EBI

Graphics image showing webinar at EMBL-EBI about Open FAIR data: the role of public data archives. The webinar will run on 25 June 2025 at 14:30 BST. The speakers are Jeena Rajan and Aybuke Kupku Yoldas. Image credit: Karen Arnott and Rebecca Nicholl, EMBL-EBI

Join our #webinar next week to learn about FAIR data, with a focus on EMBL-EBI resources Biosamples and @bioimagearchive.bsky.social! Registration is free but essential trainingcontent.embl.org/open-fair-da... #datamanagement #FAIRdata #opendata #lifescience @embl.org @ebi.embl.org #PlanetaryBiology

We will be speaking on Wednesday as part of the University of Vienna Open Science and Research Data Management Seminar Series! Join us if you want to learn about what you can expect from the BioImage Archive and the
PANGAEA repository for Earth Sciences.

💡Success stories from AI4Life: From the BioImage.IO models to @bioimagearchive.bsky.social’s AI-ready datasets, and community resources like the Helpdesk, Open Calls, and Challenges — see how it all connects in one ecosystem!

Such a beautiful (and useful) dataset! 🐟✨

It's not something we had in mind when assembling this data with @rebannjones.bsky.social, but it's very gratifying and flattering to see our zebrafish embryo images and annotations feature at the top of the AI Ready list presented by @bioimagearchive.bsky.social

www.ebi.ac.uk/bioimage-arc...

📊 What does AI-ready data actually look like?
Time to find out! Head over to @bioimagearchive.bsky.social’s gallery — it’s like an art museum for high-quality training data and metadata. Perfect for your next model!
www.ebi.ac.uk/bioimage-arc...

Did you know that Bioimage Archive has a specific database for people to share AI-ready imaging datasets? I did not until @yanlanmao.bsky.social told me! Please deposit! If people regularly submitted, it would have a huge collective impact on bioimage analysis. www.ebi.ac.uk/bioimage-arc...

Wonderful! Please keep us in mind 🙂

Outstanding work by @kenzoivanovitch.bsky.social and colleagues. And you can explore this beautiful dataset at the BIA! www.ebi.ac.uk/biostudies/b...

Mesmerising! Are these images publicly available?

We’re excited to share the amazing science our microscopes are enabling🔬

From #3Dimaging technologies to developmental biology, cancer research, spatial-omics and more!🧬🧠

Follow us for cutting-edge discoveries at @embl.org @prbb.org and discover how #mesoscopic imaging can support your research

EMBL-EBI course Microscopy data analysis: machine learning and the BioImage Archive Virtual

This week we've been joined by participants learning more about bioimaging and analysing microscopy data. Thank you to @bioimagearchive.bsky.social and Image Data Resource for your support!

Want to join us for this course next year? Register your interest: www.ebi.ac.uk/training/eve...

🧪🧬🖥️🔬

Thanks for the great lecture Esti, we love some FAIRy deep learning!

🎤 AI4Life continues its presence at the @bioimagearchive.bsky.social course! Esti presents BioImage.IO, emphasizing the importance of keeping AI models accessible, reproducible, and interoperable. With so many image analysis tools out there, common model standards are the way forward!