The BioImage Archive

Curious to see what a malaria parasite looks like during different stages of cytokinesis? 🫣 In this month’s @nfdi4bioimage.bsky.social calendar, we present a dataset of Plasmodium falciparum in EMPIAR and available as OME-Zarr via the @bioimagearchive.bsky.social, both hosted by @ebi.embl.org.

📅 Find the story behind the May image in the @nfdi4bioimage.bsky.social wall calendar and read more about what it takes to make bioimaging data truly reusable here: 👉 nfdi4bioimage.de/en/community... To the corresponding dataset on @bioimagearchive.bsky.social: 👉 www.ebi.ac.uk/biostudies/b...

More nice talks about the @bioimagearchive.bsky.social by Teresa Zulueta Coarasa, including an overview the standards MIFA and REMBI for imaging metadata and the pipeline for conversion of data into OME-Zarr

What is the value of open data for the life sciences? 📈 New report by Frontier Economics shows that EMBL-EBI data resources save users an average of 11 hours/week/person, leading to £11.8bn/year in research productivity gains. s.embl.org/EMBL-EBI-202... #opendata

I love this slide from Matthew Hartley (@bioimagearchive.bsky.social) on the repositories behind the last 50+ years of biodata management (at @gideproject.bsky.social)

A significant moment at #OME2026: Thanking Prof. Jason Swedlow, the founder of OME, who shaped this remarkable community work since the beginning of the millenium. His work & leadership were honored - even with a nod to his famous blue shirts by OME's Interim Board, nominated by Jason in Oct '25.

Matthew Hartley from EMBL-EBI, UK, demonstrating live at #OME2026 the power of recent updates around the BioImage Archive @bioimagearchive.bsky.social: Seamless image browsing enabled by OME-Zarr, and enhanced data search functionality are boosting the FAIRness of bioimage data significantly. 👏

Join us on April 23 to explore our brand-new website! 🔬 We’ll show how it makes discovering, browsing, and exploring bioimaging datasets easier than ever — with improved search and interactive visualisation right in your browser. Register here: www.ebi.ac.uk/training/eve...

How can we see where genes are active in tissues? The Spatial Transcriptomics Portal combines imaging and molecular data to map gene activity in spatial context. Explore how cells interact and develop. www.ebi.ac.uk/about/news/u... @bioimagearchive.bsky.social @expressionatlas.bsky.social

Been a minute since I visited the @bioimagearchive.bsky.social. Lots of fun new features in beta. Be sure to check it out if you need somewhere to share your imaging data w/ publication.

A significant step forward in standardizing biological imaging data. Our project partners, @gerbi-gmb.de and @bioimagearchive.bsky.social, will assure the continued development of the #FBbi ontology. Discuss this milestone and many other at our Community Event 4-6 May! tinyurl.com/26rbksyx

Curious about @bioimagearchive.bsky.social? Join the 3rd BioImage Archive User Forum to learn about new developments, share insights, and contribute to the evolution of this amazing public repository. 🗓️ March 9 Register 🔽 docs.google.com/forms/d/e/1F...

Curious about @bioimagearchive.bsky.social? Join the 3rd BioImage Archive User Forum to learn about new developments, share insights, and contribute to the evolution of this amazing public repository. 🗓️ March 9 Register 🔽 docs.google.com/forms/d/e/1F...

Join us for the third virtual BioImage Archive User Forum on March 9th! We offer two sessions: 9:00-10:30 (GMT) and 15:00-16:30 (GMT). This year we will focus on showcasing the Beta version of our new website with its new features! 📝 Registration: tinyurl.com/7cwz3puz 🗒Agenda: tinyurl.com/y87y4s28

Congratulations, @bioimagearchive.bsky.social! This pubic data repository has received @elixir-europe.org’s CDR and EDD status! Great recognition for a great resource! 🎉 Learn more🔽 www.eurobioimaging.eu/news/bioimag...

The 2nd term of our #NFDI4BIOIMAGEfromAtoZ calendar is @bioimagearchive.bsky.social, an international data repository for biological image data provided by @ebi.embl.org. It accepts data linked to a publication and promotes measures to increase the reusability of data 👉 www.ebi.ac.uk/bioimage-arc...

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)

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...

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!

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.

'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 🔬!

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!

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...

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

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

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... 🧪🧬🖥️🔬

🎤 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!

At the @training.ebi.embl.org course on Microscopy Data Analysis: Machine Learning & @bioimagearchive.bsky.social, Dominik Kutra from @ilastik-team.bsky.social introduced ilastik and how it supports image analysis. Now, it's time for a hands-on session! 🚀 #BioImageAnalysis #MachineLearning

What a wonderful week! The #EuroBioImaging All Hands Meeting is the occasion to connect with colleagues from around Europe to exchange on topics ranging from imaging technology innovation, data, training, international collaboration & more. Thanks for attending online & in person! 🤗 📸 EMBL/PhotoLab

Today we had two fantastic key note talks at #TiM2025. Matthew Hartley enlightened us about #DataSharing through @bioimagearchive.bsky.social 🔬➡️🧑‍🔬 Mayeul Collot invited us into the world of photo-convertable dyes for #highresolutionimaging! 🔴➡️🟢 Many thanks to our amazing speakers!

Kudos to Matthew Hartley of the @bioimagearchive.bsky.social for his message of global collaboration in the #bioimaging community @ #TiM2025 👏👏👏

Big news for AI4Life! Our project is a success story by the European Commission! 🇪🇺 The Directorate-General for Research and Innovation (DG RTD) highlights our mission of making AI-powered bioimage analysis accessible to researchers everywhere 🌍 Read more: ai4life.eurobioimaging.eu/ai4life-high...

Repositories are essential for #FAIR data. Our invited speakers Frances Wong from @openmicroscopy.org #IDR & Aybüke Yoldaş from @bioimagearchive.bsky.social present recent developments at @nfdi4bioimage.bsky.social All-Hands Meeting. We're excited to extend our collaborations ➡️FAIR #bioimaging #NFDI

🚨 Save the Date! 🚨 AI4Life & @globias.bsky.social are hosting a 4-part webinar series to showcase AI4Life services and lessons learned. 📅 When: Feb 13, Apr 10, Jun 12, Aug 14 🖥️ How: Online | 🎥 Recorded 🔗 Registration: bit.ly/registration...