The BioImage Archive
@bioimagearchive.bsky.social
A free, publicly available resource storing and distributing biological images from any imaging modality, at any scale. Part of EMBL-EBI. www.ebi.ac.uk/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...
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...
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...
embl.wd103.myworkdayjobs.com
November 4, 2025 at 3:18 PM
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...
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...
Reposted by The BioImage Archive
🔬 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...
www.ebi.ac.uk/biostudies/b...
BioStudies < The European Bioinformatics Institute < EMBL-EBI
BioStudies – one package for all the data supporting a study
www.ebi.ac.uk
May 23, 2025 at 9:35 PM
🔬 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...
www.ebi.ac.uk/biostudies/b...
Reposted by The BioImage Archive
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.
But seriously, look at these cells! They are so angry.
October 8, 2025 at 5:18 PM
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.
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!
Huge thanks to Joshua Talks and @rodrigofg.bsky.social for sharing the user perspective — check out the interview below!
AI has so much potential for interpreting biological images, and yet, annotated biological datasets needed to train AI tools remain scarce.
If you generate microscopy data or develop AI tools to interpret it, check it these new guidelines:
www.ebi.ac.uk/about/news/t...
#bioimaging #microscopy
🧬🔬
If you generate microscopy data or develop AI tools to interpret it, check it these new guidelines:
www.ebi.ac.uk/about/news/t...
#bioimaging #microscopy
🧬🔬
October 13, 2025 at 3:17 PM
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!
Huge thanks to Joshua Talks and @rodrigofg.bsky.social for sharing the user perspective — check out the interview below!
Reposted by The BioImage Archive
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.
If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.
#HappyFluorescenceFriday!
#microscopycommunity- want to learn open source image analysis or share your knowledge to help others? We’ve got a FREE virtual workshop Nov 17-19! Now accepting workshop session applications!
Learn more & sign up: buff.ly/esGIotD
#microscopycommunity- want to learn open source image analysis or share your knowledge to help others? We’ve got a FREE virtual workshop Nov 17-19! Now accepting workshop session applications!
Learn more & sign up: buff.ly/esGIotD
September 23, 2025 at 3:48 PM
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.
If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.
🎉 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
Community-driven standards to make bioimage data AI-ready & reusable.
👉 www.nature.com/articles/s41... #AI #Bioimaging #FAIRdata
September 15, 2025 at 9:57 AM
🎉 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
Community-driven standards to make bioimage data AI-ready & reusable.
👉 www.nature.com/articles/s41... #AI #Bioimaging #FAIRdata
Reposted by The BioImage Archive
'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...
🧬🔬
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...
🧬🔬
September 11, 2025 at 9:07 AM
'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...
🧬🔬
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...
🧬🔬
Reposted by The BioImage Archive
Honoured to be featured - and even prouder of what the @bioimagearchive.bsky.social team is building together for the life sciences community.
Meet Aybuke Kupcu Yoldas 🇹🇷🇬🇧 our BioImage Archive Data Project Leader.
Aybuke swapped telescopes for microscopes and stars ⭐ for cells a few years ago, when she pivoted from astrophysics to bioimaging.
She now helps make bioimages easy to access and reuse.
www.ebi.ac.uk/about/news/p...
Aybuke swapped telescopes for microscopes and stars ⭐ for cells a few years ago, when she pivoted from astrophysics to bioimaging.
She now helps make bioimages easy to access and reuse.
www.ebi.ac.uk/about/news/p...
We are EMBL: Aybuke Kupcu Yoldas on trading stars for cells
Aybuke Kupcu Yoldas, Senior Imaging Bioinformatician at EMBL-EBI, talks about the Bioimage Archive and her journey from astrophysics to biology
www.ebi.ac.uk
August 27, 2025 at 10:47 AM
Honoured to be featured - and even prouder of what the @bioimagearchive.bsky.social team is building together for the life sciences community.
Reposted by The BioImage Archive
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...
www.embl.org/training/ari...
ARISE2
Career Accelerator for Research Infrastructure Scientists
www.embl.org
July 14, 2025 at 9:59 AM
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...
www.embl.org/training/ari...
Reposted by The BioImage Archive
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-...
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-...
June 26, 2025 at 2:24 PM
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-...
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 🔬!
www.nature.com/articles/s41...
Here is to improving transparency and reproducibility in light and fluorescence microscopy 🔬!
Light microscopy reporting for reproducibility - Nature Cell Biology
We announce a cross-journal pilot at Nature Portfolio journals with a goal of implementing standardized light and fluorescence microscopy reporting to improve methodological description and aid in rep...
www.nature.com
June 23, 2025 at 10:21 AM
📣 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 🔬!
www.nature.com/articles/s41...
Here is to improving transparency and reproducibility in light and fluorescence microscopy 🔬!
Reposted by The BioImage Archive
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
June 17, 2025 at 9:45 AM
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.
PANGAEA repository for Earth Sciences.
June 16, 2025 at 9:17 AM
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.
PANGAEA repository for Earth Sciences.
Reposted by The BioImage Archive
💡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!
May 28, 2025 at 10:27 AM
💡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!
Reposted by The BioImage Archive
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...
www.ebi.ac.uk/bioimage-arc...
BioImageArchive < The European Bioinformatics Institute < EMBL-EBI
The BioImageArchive – a free, publicly available online resource which stores and distributes biological images
www.ebi.ac.uk
May 27, 2025 at 10:48 AM
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...
www.ebi.ac.uk/bioimage-arc...
Reposted by The BioImage Archive
📊 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...
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...
May 27, 2025 at 9:42 AM
📊 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...
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...
Reposted by The BioImage Archive
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...
BioImageArchive < The European Bioinformatics Institute < EMBL-EBI
The BioImageArchive – a free, publicly available online resource which stores and distributes biological images
www.ebi.ac.uk
May 21, 2025 at 2:53 PM
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...
May 14, 2025 at 12:51 PM
Outstanding work by @kenzoivanovitch.bsky.social and colleagues. And you can explore this beautiful dataset at the BIA! www.ebi.ac.uk/biostudies/b...
Reposted by The BioImage Archive
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
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
May 13, 2025 at 9:08 AM
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
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
Reposted by The BioImage Archive
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...
🧪🧬🖥️🔬
Want to join us for this course next year? Register your interest: www.ebi.ac.uk/training/eve...
🧪🧬🖥️🔬
April 3, 2025 at 2:17 PM
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...
🧪🧬🖥️🔬
Want to join us for this course next year? Register your interest: www.ebi.ac.uk/training/eve...
🧪🧬🖥️🔬
Reposted by The BioImage Archive
🎤 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!
April 2, 2025 at 12:20 PM
🎤 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!
Reposted by The BioImage Archive
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
April 2, 2025 at 8:51 AM
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
Reposted by The BioImage Archive
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
Thanks for attending online & in person! 🤗
📸 EMBL/PhotoLab
March 28, 2025 at 2:59 PM
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
Thanks for attending online & in person! 🤗
📸 EMBL/PhotoLab
Reposted by The BioImage Archive
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!
🔬➡️🧑🔬
Mayeul Collot invited us into the world of photo-convertable dyes for #highresolutionimaging! 🔴➡️🟢
Many thanks to our amazing speakers!
March 18, 2025 at 8:37 PM
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!
🔬➡️🧑🔬
Mayeul Collot invited us into the world of photo-convertable dyes for #highresolutionimaging! 🔴➡️🟢
Many thanks to our amazing speakers!