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Virginie Uhlmann

@virginieuhlmann.bsky.social
2K followers 86 following 53 posts

Assistant Professor in Bioimaging and Data Analysis and Director of the BioVisionCenter at UZH; Research Group Leader at EMBL-EBI. Loves image analysis, mountains, and birds.

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Virginie Uhlmann @virginieuhlmann.bsky.social · 05/10/2026
We also look ahead: what will it take for AI to deliver in microscopy data? Trustworthy models with calibrated uncertainty, computationally fluent biologists, and infrastructure that frees image data from institutional silos. Read it, share it, and tell us where you agree (or don't)!
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Virginie Uhlmann @virginieuhlmann.bsky.social · 05/10/2026
...all the way to foundation models and universal visual representations, and why biological specialization still matters (and will always do).
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Virginie Uhlmann @virginieuhlmann.bsky.social · 05/10/2026
We retrace the path from supervised models automating tedious manual tasks, to self-supervised learning finding patterns without annotations, to generative models learning the rules behind biological processes...
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Virginie Uhlmann @virginieuhlmann.bsky.social · 05/10/2026
For a long time we thought it would be great to have our perspective on the history, current developments, and future of the field written down instead of just living in our heads. Nobody asked for it, but now it exists for you all to enjoy!
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Virginie Uhlmann @virginieuhlmann.bsky.social · 05/10/2026
Together with Anna @ilastik-team.bsky.social and Florian @florianjug.bsky.social, we wrote our view of the field for @annualreviews.bsky.social, and it's out now in open access!
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Virginie Uhlmann @virginieuhlmann.bsky.social · 05/10/2026
Are you a biologist working with microscopy images? A computer scientist wanting to work with microscopy data? Their boss??? None of these, but curious how AI has transformed microscopy image analysis? 🔬🤖 This one's for you: 📄 doi.org/10.1146/annu... More in the thread! 🧵
doi.org
From Pixels to Discovery: Microscopy Image Analysis in the Age of Artificial Intelligence
Modern microscopy generates data volumes that far exceed human analytical capacity. Over the past decade, artificial intelligence (AI) has transformed microscopy image analysis into an engine for quan...
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Josh Moore @joshmoore.bsky.social · 25/09/2026
ICYMI: OME-Zarr 0.6 is out! 🎉 This is big, years in the making. @bogovicj.bsky.social & @jo-soltwedel.bsky.social perseverance brought transformations into this next major step on the road to OME-Zarr 1.0. 👏👏👏 Huge congratulations to the Johns — and to everyone who helped get us here! 🥳🙌
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Virginie Uhlmann @virginieuhlmann.bsky.social · 11/09/2026
Don't get me wrong, like you I believe that, when used from a position of power, these can be transformative tools. But I do worry when I notice how hard it is to not drift into intellectual laziness when the process of learning feels so slow and unproductive in contrast to an immediate output.
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Virginie Uhlmann @virginieuhlmann.bsky.social · 11/09/2026
Yes, but unfortunately, it turns out we humans are very good at fooling ourselves into thinking we use these tools to learn when we, in fact, have stopped thinking (doi.org/10.1145/3632...).
doi.org
The Widening Gap: The Benefits and Harms of Generative AI for Novice Programmers | Proceedings of the 2024 ACM Conference on International Computing Education Research - Volume 1
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Virginie Uhlmann @virginieuhlmann.bsky.social · 11/09/2026
Research software is costly and time-consuming to produce because it requires focused time from developers who have invested years learning to master their craft, just like art. There is nothing to celebrate about relinquishing intellectual expertise and mastery in favor of fast and cheap.
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Florian Jug @florianjug.bsky.social · 09/09/2026
Here we are, #BIC 2026 at @eccv.bsky.social is kicking off! Is this really the 11th time we’re doing this! 🥜 See full program here: bioimagecomputing.com
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Virginie Uhlmann @virginieuhlmann.bsky.social · 09/08/2026
"I pressed the wrong button and accidentally threw my friend off the chairlift and into unknown territory" 10/10 game right here
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Virginie Uhlmann @virginieuhlmann.bsky.social · 06/08/2026
The Gen III Pokemon Snorunt
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Virginie Uhlmann @virginieuhlmann.bsky.social · 01/06/2026
📢📢 We are hiring a Bioimage Analyst at the BioVisionCenter! 📢📢 Join our collaboration with the Flow Cytometry Facility and contribute back to the international efforts on open standards for bioimaging data! More information here, reach out if you have any question: jobs.uzh.ch/job-vacancie...
jobs.uzh.ch
UZH: Bioimage Analyst
The University of Zurich is the largest university in Switzerland and one of the most prominent in Europe. For research purposes the Biovision Center and Flow Cytometry Facility offer services to supp...
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Virginie Uhlmann @virginieuhlmann.bsky.social · 01/06/2026
BIC is back guys 😎 Don't go on your summer holiday before sending us your best bioimage computing papers, submission deadline on July 13!
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Human Technopole @humantechnopole.bsky.social · 22/05/2026
💡 Introducing the Multimodal #AI Across Scales Research Programme with our @florianjug.bsky.social 🤖 The new HT Programme develops open, uncertainty-aware AI tools to connect biological data from molecules and cells to patients and populations. humantechnopole.it/en/news/intr...
humantechnopole.it
Introducing the Multimodal AI Across Scales Programme with Florian Jug - Human Technopole
The new Multimodal AI Across Scales Research Programme, within Human Technopole's Computational Biology Research Centre, develops AI methods that connect biological data across modalities and scales, ...
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OME @openmicroscopy.org · 03/05/2026
#OME2026 has come to an end—what an inspiring and collaborative few days. Huge thanks to @nfdi4bioimage.bsky.social for documenting the meeting so thoroughly—definitely worth a look back through their posts! But first, enjoy the wrap-up video presented already during the closing session! 🤩
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Virginie Uhlmann @virginieuhlmann.bsky.social · 03/05/2026
If you missed this because, like me, you were busy at #OME2026, please check it out! @kevinyamauchi.bsky.social and I wrote a thing on how we can all do our part to enable the next generation of microscopy-data-driven biological discoveries. Enjoy the read!
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Virginie Uhlmann @virginieuhlmann.bsky.social · 30/04/2026
Thank you all for the incredible energy and inspiration! The OME community is a real treasure ❤️
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Caterina Fuster Barceló @cfusterbarcelo.bsky.social · 30/04/2026
Back from ICLR 2026 in Rio! 🇧🇷 Highlights: presenting my poster at the LMRL workshop, Copacabana sunsets☀️, and the best coincidence: finding out my best friend got in too without us even planning it! 👯‍♀️ So grateful to @virginieuhlmann.bsky.social for the support. Where to next? 🚀
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Joel Lüthi @joelluethi.bsky.social · 29/04/2026
Amazing to be at #OME2026 & talk about the future of OME-Zarr. @virginieuhlmann.bsky.social @lorenzocerrone.bsky.social & I were very happy to present the BioVisionCenter, ngio and Fractal yesterday. If you want to learn more, check out today’s ngio workshop: github.com/BioVisionCen...
Virginie Uhlmann giving a talk titled “Towards interoperable bioimage analysis at scaleLorenzo Cerrone presenting the ngio posterJoel presenting the Fractal poster
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NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · 28/04/2026
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.
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Joel Lüthi @joelluethi.bsky.social · 26/03/2026
🔬 Next Open Bioimaging Practices Meetup (OBPM) – Mar 31, 16:00 CET Hybrid: FMI Basel & Zoom Talk by @jo-soltwedel.bsky.social : Transforming OME-Zarr: What’s coming in v0.6 Plus short updates from the BVC & time for discussion www.biovisioncenter.uzh.ch/en/events/Up...
biovisioncenter.uzh.ch
Open Bioimaging Practices Meetup: March 2026
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OME @openmicroscopy.org · 20/03/2026
One week left for the OME2026 Community Survey! 📣 If you haven't filled it out, please do so. We'll be discussing it live at the #OME2026 meeting in April. bit.ly/ome2026-comm...
bit.ly
OME 2026 Community Survey
This year in April, the 19th OME Community Meeting will be gathering to determine the "Future and Governance of OME" during the final meeting day's guided Discussion Forum / "Unmeeting". This survey...
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Virginie Uhlmann @virginieuhlmann.bsky.social · 16/03/2026
Congrats to all of you for getting this started, I can't wait to see the amazing things you'll get done. What a time to be alive :)
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Virginie Uhlmann @virginieuhlmann.bsky.social · 16/03/2026
Things that bring me joy, episode #372: THIS!
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Virginie Uhlmann @virginieuhlmann.bsky.social · 15/03/2026
Check out @cfusterbarcelo.bsky.social's latest cool work! Domain shift, we are watching you 👀👀👀
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Erick Ratamero @erickratamero.com · 10/03/2026
Calling all OME Community members, contributors, and lurkers! Please take a minute to answer the OME 2026 Community Survey (docs.google.com/forms/d/e/1F...) to help us prepare for discussing the future of OME governance during the OME 2026 Community Meeting at the end of April.
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Virginie Uhlmann @virginieuhlmann.bsky.social · 10/03/2026
If you've been wondering what our current obsession with OME-Zarr and lego blocks is about, I have good news for you: the Fractal preprint is out! Thanks to @joelluethi.bsky.social , all co-authors, and the Fractal developers and users community for making this beautiful project a reality ❤️
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Florian Jug @florianjug.bsky.social · 28/12/2025
🚨 Alarm!!! 🚨 AI/ML course for microscopy image analysis!!! 🧐 In 2026 at Janelia (@hhmijanelia.bsky.social), no tuition, housing and meals provided! Isn’t that borderline unbelievable?!? 20 students, ~14 TAs and lecturers 🗓️ June 4-18 2026 ✍️ Jan 15 2026 ✍️ 🔁 pls!! www.janelia.org/you-janelia/...
janelia.org
Deep Learning for Microscopy Image Analysis
Topics The following will be covered extensively during lectures, exercises, and project work: Image denoising and restoration (fully supervised and self-supervised) Image translation (e.g.,
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Virginie Uhlmann @virginieuhlmann.bsky.social · 27/12/2025
A quote from H.P. Lovecraft's Festival: "Great holes secretly are digged where earth's pores ought to suffice, and things have learnt to walk that ought to crawl."
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EMBL-EBI @ebi.embl.org · 18/12/2025
The new ShapeEmbed deep learning method helps quantify shapes in bioimages 🔬 It learns to encode 2D object outlines into descriptors that are invariant to several geometric transformations. Great for robust cell shape analysis, classification & exploring phenotypes. neurips.cc/virtual/2025...
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Virginie Uhlmann @virginieuhlmann.bsky.social · 16/12/2025
Somehow this made me smile more than it should reasonably have
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Virginie Uhlmann @virginieuhlmann.bsky.social · 06/12/2025
Crank up the sound and come sing "self-supervised, we rise" with me: paper2song.com/virtual/2025... May the genius who created this be blessed with an eternity of good review karma.
paper2song.com
Paper2Song - Hear Every NeurIPS 2025 Paper as a Song
Hear research differently. 5000+ NeurIPS 2025 papers transformed into songs. Search by topic, discover ideas through music, and share what inspires you.
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Dave Barry @david-j-barry.bsky.social · 02/12/2025
Organising symposia is a whole lot less work and more fun when you've got an enthusiastic group of fellow organisers to help out. But #CBIAS2025 was my 6th and I think it's now time to step back a little. So from next year, @lankylaste.bsky.social will be taking the lead. Roll on #CBIAS2026!
Organisers of the Crick BioImage Analysis Symposium 2025
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Virginie Uhlmann @virginieuhlmann.bsky.social · 02/12/2025
If you are attending @neuripsconf.bsky.social in San Diego, go check out Anna's beautiful work on learning shape representations!
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Dave Barry @david-j-barry.bsky.social · 25/11/2025
BIOIMAGE ANALYSTS ASSEMBLE!!! #CBIAS2025
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Virginie Uhlmann @virginieuhlmann.bsky.social · 19/11/2025
So nice to see this!!!
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Joel Lüthi @joelluethi.bsky.social · 17/11/2025
We had an amazing OME-NGFF hackathon last week, Wednesday to Friday, following the inspiring OME-NGFF symposium. What a fantastic week! It’s hard to describe how motivating it is to be surrounded by so many talented, curious & friendly people who care deeply about open, FAIR bioimaging data. 1/14 🧵
Hackathon participants group picture
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Virginie Uhlmann @virginieuhlmann.bsky.social · 13/11/2025
We look forward to continuing to exchange online at the next OME-NGFF Community Call on December 16, and in person at the OME Community Meeting in Düsseldorf in April 2026. Everyone is welcome, do reach out if you are interested in more details!
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Virginie Uhlmann @virginieuhlmann.bsky.social · 13/11/2025
Finally, infinite thanks to the BioVisionCenter team (@joelluethi.bsky.social, @lorenzocerrone.bsky.social, @cfusterbarcelo.bsky.social, Valentina Marcelli, and Susanna Salas) who actually ran the show. You guys absolutely rock, thank you for being part of this adventure!
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Virginie Uhlmann @virginieuhlmann.bsky.social · 13/11/2025
This event would not have been possible without the generous support of the University of Zurich and of swissuniversities' Programme Open Science II. Thank you so much for giving us the resources to promote and develop FAIR practices in bioimaging!
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Virginie Uhlmann @virginieuhlmann.bsky.social · 13/11/2025
A gigantic thanks to all the participants for making this meeting so special! Also huge gratitude to our invited speakers who came to Zurich, some from very far away, to share their insights on next-generation file formats for microscopy data!
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Virginie Uhlmann @virginieuhlmann.bsky.social · 13/11/2025
It's inspiring to see such a vibrant community tackle the massive undertaking of building an open standard for microscopy image data, and exciting to look ahead to what we will achieve together.
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Virginie Uhlmann @virginieuhlmann.bsky.social · 13/11/2025
We wrapped up the symposium part of our 2025 International OME-NGFF workshop on Tuesday. What a phenomenal two days! I'm humbled by the incredible positive energy, talent, and enthusiasm that filled this event.
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Virginie Uhlmann @virginieuhlmann.bsky.social · 07/11/2025
She ruined so we could wreck.
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Anna Foix @afoix.bsky.social · 06/11/2025
📢 Apply now for the first DL@Janelia Bootcamp (June 4–18, 2026)! 2 weeks of hands-on deep learning for microscopy: train models on your own data, Python needed (no ML experience), housing + meals included, no registration fee 📍 Janelia Research Campus, VA 🗓️ Apply by Jan 15, 2026 🔗 shorturl.at/j4sgY
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Virginie Uhlmann @virginieuhlmann.bsky.social · 05/11/2025
Seeing our good old AURA-Net from 2021 (doi.org/10.1109/ISBI...) end up 2nd on a 2025 U-Net variants leaderboard was not on my bingo card for this year, but here we are (source: doi.org/10.48550/arX...)
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Virginie Uhlmann @virginieuhlmann.bsky.social · 22/10/2025
If you ever used napari in your research, take a moment to read this. Napari, like many other resources in the bioimaging world, is freely available despite the fact that it costs many people much time and efforts to develop and maintain it. Now you get a chance to give back, don't miss it :)
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Wolfgang Huber @wkhuber.bsky.social · 09/10/2025
My take: Engineering *is* important. Ideas are cheap. Novelty is overrated. "Hyperparameter tuning" is a cynically dismissive term for something that is in fact the real, difficult problem.
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