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Virginie Uhlmann

@virginieuhlmann.bsky.social
2K followers 86 following 47 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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Reposted by Virginie Uhlmann
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
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 · 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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Reposted by Virginie Uhlmann
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
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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Reposted by Virginie Uhlmann
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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Reposted by Virginie Uhlmann
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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Reposted by Virginie Uhlmann
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 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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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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Anna Foix @afoix.bsky.social · 23/09/2025
Thrilled to be speaking at #CBIAS2025! 🥳 CBIAS has been my scientific home since the beginning of my PhD, providing a welcoming space for early-career researchers. This year feels extra special, as I’ll be presenting my work in the final year of my PhD. Join us if you get the chance! 😃
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Crick BioImage Analysis Symposium @cbias.bsky.social · 23/09/2025
The program for the #CBIAS2025 is now live – space is limited, so register now to secure your spot! 24th-25th Nov, Wellcome Trust, London (UK) - see you there! 🔗⬇️ www.crick.ac.uk/whats-on/cri...
CBIAS2025 flier, showing the conference logo, listing the topics, confirmed speakers and sponsors. On the top right corner, a QR code is available to access the registration page.
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Virginie Uhlmann @virginieuhlmann.bsky.social · 23/09/2025
You may have heard me talk about learned shape representations for a long time, but it took @afoix.bsky.social's hard work to bring it to life 🍾 Catch her at @neuripsconf.bsky.social to find out more!!
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Joel Lüthi @joelluethi.bsky.social · 18/09/2025
Want to hack with ~40 motivated developers in the OME-Zarr space this fall in Zurich, November 12 - 14th? The application window for the 2025 OME-NGFF workflows hackathon is closing on September 30th! Apply here to be part of this exciting week about OME-Zarr: forms.gle/849cf2fBk1pJ...
forms.gle
2025 OME-NGFF Workflows Hackathon application
The 2025 OME-NGFF Workflows Hackathon has a limited number of seats. A selected number of applicants will be invited to participate by the organizing committee from their application. The hackathon is...
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Virginie Uhlmann @virginieuhlmann.bsky.social · 16/09/2025
I am in this picture and I don't like it
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The BioImage Archive @bioimagearchive.bsky.social · 15/09/2025
🎉 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
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Dave Barry @david-j-barry.bsky.social · 01/09/2025
The abstract submission deadline for #CBIAS2025 has just closed and, for the first time, we have a near perfect gender-balance in our abstract submissions. In fact, we have slightly more submissions from women than men.
media.tenor.com
a man with his arms crossed is smiling and saying noice !
ALT: a man with his arms crossed is smiling and saying noice !
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Erick Ratamero @erickratamero.com · 25/08/2025
I'll be there! Giving a talk! and hacking on _something_ for a few days!
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Virginie Uhlmann @virginieuhlmann.bsky.social · 25/08/2025
Once is an exception, twice is a trend, thrice is a tradition! Save the date for our now-traditional annual OME-NGFF extravaganza in Zurich! Whether you’ve just heard about OME-NGFF and are curious to learn more or if you are working with it every day, there is something for everyone this year!
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Virginie Uhlmann @virginieuhlmann.bsky.social · 21/07/2025
Our project BioFAIR: Towards FAIR Practices in Bioimaging has been selected for funding through the swissuniversities Open Science II Programme (www.swissuniversities.ch/en/topics/op...)! More OME-Zarr and open microscopy community events on the horizon yay!!! 🔥🔥🔥
swissuniversities.ch
Funded Projects - swissuniversities
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Virginie Uhlmann @virginieuhlmann.bsky.social · 24/06/2025
And just like that @katharinaweins.bsky.social and Elvira Isenring managed to make us look cooler than we'll ever be: www.youtube.com/watch?v=8t8R...
youtube.com
Bioimaging | UZH Research Spotlight
YouTube video by Universität Zürich
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Virginie Uhlmann @virginieuhlmann.bsky.social · 03/06/2025
Hey bioimaging folks, join us for the next OME-NGFF Community Call on June 24 at 9:00 CEST and 17:00 CEST! Details and agenda on the one and only image.sc here: forum.image.sc/t/join-us-fo...
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BioImaging North America @bioimagingna.bsky.social · 02/05/2025
#HappyFluorescenceFriday #microscopycommunity. @bioimagingna.bsky.social was at OME205 with @openmicroscopy.org this past week with the makers of BioFormats. OME-TIFF, OME-Zarr and OMERO sharing their work and listening to your challenges.
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Joel Lüthi @joelluethi.bsky.social · 29/04/2025
🚀 We just released a major Fractal update! More flexible workflows, dynamic monitoring, and a new history system for better traceability – built to handle Terabytes of high-dimensional microscopy data in #OME-Zarr. Full announcement post here: fractal-analytics-platform.github.io/news/2025-04...
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Jan Funke @janfunkey.bsky.social · 18/04/2025
How can AI help you to analyze your microscopy images? Find out at the "Machine Learning for Microscopy Image Analysis" course at the @mblscience.bsky.social in Woods Hole from Aug 22-Sep 6! Applications are due 🚨 April 30 🚨 Read on for more! 👇 www.mbl.edu/education/ad...
mbl.edu
AI@MBL: Machine Learning for Microscopy Image Analysis | Marine Biological Laboratory
The goal of this course is to familiarize researchers in the life sciences with state-of-the-art deep learning techniques for microscopy image analysis and to introduce them to tools and frameworks th...
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Etch a Cell @etchacell.bsky.social · 27/03/2025
What an incredible first week for Etch A Cell - ImmunoExplorers! 🚀 ✨ 688 volunteers have together contributed 23,474 classifications (and counting!), helping us reach 72% completion of our first dataset. Join the effort here: 🔗 www.zooniverse.org/projects/h-s... Thank you 🙌 #CitizenScience
This is a screenshot of the project's landing page, showing the statistics quoted in the tweet - 688 volunteers have made 23,474 classifications
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Etch a Cell @etchacell.bsky.social · 19/03/2025
Be a part of groundbreaking research! 🔬 Help us study immune cells & fight transplant rejection: www.zooniverse.org/projects/h-s... Together, we can make a difference! 💪 #CitizenScience #KidneyHealth #Zooniverse (6/6) ✅
This image shows most of the Etch A Cell - ImmunoExplorers project team at a Christmas Market
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