Virginie Uhlmann
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.
- Reposted by Virginie Uhlmann🚨 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/...
- Reposted by Virginie UhlmannThe 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...
- Somehow this made me smile more than it should reasonably have
- Apples xkcd.com/3180/
- 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.
- 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!!
- Reposted by Virginie UhlmannOrganising 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!
- If you are attending @neuripsconf.bsky.social in San Diego, go check out Anna's beautiful work on learning shape representations!
- We’ll be at @neuripsconf.bsky.social on Wednesday, 3 December, from 11 a.m. to 2 p.m. (San Diego time). Come and chat with us about why distance matrices and invariances are cool! 🎉 #InterdisciplinaryML #neurips2025 #bioimageanalysis #shapequantification
- Reposted by Virginie UhlmannBIOIMAGE ANALYSTS ASSEMBLE!!! #CBIAS2025
- So nice to see this!!!
- Reposted by Virginie UhlmannWe 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 🧵
- 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.
- 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.
- 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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View full threadWe 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!
- Reposted by Virginie Uhlmann📢 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
- 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...)
- 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 :)
- You might have noticed lots of activity in the napari project recently! 🚀 We're grateful for a grant from CZI that's keeping us going, but grants don't last forever: we're trying to figure out sustainable long term funding. Read our blog post to find out how you can help: napari.org/island-dispa...
- Reposted by Virginie UhlmannMy 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.
- Reposted by Virginie UhlmannThrilled 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! 😃
- The provisional program for The 6th Crick Bioimage Analysis Symposium (#CBIAS2025) is live! Join us at the @wellcomecollection.bsky.social in London in November for incredible talks, posters and insightful discussions. Space is limited - register now! www.crick.ac.uk/whats-on/cri...
- Reposted by Virginie UhlmannThe 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...
- 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!!
- Happy to share that ShapeEmbed has been accepted at @neuripsconf.bsky.social 🎉 SE is self-supervised framework to encode 2D contours from microscopy & natural images into a latent representation invariant to translation, scaling, rotation, reflection & point indexing 📄 arxiv.org/pdf/2507.01009 (1/N)
- Reposted by Virginie UhlmannWant 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...
- We're happy to announce the 2025 International OME-NGFF workshop 🎉 📅 Dates: - Symposium: Nov 10–11, 2025 - Hackathon: Nov 12–14, 2025 📍 Location: Zurich, Switzerland Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up... #bioimaging #openscience #OMENGFF #OMEZarr (1/x 🧵)
- I am in this picture and I don't like it
- Reposted by Virginie Uhlmann🎉 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
- Reposted by Virginie UhlmannThe 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.
- Reposted by Virginie UhlmannI'll be there! Giving a talk! and hacking on _something_ for a few days!
- We're happy to announce the 2025 International OME-NGFF workshop 🎉 📅 Dates: - Symposium: Nov 10–11, 2025 - Hackathon: Nov 12–14, 2025 📍 Location: Zurich, Switzerland Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up... #bioimaging #openscience #OMENGFF #OMEZarr (1/x 🧵)
- 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!
- We're happy to announce the 2025 International OME-NGFF workshop 🎉 📅 Dates: - Symposium: Nov 10–11, 2025 - Hackathon: Nov 12–14, 2025 📍 Location: Zurich, Switzerland Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up... #bioimaging #openscience #OMENGFF #OMEZarr (1/x 🧵)
- 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!!! 🔥🔥🔥
- 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...
- 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...
- Reposted by Virginie Uhlmann#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.
- Reposted by Virginie Uhlmann🚀 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...
- Reposted by Virginie UhlmannHow 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...
- Reposted by Virginie UhlmannWhat 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
- Reposted by Virginie UhlmannBe 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) ✅
- Share this with everyone you know and help us hunt the immune cells!!!
- Reposted by Virginie UhlmannCalling all... 🔬 Microscopists 💻 BioImage Analysts 👩🔬 Life Scientists 📅 Save the Date The 5th edition of the Crick BioImage Analysis Symposium will take place on November 24/25th 2025. More details to follow... #CBIAS2025
- Reposted by Virginie UhlmannBuilding a truly interdisciplinary bioimaging culture! 👯 Our latest article explores how #opendata sharing can create interdisciplinary collaboration and scientific discovery: doi.org/10.1242/jcs.... Find out, how NFDI4Bioimage contributes to this vision: nfdi4bioimage.de/about-us/goa...
- Reposted by Virginie Uhlmann🌍 Who joined us? 👩🔬 43 participants from academia & industry 🏢 40 affiliations 📍 11 countries across Europe & the US OME-Zarr is a global effort! 🧵 (11/15)
- Turns out that when a group of interesting and enthusiastic scientists who care about open standards sit together for a couple of days, they do great things 🔥🔥🔥
- 🚀 We’re very excited to share our latest preprint on OME-Zarr! 🚀 Our report on the 2024 OME-NGFF Workflows Hackathon is a deep dive into the status of OME-Zarr and the great work that happened last November at the BioVisionCenter in Zurich. 🔗 Read the preprint: osf.io/preprints/bi... 🧵 (1/15)
- Reposted by Virginie Uhlmann@virginieuhlmann.bsky.social talked @tlmcambridge.bsky.social online seminar series about: Turning morphology into numbers across microscopy scales and modalities; a perforce ride from imaging to image analysis to model generation to prediction. bio-mat-sketches-mor.blogspot.com/2025/03/virg...
- Join us at the Open Microscopy Community meeting 2025! 🦞🦞🦞
- Happy #FluorescenceFriday! #microscopycommunity. Join the Open Microscopy Community meetings #OME2025 at MBL, MA, April 28-May 1. Register today buff.ly/3CYC0tS to join the conversation on image data sharing & formats ...BioFormats, OME-Zarr... @bioimagingna.bsky.social @openmicroscopy.org
- Herausgeberannahmefreude: the joy of hitting the "accept" button in the editorial manager.
- Different year, different conference, same vibe.
- Because the real treasure wasn't the Science paper, but the friends we made along the way: thenode.biologists.com/behind-the-p...
- Reposted by Virginie UhlmannKnow someone looking for a new start in 2025? 🔍 Colleagues of #BlueSci, help flex this new social muscle! 🦾
- A library.
- #CBIAS2024 attendees group photo. Is there a collective noun for a dense group of image analysts?
- Reposted by Virginie UhlmannThis week, we're hosting the #OME_NGFF_Hackathon 2024 at the BioVisionCenter at the University of Zurich. We're bringing together 40 motivated researchers and specialist for #OMEZarr workflows, #OMEZarr Python tools & #OMEZarr Java tools. (1/3)
- Reposted by Virginie UhlmannThere's still time to register for #CBIAS2024 - join us online if you can't make it in person
- Leaving Twitter like
- Reposted by Virginie UhlmannI don't think I saw this on social media at all: a bunch of very clever people (including our team) has put together a federated bioimage repository based on OME-Zarr with 500TB of data in 4 months! ome.github.io/ome2024-ngff...
- Bioimage analysts have a huge impact on modern biology research and can enable so much more when appropriately resourced. Read our piece and maybe also casually drop it on the desk of your PI/Head of Department/Dean/rich uncle!
- New from a huge cast of amazing #bioimage analysts in the Journal of Cell Science - "The crucial role of bioimage analysts in scientific research and publication" journals.biologists.com/jcs/article/... . Hop into 🧵to learn more! (1/x) #bioimaging #microscopy #bioimageanalyst
- If you didn't yet have enough good reasons to share your bioimage data, Matthew, Josh (@joshmoore.bsky.social), Erin, Assaf and I are here with squirrel drawings to convince you that you should do it: journals.biologists.com/jcs/article/...
- Reposted by Virginie UhlmannI made to the #BioVisionCenter kick-off symposium! I’m so excited about this place being built in the heart of Zurich. And… OMG… the vision is great and first hires pure gold! @virginieuhlmann.bsky.social and Joel Lüthi (not on bsky?). biovisioncenter.uzh.ch/de.html
