Behold: The full JUMP Cell Painting chemical dataset preprint! Images + 1.53 billion single-cell profiles for 115,796 compounds in human cells, made across 12 labs. All freely available 🧵 www.biorxiv.org/content/10.1...
Damian Dalle Nogare
@damiandn.bsky.social
Leading the bioimage analysis facility at Human Technopole Milan. Formerly cell and developmental biologist at the NIH. Serial immigrant 🇦🇺➡️🇳🇿➡️🇺🇸➡️🇮🇹🇪🇺. Fan of dogs, open source tools, and gin.
Early morning at the airport on my way to Dortmund for Globias 🔬💻
Hi everyone! I am looking for postdoc positions that would require strong microscopy and image analysis skills! I'm very open and willing to learn about different model systems and different microscopy approaches, (EM, SPIM, superresolution) And of course, lots and lots of image analysis!
🚨 Open PhD Positions @humantechnopole.bsky.social 🚨 Please repost and help us spread the word! 🙏 We are hiring 3 fully funded PhD positions. Here, in beautiful Milan, in the labs of myself and @janfunkey.bsky.social! 🤩 Read up on our mission here: www.linkedin.com/pulse/introd... Short 🧵...
Introducing the Multimodal AI Across Scales Programme at Human Technopole
At Human Technopole in Milan, we've spent the last year building something we think is genuinely needed: a coordinated research effort to develop AI that works across biological scales and data modali...
linkedin.com
Eat shit Republicans. You earned every bit of this.
The Napari team has really been on it with the updates recently 💪🏻
napari@napari.fosstodon.org.ap.brid.gy · 2w agonapari 0.10.0 is out! 🚀 This is a substantial release, with long-awaited new features, lots of bugfixes and improvements, and many new contributors! https://napari.org/stable/release/release_0_10_0.html Some highlights in the thread below 👇
🎉 It's out! After a long journey, I'm happy to announce that my first paper as first author is now published in Microscopy Research and Technique! 😊 "DINOSim: Training-Free Semantic Segmentation on Microscopy Images" 🧵👇
AI in Microscopy: A BioImaging Guide (bioimagingai.janelia.org) is available now! This free, online textbook bridges the gap between tool developers & microscopists + biologists. Whether you’re new to AI or already using it, we hope this book gives you the confidence to apply AI in your research.
AI in Microscopy: A BioImaging Guide
bioimagingai.janelia.org
I do think when historians look back the period the exact moment where it flipped and started going the other way won’t be anything any politician did but my Minneapolis neighbors weathering the worst of the regime in the streets, rallying together, fighting back, and winning
#HappyFluorescenceFriday #microscopycommunity - Congrats to the winner of the Wayne S. Rasband Open Source Imaging Award! Wayne S. Rasband Open Source Imaging Award – Curtis Rueden Learn more: buff.ly/hwKCCwU
We completed the publication project "Focus on the methods reproducibility of bioimage analysis", started in #GloBIAS 2024. Here is the editorial for the special issue of the Journal of Microscopy explaining the aim of this action (open access). onlinelibrary.wiley.com/doi/10.1111/...
Focus on the methods reproducibility of bioimage analysis
Click on the article title to read more.
onlinelibrary.wiley.com
We have a position open in our core facility in the @pasteur.fr . Please share it and / or apply! forum.image.sc/t/research-e...
Research engineer in Bioimage Analysis. Institut Pasteur, Image Analysis Hub - 2026
Dear all Below is an announcement for a permanent position as a Research Engineer in the Institut Pasteur, Paris. There is a flyer attached at the bottom. We are looking ideally for a Bioimage An...
forum.image.sc
🚀 napari is hiring Remote Developers-in-Residence! Join us to build the future of interactive n-dimensional data visualization in Python. 💻 60% Dev / 20% Maintenance / 20% Community & Outreach 💰 $59.50/hr (Contract, 14–35 hrs/wk) 🌍 100% Remote, open globally Learn more and apply today […]
Original post on fosstodon.org
fosstodon.org
Not to put too fine a point on it, but I have been yelling at anyone who will listen about these kinds of pseudo fluorescence i2i methods for years now. For sure some valid use cases, but infinitely many more ways it can (and will) be abused.
Christophe 🔬 Leterrier@christlet.bsky.social · 2mo agoFrom the new info my bet is fluo labeling inference pushed to 11. Hallucinating nonsensical DAPI nuclei, mitochondria stain, membrane labeling from a kind of phase contrast image: wrong localization, wrong scale, wrong movement. Keeping this movie as SWiM winner is a disgrace to the competition
What if any dataset, any size, any number of dimensions, opened in a browser tab from a link? 🔬🧪💻 Luxar is out today: write it in Python, share it as a link, explore it in any browser. Open source. 🧵 @biohub.org Preprint: doi.org/10.5281/zen... Code: github.com/royerlab/luxar
I don't know this technique, but If they're using label free imaging followed by some kind of image-to-image translation task to generate pseudo fluorescence, that would explain a lot of the weird artifacts. But, really stretching the definition of "light microscopy" here Nikon.
Kirsty Wan@micromotility.bsky.social · 2mo agoThe link states that the cilia were imaged with "diffractive super resolution microscopy" which is not a technique I have ever heard of... anyone?? Apparently based on this paper? (which at first glance does not seem as outrageous as the Nikon video) arxiv.org/abs/2512.13432
Even with all the advancements in automated cell tracking getting us to 90%+ accuracy...that's still a lot of broken tracks over long movies! Our brains are pretty good at this so I made Vizsla 🐕, a little @napari.org plugin, to help you fix your tracks manually. 👉 pypi.org/project/napa...
FOCUS-3D: Robust, generalizable volumetric cell segmentation for three-dimensional fluorescence microscopy https://www.biorxiv.org/content/10.64898/2026.08.25.746907v1
I have 3, I could auction them off to highest bidder, proceeds to resistance groups :) For sticker DIY use the template: figshare.com/articles/fig...
Woody Gurthrie - "This Machine Kills Fascists", Microsopy edition
A sticker reminding biologists/life scientists that, just like Woody Gurthrie had his guitar, they also have training and tools to help fight fascism. Biology equips us to See, Understand, Document, Report - and we can apply these in politics.
figshare.com
Had an abundance of cherry tomatoes from the garden so we're making one of the simplest - and best - pasta sauces. Garlic and tomatoes in a pot, cook long and slow with salt until they've broken down completely, add fresh basil at the end.
Spatialproteomics: a Python-based toolbox for end-to-end analysis of highly multiplexed imaging data. www.nature.com/articles/s41...
Spatialproteomics: an interoperable toolbox for analyzing highly multiplexed fluorescence image data - Nature Methods
Spatialproteomics is a Python-based toolbox that supports end-to-end analysis of highly multiplexed imaging data.
nature.com
Microscopy Nodes 3.1 is out for Blender 5.2! 🎉 This has cool new features for conditional masking, working with even larger data (regional upscaling), and data manipulation! Watch the new youtube tutorials that explain the features: www.youtube.com/playlist?lis...
