Alex Kalinin
AI x Bioimaging @biohub.org | prev Broad Institute, CUHK-SZ & UMich
- Reposted by Alex Kalinin🚨 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/...
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- Excited to be in sunny San Diego for #NeurIPS2025 🌴 Biohub @czbiohub.bsky.social has a booth! Stop by to see cool demos from our computational imaging group and chat about AI for bioimaging.
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- Today is the last chance to register for #CytoData2025. Don’t miss a fantastic program covering the full spectrum of image-based profiling! cytodata25.eu-openscreen.eu
- 💡Just presented our new paper at the @iccv.bsky.social BioImage Computing workshop: cubic: CUDA-accelerated 3D Bioimage Computing. We introduce a simple way to add GPU acceleration to scikit-image–based bioimage processing pipelines by swapping import statements. 🧵 1/6 #iccv2025
- scikit-image is widely used across bioimage analysis (incl. under the hood in CellProfiler), but with large 3D volumes and long time-lapse datasets, CPU execution often becomes the bottleneck. 2/6
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- Reposted by Alex KalininMorph Map is now published in Nature Methods. Excited to see what the community discovers with this resource mapping ~15,000 human genes! rdcu.be/ezGre
- Now on biorxiv! The JUMP-Cell Painting Consortium’s paper: “Morphological map of under- and over-expression of genes in human cells” This is the genetic perturbation portion of the JUMP’s dataset; our chemical perturbation paper will come in a few months www.biorxiv.org/content/10.1...
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- 🔬🤖 Introducing Spotlight: virtual staining (VS) improved by focusing on cells VS models often learn to predict both cells and noisy background, because training treats all pixels equally. We address this by explicitly training models to prioritize foreground. 1/5
- 🔬API-first feature extraction for image-based profiling workflows If you need to obtain interpretable features from your segmented microscopy images, but want to do it in a fully automated way, we know the struggle. 1/6
- We felt there were a limited number of programmatic tools for featurizing segmented cell images, and CellProfiler is the de-facto standard for interpretable features. 2/6
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- Reposted by Alex KalininThe 2nd AI4Life Challenge is live! Calling the AI & bioimaging community to tackle a key microscopy challenge: removing noise while preserving detail. 📦 Paired noisy/clean datasets 📈 Ground-truth evaluation 🧠 DL focus Build, test, compete 👉 ai4life.eurobioimaging.eu/challenge-2/
- There is still time to submit an abstract to CytoData 2025!
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- 🚨 New paper alert! We developed a versatile information retrieval framework that uses mean average precision (mAP) to robustly quantify sample activity and similarity in large-scale profiling data. Now out @natcomms.nature.com: doi.org/10.1038/s414... More in the 🧵 below: 1/7
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- CytoData is going to Berlin this November! Submit an abstract for oral presentation by June 25, 2025.
- Turns out Transformers do outperform Cellpose when trained by Marius and Carsen 😄 Super exiting to see this being released and can't wait to try it out on our data!
- 🚀🔬🦠 Releasing 🤖Cellpose-SAM🤖, a cellular segmentation algorithm with superhuman generalization 🦸♀️. Try it now on 🤗 huggingface.co/spaces/mouse... paper: www.biorxiv.org/content/10.1... w/ @computingnature.bsky.social 1/n
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- Reposted by Alex KalininInventors of flow matching have released a comprehensive guide going over the math & code of flow matching! Also covers variants like non-Euclidean & discrete flow matching. A PyTorch library is also released with this guide! This looks like a very good read! 🔥 arxiv: arxiv.org/abs/2412.06264
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- Excited to see this being out! It was so great to work with such a star team on this project and can't wait to see what opportunities these data can open.
- Now on biorxiv! The JUMP-Cell Painting Consortium’s paper: “Morphological map of under- and over-expression of genes in human cells” This is the genetic perturbation portion of the JUMP’s dataset; our chemical perturbation paper will come in a few months www.biorxiv.org/content/10.1...
