The Cimini lab is hiring for both postdocs and interns! The postdoc role will cover bioimage analysis projects and educational material creation; the intern will be working on our Bilayers project for helping distribute and access deep learning tools for bioimage analysis. Click below to learn more!

1/ 🚀 Excited to release: napari-mcp - agentic control of napari from any MCP-capable AI assistant! Use it for interactive image processing, analysis, and visualisation! Really cool project from @ilan-theodoro.bsky.social from my team! #napari #bioimageanalysis #MCP @biohub

🚨 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/...

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...

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.

A game changer in our hands... www.nature.com/articles/s41...

Janelia is hosting a course on DL for bioimage analysis www.janelia.org/you-janelia/...

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

Segment large images without tiling artifacts: sharing our work that should have been presented at ICCV in 2 weeks - the brilliant first author Elena can’t go because of visa issues. The paper: arxiv.org/abs/2503.19545 1/🧵

Morph 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

Today @nature.com www.nature.com/articles/d41...

🔬🤖 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

If you’re interested in single cell data analysis, come give Image based profiles a try! Huge dataset being made available for exploration at this hackathon (+ symposium): Berlin, November cytodata25.eu-openscreen.eu

The 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!

The submission for 2025's BioImage Computing @iccv.bsky.social is now open. If things go like the last years, I am looking forward to all you brilliant submissions. www.bioimagecomputing.com

🚨 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

The #CVPR2025 main conference open access proceedings is up: openaccess.thecvf.com/CVPR2025 Workshop papers will be posted shortly. Stay tuned...

Our work “AI4CellFate: Interpretable Early Cell Fate Prediction with Generative AI” is finally out in @biorxivpreprint.bsky.social !!! 😍❤️ biorxiv.org/content/10.1... @scilifelab.se , @crick.ac.uk . More about it in the thread #AI4CellFate (1/n)⬇️

Lovely article from our colleague Kseniia Petrova, who has been wrongfully imprisoned for months: www.nytimes.com/2025/05/13/o...

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!

🌟 Call for Proposals: Host CytoData 2026! 🌟 We invite North American institutions to submit proposals for the 2026 symposium, whether in-person or hybrid. Nominate your institution by September 1, 2025. Join us in shaping the future of image-based profiling! docs.google.com/forms/d/e/1F...

👋 We are CytoData Society (CytoDS)! 🌟 We build and maintain an active community around image-based profiling of biological phenotypes induced by genetic, chemical, or other perturbations of biological systems. Join us to explore, share, and innovate together! #CytoData #Community

Great to see that many noise2void inspired denoising algorithms have been ported to @pytorch.org! Kudos to @florianjug.bsky.social and many others ... github.com/CAREamics/ca...

This summer, we are running a one-week intensive workshop on Python-based BioImage Analysis. Are there better ways to spend 6 days in mid-July in Boston?Probably. Would you learn as much as you will here? Probably not. Apply here: iac.hms.harvard.edu/bobiac/2025

Inexplicably, US administration has launched an unprecedented assault on science, on research institutions & on vital international organizations & initiatives. An assault on science anywhere is an assault on science everywhere; the global community must unite 🧪 www.nature.com/articles/d41...

📢 Submissions are now open for the CellMap Segmentation Challenge. Build the best method for segmenting cellular organelles in vEM using our 289 annotated volumes, 40 organelle classes, and 22 diverse cell and tissue types. 🔗 hhmi.news/410evJQ

As the aughties fade into history, let's recount the many lessons of the first leaderboard competition: The Netflix Prize.

Many still believe in overfitting. Here’s a post trying to pin down what they mean and reach some common ground. www.argmin.net/p/flavors-of...

Overfitting, as it is colloquially described in data science and machine learning, doesn’t exist. www.argmin.net/p/thou-shalt...

Very good (technical) explainer answering "How has DeepSeek improved the Transformer architecture?". Aimed at readers already familiar with Transformers. epoch.ai/gradient-upd...

The Illustrated DeepSeek-R1 Spent the weekend reading the paper and sorting through the intuitions. Here's a visual guide and the main intuitions to understand the model and the process that created it. newsletter.languagemodels.co/p/the-illust...

Excited to announce the publication of "Diffusion models for super-resolution microscopy" in JPhysPhoton! Work led by @harshithb.bsky.social with a step-by-step guide to building diffusion models to transform microscopy images from low- to high-resolution. iopscience.iop.org/article/10.1...

And to start 2025 strong… Our work #NanoPyx is out in Nature Methods 😍❤️ DOI: doi.org/10.1038/s415... #NanoPyx is a Python framework that uses the #LiquidEngine to efficiently accelerate bioimage analysis for any user! (1/n) ⬇️

Happy to share our last contribution for this year! As it turns out a spoonful of physics helps mitigate hallucinations in computational super-resolution microscopy achieved through gen #AI www.nature.com/articles/s44... @hzdr.bsky.social @mdc-berlin.bsky.social

Taking pictures of cells with a microscope, then extracting thousands of features from them is uncannily effective for quantifying cell state, esp. for genes and chemicals (e.g., Cell Painting). But we often average the rich single-cell data to simplify analysis. Can we do better? #bioML 🧪 1/n

We've a postdoc opening for our lab at the Broad: Cambridge MA! Must have experience in toxicology + data science Work on the wonderful OASIS dataset we are producing... Cell Painting, transcriptomics, proteomics in various liver cell and tissue models! broad.io/mlcbpostdoc

New Year, new job? Delighted to announce two early-career-level (post-BA/BS or MA) positions in my lab, and an open call for computational postdocs at the Broad! First, an image analysis associate - work on high content screens for all kinds of cells and dimensionalities! See more at link (1/4)

Excited to present our spotlight paper at #NeurIPS! MOTIVE is a new dataset + benchmark for predicting drug-target interactions, using Cell Painting data Location: Fri 13 Dec 4:30 p.m. PST @ East Exhibit Hall A-C #4208 Poster: neurips.cc/virtual/2024... Paper: arxiv.org/abs/2406.08649

🎉 I'm starting my own lab at EMBL-EBI (Cambridge, UK; June 2025) 🎉 We will focus on identifying and characterizing chemical hazards to humans and ecosystems using computational biology methods. I am beginning the search for two postdocs now - stay tuned for more details! ewaldlab.org

Inventors 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

Our preprint list is now up on FocalPlane. This week we focus on research in #bioimageanalysis. Drop us a message if we’re missing any preprints that you’ve been reading or writing! focalplane.biologists.com/2024/11/29/m...

Made a starter pack for microscopy and image analysis - please (self-)nominate additions! go.bsky.app/Nwa91pC

We’re thrilled to share our Nature Methods review on #CellPainting — your go-to resource for mastering Cell Painting! From MOA and toxicity prediction to contributing to candidate drugs in clinical trials, we’ve distilled 10 years of insights!

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.

Anne Gagneux, Ségolène Martin, @quentinbertrand.bsky.social Remi Emonet and I wrote a tutorial blog post on flow matching: dl.heeere.com/conditional-... with lots of illustrations and intuition! We got this idea after their cool work on improving Plug and Play with FM: arxiv.org/abs/2410.02423