💡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

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

Big shout out to the whole team: Alán F. Muñoz, Tim Treis, @shatavishadg.bsky.social , @fabiantheis.bsky.social ntheis.bsky.social, @drannecarpenter.bsky.social, @shantanu-singh.cc 6/6

🔬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

🌟 𝗥𝗲𝗺𝗶𝗻𝗱𝗲𝗿 🌟 The deadline for abstract submissions for oral presentations at Cytodata 2025 in Berlin is approaching! 👉 𝗦𝘂𝗯𝗺𝗶𝘁 𝘆𝗼𝘂𝗿 𝗮𝗯𝘀𝘁𝗿𝗮𝗰𝘁 𝗯𝘆 𝗝𝘂𝗻𝗲 25! cytodata25.eu-openscreen.eu/registration/ #BerlinConference #Imageanalysis #Microscopy

Delighted to see this out in print! It captures everything several of us in the field have been thinking about on the topic of measuring signal in high-dimensional profiling data, and I couldn't think of a better torchbearer and storyteller than @alxndrkalinin.bsky.social to champion this work.

🚨 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

Aleatoric and epistemic uncertainty are clear-cut concepts, right? ... right? 😵‍💫 In our new ICLR blogpost we let different schools of thought speak and contradict each other, and revisit chatbots where “the character of aleatory ‘transforms’ into epistemic” iclr-blogposts.github.io/2025/blog/re...

🚀🔬🦠 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

"Ich askid ChatGPT," Well Ich askid the stones, and the forest, and the rayne, and the wynde, and what thei seyde was learninge, and dreames, and growinge thinges, and a worlde wher we talke to each othir.

📚😅🎉 Yay!! I just submitted the complete manuscript of my upcoming book to the publisher! Learn to easily and clearly interpret (almost) any stats model w/ R or Python. Simple ideas, consistent workflow, powerful tools, detailed case studies. Read it for free @ marginaleffects.com #RStats #PyData

🚨Latin American Workshop Series🚨 The team from @bethcimini.bsky.social‘s lab at @broadinstitute.org and the Center for Open Bioimage Analysis will host three free online image analysis workshops for LATAM ... in SPANISH🇪🇸 and PORTUGUESE🇧🇷!!!🎉🎊 broad.io/latam_worksh... Deadline: April 23rd, 2025

Delighted to announce that @erinweisbart.bsky.social and I have teamed up to create a new bioimage analysis video podcast called Ask Erin/Dear Beth - you can check it out at the link below! It will highlight common challenges in #bioimageanalysis, as well as our favorite solutions to them. (1/x)

We're once again hiring a summer (+?) #bioimage #bioimageanalysis #software intern! Due to requirements of the funding program, you must be a current student, as well as work onsite in MA (+ have US work permission). Details at the link below. Spend your summer making great tools with fun people!

This is a room where we turn very modest salaries and budgets (and lots of coffee) into new knowledge, life-saving innovations, and technology that feeds business growth. It's literally the loom that spins hay into gold but these numpties are suddenly worried about the cost of hay.

Our paper “A genome-wide atlas of human cell morphology” is finally out today in @naturemethods.bsky.social ! www.nature.com/articles/s41... (I tweeted about our preprint in 2023 over at the bad place, but deactivated my account, so here we go again!)

🧪 Summer internship alert, Feb 7 deadline New URL: hsph.harvard.edu/fellowship-s... (+ @harvardchanschool.bsky.social is now on 🦋!)

Hey #StatsSky, what are you favorite papers to cite when you need to justify something that is obvious (I once had a reviewer ask we justify the use of logistic regression on a binary outcome) or when you need to push-back on silly reviewer requests (e.g., asking for p-values in table 1)?

I don't think it's widely clear to the #RadiologyAI community just how poorly GPT-4V compares with the top report generation models on chest X-rays, like MedVersa or MAIRA-2. It's clear we need a way to track progress.

Instead of listing my publications, as the year draws to an end, I want to shine the spotlight on the commonplace assumption that productivity must always increase. Good research is disruptive and thinking time is central to high quality scholarship and necessary for disruptive research.

Over the long term there will be progress in closing the "capability-reliability gap" for agents, but for now, I think successful applications will be ones where (1) the user is in the loop, (2) errors are relatively easy to spot and (3) aren't a deal-breaker if not spotted.

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

True luxury is found in the simplest moments.

“The climate crisis that is coming our way is not just about polar bears, and it’s not just about green jobs,” Mr. Whitehouse said. “It actually is coming through your mail slot, in the form of insurance cancellations, insurance nonrenewals and dramatic increases in insurance costs.” Gift link:

🧪 So proud of this work by the dream team of @johnarevalo.bsky.social and Ellen Su: a new graph dataset for predicting drug-target interactions, using information from Cell Painting. Stop by their poster in a few hours @ #NeurIPS! (details below) PS: John is on the job market 🚀 #bioML #MLSky

🎉 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

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

Related: Specialized Foundation Models Struggle to Beat Supervised Baselines arxiv.org/abs/2411.02796

Please join me in contributing to this worthy researcher's work (& support solar energy at the same time!)

A little fun with numbers on this Sunday, showing just how successful DNA really is. First, here's what DNA looks like. I'll draw your attention to the "rise" in DNA, that is, the distance between two basepairs, which is 3.4 Angstroms, also known as 3.4x10^-10 meters...

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...

This is really horrific. These single cell reference atlases are widely used as is to train all kinds of models! This is one of the reasons I've constantly harping about uniform reprocessing & extremely careful QC of large atlases. 1/

Reposting two starter packs with researchers working on AI4Science for those who are newly joining 🦋. So many wonderful folks on these lists, help me add more by sending names (including your own 😊). Starter Pack 2: go.bsky.app/GnFTUM6 Starter Pack 1: go.bsky.app/JeFdryY

Three BioML starter packs now! Pack 1: go.bsky.app/2VWBcCd Pack 2: go.bsky.app/Bw84Hmc Pack 3: go.bsky.app/NAKYUok DM if you want to be included (or nominate people who should be!)

My #I2K204 workshop is admittedly pretty specific, but if you're interested in accessing Cell Painting data on the Cell Painting Gallery, hopefully you find it helpful! Up on YouTube now. www.youtube.com/watch?v=ikzP... Thanks @bioimagingna.bsky.social for getting all the sessions up on YouTube!

PCPs on #MedSky must share this clear, compelling data with their >65 yo patients: getting last year’s COVID shot made you about 2.5 times less likely to end up in the hospital and 4 times less likely to die from COVID last winter—even if you’d had all the earlier shots and COVID before.

This is very interesting and highly relevant paper to clinical genetics and rare disease researchers. I wrote the accompanying News & Views piece. Free sharing link here: rdcu.be/d0VlK

One full year to get ready: join us next year in Berlin-Buch if you're into spatial biology, morphology and/or high-content perturbation screens! 🔬💻 #CytoData #Microscopy #ImageBasedProfiling

I must admit that this annotated Nature abstract remains a useful recipe for constructing a summary paragraph. I show it to my students every time we get started.

I really hope we can keep this place fun, informative, relevant, and a place for engaging scientific discussion, where we all take the most charitable interpretation possible of those we're engaging with, ie the opposite of Twitter. Hence, trying to avoid boosting accts with hot takes, snark, etc.!

A delightful thread on the follow-up to the U-turn on double descent paper, extending explanations to neural network learning Context: 1. Seminal article on double descent arxiv.org/abs/2105.14368 2. U-turn paper, which ~demystified double descent (but not for NNs) arxiv.org/abs/2310.18988

From double descent to grokking, deep learning sometimes works in unpredictable ways.. or does it? For NeurIPS(my final PhD paper!), @alanjeffares.bsky.social & I explored if&how smart linearisation can help us better understand&predict numerous odd deep learning phenomena — and learned a lot..🧵1/n

@drannecarpenter.bsky.social @shantanuxsingh.bsky.social #preprint We developed NeuroPainting, an advanced morphological profiling tool adapted from Cell Painting, tailored for neural cells. This method captures over 4,000 cellular traits, setting a new standard for neuropsychiatric research. 🧠🔍

Absolutely! There’s this great talk with Meredith and Arvind which is such a treat. cdh.princeton.edu/events/2023/...

Student Researcher positions in EMEA now accepting applications! Please repost. www.google.com/about/career...

Now that "scale is all we need" has predictably faltered... 1. Small AI models often perform better in context. 2. Obsession w bigness has bad consequences, from climate, to power concentration, to research capture. Me + @gaelvaroquaux.bsky.social @sashamtl.bsky.social arxiv.org/abs/2409.14160

Janelia is recruiting AI scientists and theory fellows to collaborate with experimental scientists on hard biological problems - these positions have a considerable level of independence and very competitive salaries. Join our great community! Ai.hhmi.org janelia.org/theoryfellow #neuroscience #AI

How to write an excellent Review article https://www.nature.com/articles/s44222-024-00256-4 (read free: https://rdcu.be/d0aKY)

🧪 Excited to see this go live today! We wrote a Preview article exploring the stunning work by Lacoste, Haghighi and colleagues @drannecarpenter.bsky.social @shantanuxsingh.bsky.social @mike_tilapia in the latest edition of Cell. doi.org/10.1016/j.xg...

You have 10 more days to apply for an internship with me, Ava Amini, Alex Lu, Lorin Crawford, or Kristen Severson! Make sure you include a research statement with your application. jobs.careers.microsoft.com/global/en/jo...