Ep 23 - So what actually IS CellPainting anyway? You may have heard of it if you're say, a fan of the @drannecarpenter.bsky.social - @shantanu-singh.cc lab (and who isn't????), but what, you know, is it? Let @erinweisbart.bsky.social break it down for you! youtu.be/9-d6DoHtgUY

Introduction to the Cell Painting Assay - AskErinDearBeth Episode 23

YouTube video by Ask Erin, Dear Beth

youtu.be

Beth Cimini 🔬💻📊@bethcimini.bsky.social · 7mo ago

Ep 22 - while we all love CellProfiler (right??), we know that often the challenging part is handling the "bookkeeping" to get your data into it in the first place. @erinweisbart.bsky.social and I do a quick overview, and then point to great longer-form materials. Welcome to AE/DB 2026!

💡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

Morphological map of under- and overexpression of genes in human cells

Nature Methods - This Resource presents the genetic subset of the 136,000 chemical and genetic perturbations tested by the Joint Undertaking for Morphological Profiling (JUMP) Cell Painting...

rdcu.be

Anne Carpenter@drannecarpenter.bsky.social · 2y ago

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...

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.

Alex Kalinin@alxndrkalinin.bsky.social · last yr.

🚨 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

🚨 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

A versatile information retrieval framework for evaluating profile strength and similarity - Nature Communications

Profiling assays measure thousands of features to uncover biological insights but lack reliable methods for quality evaluation. Here, the authors develop a versatile information retrieval framework to...

doi.org

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)

Ask Erin, Dear Beth

On Ask Erin/Dear Beth, bioimage analysis experts Beth Cimini and Erin Weisbart, of the Imaging Platform at the Broad Institute of MIT and Harvard, answer your image analysis questions! Whether it’s ab...

youtube.com

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!

Software engineering intern - summer/fall 2025 - Cambridge, MA USA

If you are a current student (undergraduate/masters/PhD) with permission to work in the US and ability to work in-person in Cambridge, MA, US, consider a summer internship in the Broad Institute Imagi...

forum.image.sc

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!)

A genome-wide atlas of human cell morphology - Nature Methods

An optical pooled cell profiling platform (PERISCOPE) based on Cell Painting and optical sequencing of molecular barcodes was used to develop the first unbiased genome-wide morphology-based perturbati...

nature.com

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

Shantanu Singh@shantanu-singh.cc · 2y ago

Please share: The Harvard School of Public Health has a paid summer research internship in biological sciences for underrepresented undergrads. Incredible opportunity to gain lab experience & mentorship while working on key public health issues. Apply by Feb 7! www.hsph.harvard.edu/biological-s...

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:

Insurers Are Dropping Homeowners as Climate Shocks Worsen (Gift Article)

Without insurance, it’s impossible to get a mortgage; without a mortgage, most Americans can’t buy a home.

nytimes.com

🧪 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

John Arevalo@johnarevalo.bsky.social · 2y ago

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

Ewald Lab

@ EMBL-EBI. We identify and characterize chemical hazards to both humans and ecosystems with cell profiling data, machine learning, and integrative data analysis.

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

Stephen Turner@stephenturner.us · 2y ago

DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA https://arxiv.org/abs/2412.05430 🧬🖥️🧪 https://github.com/kundajelab/DART-Eval

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

@emmannaemeka.bsky.social · 2y ago

forum.effectivealtruism.org/posts/May2wy... @drannecarpenter.bsky.social @daslabpombe.com The previous campaign had issues. Please support our efforts to get solar for our lab @sfv.bsky.social @solarenergyuk.bsky.social