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Shantanu Singh

@shantanu-singh.cc
3.8K followers 886 following 62 posts

computation biology, drug discovery, computer vision, microscopy, statistics, machine learning, all happening at carpenter-singh-lab.broadinstitute.…

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Reposted by Shantanu Singh
Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 20/01/2026
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
youtu.be
Introduction to the Cell Painting Assay - AskErinDearBeth Episode 23
YouTube video by Ask Erin, Dear Beth
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Alex Kalinin @alxndrkalinin.bsky.social · 23/10/2025
💡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
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Niranj Chandrasekaran @niranjchandrasekaran.com · 07/08/2025
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
rdcu.be
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...
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Alex Kalinin @alxndrkalinin.bsky.social · 08/07/2025
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
ntheis.bsky.social
Bluesky
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Alex Kalinin @alxndrkalinin.bsky.social · 08/07/2025
🔬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
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cytodata.bsky.social @cytodata.bsky.social · 20/06/2025
🌟 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
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Shantanu Singh @shantanu-singh.cc · 11/06/2025
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.
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Alex Kalinin @alxndrkalinin.bsky.social · 10/06/2025
🚨 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
doi.org
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...
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Michael Kirchhof @mkirchhof.bsky.social · 08/05/2025
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...
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Marius Pachitariu @marius10p.bsky.social · 03/05/2025
🚀🔬🦠 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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Chaucer Doth Tweet @levostregc.bsky.social · 07/05/2025
"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.
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Vincent Arel-Bundock @vincentab.bsky.social · 10/04/2025
📚😅🎉 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
Model to Meaning: How to interpret statistical models with marginaleffects for R and Python
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Esteban Miglietta @emiglietta.bsky.social · 10/04/2025
🚨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
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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 07/04/2025
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)
youtube.com
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...
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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 07/03/2025
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!
forum.image.sc
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...
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c0nc0rdance @c0nc0rdance.bsky.social · 10/02/2025
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.
A research lab from Northwestern, chosen because it's generic and sort of zoomed out.  Three scientists are visible in lab coats, and there are benches and shelving, with glass along one wall showing another high-rise building nearby. Overhead fluorescents provide light.
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JT Neal @jtneal.bsky.social · 27/01/2025
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!)
nature.com
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...
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Shantanu Singh @shantanu-singh.cc · 08/01/2025
🧪 Summer internship alert, Feb 7 deadline New URL: hsph.harvard.edu/fellowship-s... (+ @harvardchanschool.bsky.social is now on 🦋!)
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Mattan S. Ben-Shachar @mattansb.msbstats.info · 06/01/2025
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)?
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Pranav Rajpurkar PhD @rajpurkar.bsky.social · 18/12/2024
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.
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Rosa Ritunnano @rritunnano.bsky.social · 20/12/2024
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.
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Arvind Narayanan @randomwalker.bsky.social · 20/12/2024
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.
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Shantanu Singh @shantanu-singh.cc · 19/12/2024
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
(a) Human U2OS cells treated with dimethyl sulfoxide (DMSO) and stained using the Cell Painting assay, which employs six dyes in five channels to label eight cellular compartments. The top row (from left to right) shows mitochondrial staining; actin, Golgi, and plasma membrane staining; and nucleolar and cytoplasmic RNA staining. The bottom row (from left to right) displays endoplasmic reticulum staining, DNA staining, and a montage of all five channels (from Cimini et al. [21]). (b) Thousands of features are extracted from each segmented cell in microscopy images of wells. A learned function f(x) (CytoSummaryNet) aggregates this data into a single feature vector: the sample’s profile. (c) An in-depth look at the model architecture used in this study. The model consists of three elements: a function φ(x), which maps the input data from ℝD to ℝL space, a summation, which collapses the cell dimension, and ρ(z), which maps the collapsed representation from ℝN to ℝL space. (d) During training, replicate compound profiles are forced to attract each other (green arrows) and simultaneously repel every other compound (red arrows) in the learned feature space. Here, all forces are drawn for a single profile of compound B.
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Daniel Rolph Author @danielrolphauthor.bsky.social · 18/12/2024
True luxury is found in the simplest moments.
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Omar Wasow @owasow.bsky.social · 18/12/2024
“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:
nytimes.com
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.
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Shantanu Singh @shantanu-singh.cc · 13/12/2024
🧪 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
Diagram showing 3.6k drugs, 11.5k genes, and the counts of "ground truth" relationships among them.
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Jess Ewald @ewaldlab.org · 13/12/2024
🎉 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
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.
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John Arevalo @johnarevalo.bsky.social · 13/12/2024
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
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Stephen Turner @stephenturner.us · 12/12/2024
Related: Specialized Foundation Models Struggle to Beat Supervised Baselines arxiv.org/abs/2411.02796
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Anne Carpenter @drannecarpenter.bsky.social · 12/12/2024
Please join me in contributing to this worthy researcher's work (& support solar energy at the same time!)
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John Doench @johndoench.bsky.social · 08/12/2024
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...
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Anne Carpenter @drannecarpenter.bsky.social · 04/12/2024
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...
biorxiv.org
Morphological map of under- and over-expression of genes in human cells
Cell Painting images offer valuable insights into the state of a cell and enable many biological applications, but publicly available arrayed datasets only include hundreds of genes perturbed. The JUM...
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Anshul Kundaje @anshulkundaje.bsky.social · 04/12/2024
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/
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Ben Blaiszik @benblaiszik.bsky.social · 03/12/2024
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
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 03/12/2024
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!)
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Erin Weisbart @erinweisbart.bsky.social · 26/11/2024
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!
youtube.com
Browsing, Filtering, and Downloading Data in the Cell Painting Gallery
YouTube video by I2K Conference
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Shantanu Singh @shantanu-singh.cc · 21/11/2024
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.
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Gerome Breen @psychgenomics.bsky.social · 20/11/2024
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
rdcu.be
Common genetic variants contribute more to rare diseases than previously thought | Nature
In rare diseases, rare mutations have long been thought of as the only contributor. Genetic analyses of people with such conditions now suggest that the effects of common genetic variants can stack up and contribute to disease risk. Assessing the influence of common mutations on rare disease risk.
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Loan Vulliard @lvulliard.bsky.social · 20/11/2024
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
Poster for the CytoData 2025 event on image-based profiling: Hackathon November 17-19, 2025 and Symposium November 20-21, 2025.
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Itai Yanai @itaiyanai.bsky.social · 19/11/2024
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.
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Stephen Turner @stephenturner.us · 19/11/2024
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.!
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Shantanu Singh @shantanu-singh.cc · 19/11/2024
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
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Alicia Curth @aliciacurth.bsky.social · 18/11/2024
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
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Matthew Tegtmeyer @tegtmeyerlab.bsky.social · 18/11/2024
@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. 🧠🔍
biorxiv.org
Combining NeuroPainting with transcriptomics reveals cell-type-specific morphological and molecular signatures of the 22q11.2 deletion
Neuropsychiatric conditions pose substantial challenges for therapeutic development due to their complex and poorly understood underlying mechanisms. High-throughput, unbiased phenotypic assays presen...
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Stefanie Sirén-Heikel @mssiren.bsky.social · 18/11/2024
Absolutely! There’s this great talk with Meredith and Arvind which is such a treat. cdh.princeton.edu/events/2023/...
cdh.princeton.edu
LLM Forum: Meredith Whittaker with Arvind Narayanan (topic: society)
LLM Forum: Meredith Whittaker with Arvind Narayanan (topic: society)
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Marc Lanctot @sharky6000.bsky.social · 18/11/2024
Student Researcher positions in EMEA now accepting applications! Please repost. www.google.com/about/career...
google.com
Student Researcher, 2025 — Google Careers
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Meredith Whittaker @meredithmeredith.bsky.social · 17/11/2024
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
arxiv.org
Hype, Sustainability, and the Price of the Bigger-is-Better Paradigm in AI
With the growing attention and investment in recent AI approaches such as large language models, the narrative that the larger the AI system the more valuable, powerful and interesting it is is increa...
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Carsen Stringer @computingnature.bsky.social · 14/11/2024
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
AI at hhmi, link ai.hhmi.org; theory fellows, link janelia.org/theoryfellow
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Stephen Turner @stephenturner.us · 14/11/2024
How to write an excellent Review article www.nature.com/articles/s44222-024-… (read free: rdcu.be/d0aKY)
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Lucy Dornan @lucygdornan.bsky.social · 13/11/2024
🧪 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...
This image portrays a graphical abstract for the Cell Genomics Preview article by Dornan & Simpson (2024). This graphical abstract summarises the workflow and key findings of a research paper by Lacoste, Haghighi and colleagues in the most recent edition of Cell. In summary, 3,448 variants from a collection of 1,269 genes were GFP-tagged and transfected into cells. Using high-content screening microscopy, the researchers identified that improper localisation of proteins encoded by the gene variants accounted for a huge 16% of all pathogenic variants studied. Upon further investigation, they also found that mislocalisation correlated with disease severity, and that mislocalised proteins also tended to be unstable and misfolded. This work has highlighted the importance of correct protein localisation, and developed a highly effective and useful screening system for the identification of mislocalised proteins which has huge implications for alternative and innovative drug discovery methods.
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