Shantanu Singh
@shantanu-singh.cc
computation biology, drug discovery, computer vision, microscopy, statistics, machine learning, all happening at https://carpenter-singh-lab.broadinstitute.org/
Reposted by Shantanu Singh
💡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
1/6 #iccv2025
October 23, 2025 at 6:01 PM
💡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
1/6 #iccv2025
Reposted by Shantanu Singh
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/ezGre
August 7, 2025 at 1:36 PM
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/ezGre
Reposted by Shantanu Singh
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
6/6
Bluesky
ntheis.bsky.social
July 8, 2025 at 7:22 PM
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
6/6
Reposted by Shantanu Singh
🔬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 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
July 8, 2025 at 7:22 PM
🔬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 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
Reposted by Shantanu Singh
🌟 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
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
June 20, 2025 at 10:35 AM
🌟 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
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
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
June 11, 2025 at 12:59 PM
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.
Reposted by Shantanu Singh
🚨 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
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
June 10, 2025 at 7:54 PM
🚨 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
More in the 🧵 below:
1/7
Reposted by Shantanu Singh
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...
May 8, 2025 at 8:18 AM
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...
Reposted by Shantanu Singh
🚀🔬🦠 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
paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n
May 3, 2025 at 7:12 PM
🚀🔬🦠 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
paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n
Reposted by Shantanu Singh
"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.
May 7, 2025 at 3:45 AM
"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.
Reposted by Shantanu Singh
📚😅🎉
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
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
April 10, 2025 at 7:06 PM
📚😅🎉
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
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
Reposted by Shantanu Singh
🚨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
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
April 10, 2025 at 1:36 PM
🚨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
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
Reposted by Shantanu Singh
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...
www.youtube.com
April 7, 2025 at 10:11 PM
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)
Reposted by Shantanu Singh
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
March 7, 2025 at 2:23 PM
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!
Reposted by Shantanu Singh
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.
It's literally the loom that spins hay into gold but these numpties are suddenly worried about the cost of hay.
February 10, 2025 at 11:59 PM
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.
It's literally the loom that spins hay into gold but these numpties are suddenly worried about the cost of hay.
Reposted by Shantanu Singh
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!)
(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...
www.nature.com
January 27, 2025 at 6:23 PM
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!)
(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 🦋!)
New URL: hsph.harvard.edu/fellowship-s...
(+ @harvardchanschool.bsky.social is now on 🦋!)
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...
www.hsph.harvard.edu/biological-s...
January 8, 2025 at 3:27 PM
🧪 Summer internship alert, Feb 7 deadline
New URL: hsph.harvard.edu/fellowship-s...
(+ @harvardchanschool.bsky.social is now on 🦋!)
New URL: hsph.harvard.edu/fellowship-s...
(+ @harvardchanschool.bsky.social is now on 🦋!)
Reposted by Shantanu Singh
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)?
or when you need to push-back on silly reviewer requests (e.g., asking for p-values in table 1)?
January 6, 2025 at 8:15 AM
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)?
or when you need to push-back on silly reviewer requests (e.g., asking for p-values in table 1)?
Reposted by Shantanu Singh
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.
It's clear we need a way to track progress.
December 18, 2024 at 8:48 PM
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.
It's clear we need a way to track progress.
Reposted by Shantanu Singh
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.
December 20, 2024 at 11:18 AM
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.
Reposted by Shantanu Singh
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.
December 20, 2024 at 9:32 PM
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
#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.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:raswr6mjt7sbppdo6kcce4mz/bafkreicppuq2utmxkx5kpaggndigq7qcat6ppdqqajxhphpyi53ydlbbeq@jpeg)
December 19, 2024 at 11:31 PM
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
#bioML 🧪
1/n
Reposted by Shantanu Singh
True luxury is found in the simplest moments.
December 18, 2024 at 8:59 PM
True luxury is found in the simplest moments.
Reposted by Shantanu Singh
“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.
www.nytimes.com
December 18, 2024 at 9:07 PM
“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
Stop by their poster in a few hours @ #NeurIPS! (details below)
PS: John is on the job market 🚀
#bioML #MLSky
December 13, 2024 at 9:43 PM
🧪 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
Stop by their poster in a few hours @ #NeurIPS! (details below)
PS: John is on the job market 🚀
#bioML #MLSky