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Erin Weisbart

@erinweisbart.bsky.social
210 followers 62 following 14 posts

Bioimage Analyst. I help people turn pictures into numbers. Overly passionate about documentation and FAIR data. Senior Staff Scientist in the Cimini Lab at the Broad. I also read, knit, sew, bake, and herd cats.

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 07/05/2026
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!
forum.image.sc
Postdoctoral Associate and Data Science Intern roles - Broad Institute, Cambridge MA USA
The Broad Institute Imaging Platform (the team behind CellProfiler, Piximi, and Bilayers) is currently hiring for postdoctoral and intern roles! Postdoc role: we are looking for 1-2 candidates who ha...
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Ask Erin / Dear Beth @askerindearbeth.bsky.social · 13/04/2026
We're turning 29 episodes old! Learn from @erinweisbart.bsky.social and @bethcimini.bsky.social about Pooled Cell Painting, Cell Painting's version of Optical Pooled Screening. It's high-throughput heaven!
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Introduction to Pooled Cell Painting - AskErinDearBeth Episode 29
YouTube video by Ask Erin, Dear Beth
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Ask Erin / Dear Beth @askerindearbeth.bsky.social · 30/03/2026
Ep 28 - part 3/3 in our thresholding series! Find out from @bethcimini.bsky.social and @erinweisbart.bsky.social why threshold correction factors and bounds are SO critical for making your workflows scale, and great ways to bring the biology you know into your workflow. Don't sleep on them!
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Thresholding in CellProfiler Part 3: Correction Factor and Limits - AskErinDearBeth Episode 28
YouTube video by Ask Erin, Dear Beth
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Erin Weisbart @erinweisbart.bsky.social · 27/03/2026
Are you interested in the Cell Painting Assay but have some questions? We've curated a whole bunch of resources into a comprehensive and friendly "Cell Painting for Biologists" guide ciminilab.github.io/GuideToCellP...
ciminilab.github.io
Guide to Cell Painting for Biologists
Overview of resources for biologists interested in Cell Painting. Covers introduction, application, modification, image analysis, profile generation, biology exploration, and more!
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Ask Erin / Dear Beth @askerindearbeth.bsky.social · 02/03/2026
Ep 26! A whole year of AE/DB - thanks for making this first year fantastic! Cont. our deep dive on thresholding from Ep 24, @bethcimini.bsky.social and @erinweisbart.bsky.social walk through the algorithms in CellProfiler and when you might use them - our math-free logic for picking the right one!
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Thresholding in CellProfiler Part 2: Picking the Right Algorithm - AskErinDearBeth Episode 26
YouTube video by Ask Erin, Dear Beth
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OME @openmicroscopy.org · 26/02/2026
We have integrated the Allen Institute's BioFile Finder app with IDR. You can quickly Group and Filter all images in a study. Data is served by the IDR search engine and supports up to a million images at a time. BioFile Finder links are on each study page e.g. idr.openmicroscopy.org/study/idr0056/
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Ask Erin / Dear Beth @askerindearbeth.bsky.social · 17/02/2026
Ep 25 - from our new AE/DB Bsky account! It's a great one from @erinweisbart.bsky.social - once we've done Cell Painting and gotten our data, how do we interpret the measurements into biology? She and @bethcimini.bsky.social walk you through it. PLUS, in honor of our silver episode, bonuses (1/2)
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Interpreting Cell Painting Features: Classic Cell Profiler Features - AskErinDearBeth Episode 25
YouTube video by Ask Erin, Dear Beth
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Erin Weisbart @erinweisbart.bsky.social · 02/02/2026
We answered our first viewer-submitted question in our "advice column" podcast! Thresholding when some areas are bright and some are dark is easy in CellProfiler with just one setting! Part 1/3 of a series on thresholding so keep an eye out for more w/ @bethcimini.bsky.social youtu.be/ynrPqsOZVYE
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Thresholding in CellProfiler Part 1: Adaptive Thresholding - AskErinDearBeth Episode 24
YouTube video by Ask Erin, Dear Beth
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Erin Weisbart @erinweisbart.bsky.social · 26/01/2026
@bethcimini.bsky.social and I talk about the Cell Painting Assay a LOT, especially on our podcast Ask Erin/Dear Beth, so we figured it was about time to talk about what it actually is! youtu.be/9-d6DoHtgUY h/t @drannecarpenter.bsky.social #science #biology #cellpainting #microscopy #imageanalysis
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Introduction to the Cell Painting Assay - AskErinDearBeth Episode 23
YouTube video by Ask Erin, Dear Beth
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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 08/12/2025
20 eps - wow! Today, @erinweisbart.bsky.social and I introduce BioimagingGuide.org, a fantastic resource we made in partnership with @bioimagingna.bsky.social , your guide to "what you don't know you don't know" about imaging and analysis. Friendly and in 4 languages (and counting!); check it today!
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Intro to the Bioimaging Guide - AskErinDearBeth Episode 20
YouTube video by Ask Erin, Dear Beth
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Erin Weisbart @erinweisbart.bsky.social · 11/11/2025
This week on AskErinDearBeth, @bethcimini.bsky.social and I ask some hard hitting questions, (wo)man-on-the-street-style, at SBI2 2025 conference. Let us know, what's *your* favorite CellProfiler feature? And chime in on the debate: confocal or wide field microscopy? youtu.be/99L2ESvAt5I
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Women on the Street Interviews: Hard Hitting Questions at SBI2 2025 - AskErinDearBeth Episode 18
YouTube video by Ask Erin, Dear Beth
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Erin Weisbart @erinweisbart.bsky.social · 31/10/2025
Had a fab time collaborating with @assafzaritsky.bsky.social's group on this paper! So cool to have Cell Painting profiles that start with classic CellProfiler-derived morphological profiles, use self-supervised DL for improved profile strength, but also retain *~*feature interpretability*~* !!!
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Reposted by Erin Weisbart
Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 14/10/2025
Big news! Our week-long #bioimageanalysis bootcamp is BACK! Learn how to think about bioimage analysis like the pros do, learn what corrections you should (and shouldn't!) apply to your images, learn open source tools, and more. Apply NOW at broad.io/BAB3 for our January 2026 course!
A flyer for the Bioimage Analysis Beginnings Bootcamp - blue and white with a picture of cells on the top. It says "Learn core bioimage analysis skills using open-source tools for light microscopy. Open to participants at all skill levels." It also says it will be held a the Broad Institute, 415 Main Street, Cambridge MA USA, on Monday to Friday January 12th-16, 2026, from 9-5pm. Registration is $750 academic, $1250 industry, and applications are open at broad.io/BAB3
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Erin Weisbart @erinweisbart.bsky.social · 09/09/2025
While image analysis may be our primary focus, @bethcimini.bsky.social and I have many shared nerderies. Love of #GBBO is one of them. Hear about my family's Great British Bake Off fantasy league and a couple of our favorite recipes on this ~bonus~ episode of AskErinDearBeth! youtu.be/hKEO9UeP1yw
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Baking Nerds Talk GBBO - AskErinDearBeth Episode 13 5
YouTube video by Ask Erin, Dear Beth
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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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Erin Weisbart @erinweisbart.bsky.social · 03/06/2025
I cannot overstate how amazing it is to work in a supportive, kind, collaborative environment and - even better - with my best friend. Scary times aren't quite as scary and we do better science. Beth and I talk about this in a recent AskErinDearBeth! youtu.be/9gKE9euaUJo
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AskErinDearBeth Bonus Episode 6.5 - In the beginning
YouTube video by Ask Erin, Dear Beth
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Erin Weisbart @erinweisbart.bsky.social · 03/06/2025
LoadData is how I bypass the use of my nemesis (the NamesAndTypes module) and a super handy way to pass file information and metadata into CellProfiler. Wanna hear me and Beth explain what it is and how to use it? Check out the latest episode of AskErinDearBeth!
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Reposted by Erin Weisbart
Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 01/05/2025
BIG NEWS - for the first time ever, we're running a Bioimage Analysis Beginnings Bootcamp. Learn #bioimageanalysis from awesome folks, and gain familiarity with some new tools as well as how to pick the right tool in the first place. Aug 4th-8th - apply here (soon!) forms.gle/d2fCXsrWHVP8...
Ad for the Bioimage Analysis Beginnings Bootcamp at the Broad Institute. 

Where & When
Broad Institute, 415 Main Street, Cambridge MA (in-person only)
Monday–Friday, August 4–8, 20259:00 AM – 5:00 PM

About the Bootcamp
Learn core bioimage analysis skills using open-source tools for light
microscopy in this hands-on, in-person course. The Bootcamp
covers annotation, segmentation, and deep learning fundamentals.

Fee: $600 (Academic/Non-Profit) | $1000 (Industry/For-Profit)
For more information email ImagingAdmin@broadinstitute.org
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Reposted by Erin Weisbart
Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 28/04/2025
Episode 4 - in which @erinweisbart.bsky.social and I fight the commonest @cellprofiler.bsky.social battle yet - with a million ways to read in your data, what is the right way for YOUR data? Shall a new hope arise? Will we find only one way to do things? Watch and find out!
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AskErinDearBeth Episode 4 - Proprietary File Formats in Fiji and CellProfiler
YouTube video by Ask Erin, Dear Beth
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Erin Weisbart @erinweisbart.bsky.social · 14/04/2025
Now out: Episode 3 of Ask Erin/Dear Beth in which @bethcimini.bsky.social and I overview the method we use for QC on high content imaging datasets. It's great for ~*~vibes~*~ and to QC segmentation along with catching debris, confluency, or focus issues. youtu.be/5pAcdd_Nn00
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AskErinDearBeth Episode 3 - QC on High Content Imaging Datasets using CellProfiler and FIJI
YouTube video by Ask Erin, Dear Beth
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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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Reposted by Erin Weisbart
Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 08/04/2025
Bioimaging and bioimage analysis friends, some help if you have 2-3 mins; for a paper, we're trying to estimate the number of biologists trained in open source software or tools in the last ~5 years. (1/2) #bioimaging #microscopy #bioimageanalysis
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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)
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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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Jess Ewald @ewaldlab.org · 05/03/2025
🚨 We're hiring! 🚨 The Ewald Lab at EMBL-EBI is looking for a postdoctoral researcher in multi-omics, machine learning, and predictive toxicology to analyze a groundbreaking toxicology dataset as part of the OASIS Consortium. More details & application here: lnkd.in/eHD7DMdX
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Jennifer Waters @jencwaters.bsky.social · 09/01/2025
Quantitative Imaging From Acquisition to Analysis applications are due Jan 31! 2 weeks of total microscopy & image analysis immersion with me, @talleylambert.bsky.social, @bethcimini.bsky.social, @florianjug.bsky.social & Hunter Elliott! See comments... (1/5) meetings.cshl.edu/courses.aspx...
meetings.cshl.edu
Quantitative Imaging: From Acquisition to Analysis
Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.
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Danish BioImaging @danishbioimaging.bsky.social · 09/01/2025
Do you want to learn how to →run simple python scripts for automating image analysis, →understand the principles of image processing, →gain insight into how machine learning methods work? Join the Python for BioImage Analysis Course - March 31st to April 2nd eventsignup.ku.dk/pythonforbio...
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Erin Weisbart @erinweisbart.bsky.social · 16/12/2024
Come work with us in the Cimini Lab! The image analysis associate position we're hiring will be working directly with me!
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Jonathan Edward Durham @thisone0verhere.bsky.social · 12/12/2024
One good thing about self-checkout is it never asks me what kind of party I'm having when I ring up $115 worth of cheese I’ve just bought for myself. If you must know, I'm having an “I'm an adult and nobody can tell me how much cheese I can buy for myself" party and it's gonna be totally awesome
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Jonathan Edward Durham @thisone0verhere.bsky.social · 05/12/2024
Never forget that in 1861 Charles Darwin wrote in a letter to a friend.. “But I am very poorly today and very stupid and hate everybody and everything" ...because this is my favorite reminder that we can do great things even if we don't always have great days
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Srijit Seal 🇺🇸🇬🇧🇩🇪🇯🇵🇮🇳 @srijitseal.com · 05/12/2024
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!
nature.com
Cell Painting: a decade of discovery and innovation in cellular imaging - Nature Methods
This Review synthesizes the literature from over 10 years of Cell Painting for image-based profiling and highlights how advances in this technology enable new biological discovery of cellular phenotyp...
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Josh Moore @joshmoore.bsky.social · 04/12/2024
"Scientists collaborate — funders must, too" @dartar.bsky.social & @k8hert.bsky.social www.statnews.com/sponsor/2024...
statnews.com
New report highlights the scientific impact of open source software
Two of the scientists who won this year’s Nobel Prize for cracking the code of proteins’ intricate structures relied, in part, on a series of computing
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Erin Weisbart @erinweisbart.bsky.social · 04/12/2024
Super proud to be part of this effort along with so many other talented and hardworking folks! Also pretty fun to get to say that I touched every single ORF image to turn it from a picture to numbers :)
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Li Chen @exocomics.com · 27/11/2024
dabbling again
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Ferris Jabr @ferrisjabr.bsky.social · 27/11/2024
I was deeply disappointed by the lack of nature/science/climate/enviro on many major end-of-year book lists—so I decided to make my own! Introducing: ✨🎁📚 The 2024 Holiday Gift Guide to Nature & Science Books ✨🎁📚 Please share: Let's make this go viral in time for Black Friday / holiday shopping!
A collage of book covers of new nature & science books. Featured here are Atlas Obscura Wild Life, Dinosaurs at the Dinner Party, Every Living Thing, Alien Earths, Becoming Earth, and Deep WaterA collage of book covers of new nature & science books. Featured here are Frostbite, The Inner Clock, How to Kill an Asteroid, The Great River, The Last Fire Season, and Hoof BeatsA collage of book covers of new nature & science books. Featured here are The Serviceberry, Not the End of the World, Nature's Ghosts, Meet the Neighbors, The Light Eaters, and Our MoonA collage of book covers of new nature & science books. Featured here are Turning to Stone, The Weight of Nature, What If We Get It Right?, Waves in An Impossible Sea, The Tree Collectors, and Why We Remember
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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!
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Browsing, Filtering, and Downloading Data in the Cell Painting Gallery
YouTube video by I2K Conference
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Markus Eichhorn @markuseichhorn.bsky.social · 22/11/2024
Who should you nominate as reviewers for your manuscript? After a long chat with a post-grad it appears that there's a lot of misguided advice out there. Thread 👇
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Erin Weisbart @erinweisbart.bsky.social · 22/11/2024
Here's what my science clouds like: shiny.rcg.sfu.ca/u/rdmorin/sc...
Word cloud of terms including profiling, analysis, cell, platform, CellProfiler, perturbations, containers, morphology, python
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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 21/10/2024
Have you ever analyzed a #microscope image before- even just a single one? Please take our survey on progress and places to still improve for image analysis software! #microscopy #imageanalysis #bioimageanalysis forum.image.sc/t/2024-image...
forum.image.sc
2024 Image Analysis Survey
The Center for Open Bioimage Analysis , Bioimaging North America , the Royal Microscopical Society, and the Global Bioimage Analysts’ Society have now released a new and improved edition of our biannu...
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