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!

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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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!

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 · 4mo ago

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!

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!

Thresholding in CellProfiler Part 3: Correction Factor and Limits - AskErinDearBeth Episode 28

YouTube video by Ask Erin, Dear Beth

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Ask Erin / Dear Beth@askerindearbeth.bsky.social · 5mo ago

Ep 27- have you heard deep learning called a "black box"? It often is, but this week, @erinweisbart.bsky.social tells @bethcimini.bsky.social about a cool paper from the @assafzaritsky.bsky.social team (and Erin!) using DL to make Cell Painting even more powerful, but still interpretable. So fun!

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...

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!

Thresholding in CellProfiler Part 2: Picking the Right Algorithm - AskErinDearBeth Episode 26

YouTube video by Ask Erin, Dear Beth

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Ask Erin / Dear Beth@askerindearbeth.bsky.social · 6mo ago

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)

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/

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)

Interpreting Cell Painting Features: Classic Cell Profiler Features - AskErinDearBeth Episode 25

YouTube video by Ask Erin, Dear Beth

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Beth Cimini 🔬💻📊@bethcimini.bsky.social · 6mo ago

Ep 24 - Understanding your thresholding options is the diff between a win and a loss in SO MANY workflows - gain that intuition, and SO MUCH is easier. The 1st of 3 episodes discussing why - inspired by OUR FIRST REAL READER QUESTION. @erinweisbart.bsky.social and I are actual advice columnists now!

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

Thresholding in CellProfiler Part 1: Adaptive Thresholding - AskErinDearBeth Episode 24

YouTube video by Ask Erin, Dear Beth

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@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

Introduction to the Cell Painting Assay - AskErinDearBeth Episode 23

YouTube video by Ask Erin, Dear Beth

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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!

Intro to the Bioimaging Guide - AskErinDearBeth Episode 20

YouTube video by Ask Erin, Dear Beth

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Beth Cimini 🔬💻📊@bethcimini.bsky.social · 8mo ago

Was lovely to see many of you @ I2K! Despite having major FOMO about missing so much stuff this fall (GloBIAS! CytoData! FoundingGIDE! CBIAS!), conferences ARE usually a great way to find @erinweisbart.bsky.social and I. In Episode 19, we talk through great societies/meetings we think you'll enjoy!

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

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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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*~* !!!

Assaf Zaritsky@assafzaritsky.bsky.social · 9mo ago

Our paper is out ✨ doi.org/10.1016/j.ce... We propose a self-supervised anomaly representation that encodes morphological inter-feature dependencies for high-content image-based cell phenotyping! 1/3

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!

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

Baking Nerds Talk GBBO - AskErinDearBeth Episode 13 5

YouTube video by Ask Erin, Dear Beth

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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...

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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...

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

AskErinDearBeth Bonus Episode 6.5 - In the beginning

YouTube video by Ask Erin, Dear Beth

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Beth Cimini 🔬💻📊@bethcimini.bsky.social · last yr.

Literally everything is terrible right now in the world, but @erinweisbart.bsky.social and I just filmed a podcast bonus episode about how fun it is to work with your best friend and that seems as good a time as any to start a (daily?) gratitude thread amongst the creeping gloom.

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!

Beth Cimini 🔬💻📊@bethcimini.bsky.social · last yr.

Gah! I was traveling last week and forgot to tell you re: Episode 6 - in which @erinweisbart.bsky.social and I dig into yet another way to get data into Cell Profiler, via CSV. Super useful for big data! But as a silver lining, I get to shout out our first BONUS EPISODE (1/2)

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...

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!

AskErinDearBeth Episode 4 - Proprietary File Formats in Fiji and CellProfiler

YouTube video by Ask Erin, Dear Beth

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Beth Cimini 🔬💻📊@bethcimini.bsky.social · last yr.

New episode of Ask Erin/Dear Beth just dropped! See how Erin handles figuring out experiment quality and segmentation performance for multi-well plate data! See Beth force Erin to define things (very well!) she didn't want to define! Learn to ensure your large experiments have only the best vibes.

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

AskErinDearBeth Episode 3 - QC on High Content Imaging Datasets using CellProfiler and FIJI

YouTube video by Ask Erin, Dear Beth

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🚨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

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

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...

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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...

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🚨 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

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...

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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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...

Come work with us in the Cimini Lab! The image analysis associate position we're hiring will be working directly with me!

Beth Cimini 🔬💻📊@bethcimini.bsky.social · 2y ago

New Year, new job? Delighted to announce two early-career-level (post-BA/BS or MA) positions in my lab, and an open call for computational postdocs at the Broad! First, an image analysis associate - work on high content screens for all kinds of cells and dimensionalities! See more at link (1/4)

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

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