Erin Weisbart

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!

YouTube video by Ask Erin, Dear Beth Women on the Street Interviews: Hard Hitting Questions at SBI2 2025 - AskErinDearBeth Episode 18

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

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*~* !!!

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

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!

YouTube video by Ask Erin, Dear Beth Baking Nerds Talk GBBO - AskErinDearBeth Episode 13 5

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

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

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

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!

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

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!

YouTube video by Ask Erin, Dear Beth AskErinDearBeth Episode 3 - QC on High Content Imaging Datasets using CellProfiler and FIJI

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

🚨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

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...

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)

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...

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!

🚨 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 Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.

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...

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!

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

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...

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!

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

"Scientists collaborate — funders must, too"

@dartar.bsky.social & @k8hert.bsky.social

www.statnews.com/sponsor/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 :)

dabbling again

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 Water

A 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 Beats

A 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 Moon

A 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

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!

GitHub - DistributedScience/Distributed-OMEZarrCreator: Run encapsulated docker containers with BioFormats2Raw in the Amazon Web Services infrastructure. Run encapsulated docker containers with BioFormats2Raw in the Amazon Web Services infrastructure. - DistributedScience/Distributed-OMEZarrCreator

What's your threshold for inclusion 😜? I did make an OME-Zarr tool... (Distributed-OMEZarrCreator wraps the BioFormats2Raw Docker to simplify running it at scale in AWS). But I can't say I've gotten the chance to do much with it recently...
github.com/DistributedS...

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!

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 👇

Word cloud of terms including profiling, analysis, cell, platform, CellProfiler, perturbations, containers, morphology, python

Here's what my science clouds like:
shiny.rcg.sfu.ca/u/rdmorin/sc...