Erin Weisbart
@erinweisbart.bsky.social
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.
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
youtu.be
November 11, 2025 at 1:50 AM
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*~* !!!
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
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
October 31, 2025 at 7:19 PM
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*~* !!!
Reposted by Erin Weisbart
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!
October 14, 2025 at 9:31 PM
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
youtu.be
September 9, 2025 at 4:36 PM
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
Reposted by Erin Weisbart
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
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
June 3, 2025 at 4:43 PM
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!
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)
June 3, 2025 at 4:35 PM
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!
Reposted by Erin Weisbart
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...
May 1, 2025 at 9:22 PM
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...
Reposted by Erin Weisbart
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!
April 28, 2025 at 12:07 PM
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!
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
youtu.be/5pAcdd_Nn00
AskErinDearBeth Episode 3 - QC on High Content Imaging Datasets using CellProfiler and FIJI
YouTube video by Ask Erin, Dear Beth
youtu.be
April 14, 2025 at 9:31 PM
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
youtu.be/5pAcdd_Nn00
Reposted by Erin Weisbart
🚨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 Erin Weisbart
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
April 8, 2025 at 2:32 PM
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
Reposted by Erin Weisbart
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 Erin Weisbart
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 Erin Weisbart
🚨 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
More details & application here: lnkd.in/eHD7DMdX
March 5, 2025 at 5:31 PM
🚨 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
More details & application here: lnkd.in/eHD7DMdX
Reposted by Erin Weisbart
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.
meetings.cshl.edu
January 9, 2025 at 3:43 PM
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...
Reposted by Erin Weisbart
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...
→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...
January 9, 2025 at 9:17 AM
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...
→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!
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)
First, an image analysis associate - work on high content screens for all kinds of cells and dimensionalities! See more at link (1/4)
Image analysis associate job description
Image Analysis Associate Broad Institute of MIT and Harvard, Cambridge, MA Impact the discovery of new disease therapies in the Cimini laboratory at the Imaging Platform Join our vibrant, world-clas...
docs.google.com
December 16, 2024 at 3:51 PM
Come work with us in the Cimini Lab! The image analysis associate position we're hiring will be working directly with me!
Reposted by Erin Weisbart
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
December 12, 2024 at 8:47 PM
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
Reposted by Erin Weisbart
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
“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
December 5, 2024 at 7:30 PM
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
“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
Reposted by Erin Weisbart
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!
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...
www.nature.com
December 5, 2024 at 5:35 PM
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!
Reposted by Erin Weisbart
"Scientists collaborate — funders must, too"
@dartar.bsky.social & @k8hert.bsky.social
www.statnews.com/sponsor/2024...
@dartar.bsky.social & @k8hert.bsky.social
www.statnews.com/sponsor/2024...
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
www.statnews.com
December 4, 2024 at 10:21 AM
"Scientists collaborate — funders must, too"
@dartar.bsky.social & @k8hert.bsky.social
www.statnews.com/sponsor/2024...
@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 :)
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...
“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...
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...
www.biorxiv.org
December 4, 2024 at 6:02 PM
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 :)
Reposted by Erin Weisbart
Reposted by Erin Weisbart
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!
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!
November 27, 2024 at 7:08 PM
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!
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!