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!
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 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!
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!
Extra special bonus - video of Erin and I in the same place! It does happen!
This new Bsky account! A new LinkedIn page! (www.linkedin.com/company/ask-...). Website refreshes to our materials page (ciminilab.github.io/AskErin_Dear...)! And a fun new blogpost on @focalplane.bsky.social focalplane.biologists.com/2026/02/16/a... . Thanks for coming with us on this journey!(2/2)
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)
Check out this fun post from @bethcimini.bsky.social & @erinweisbart.bsky.social, where they interview each other about their popular image analysis video podcast, ‘Ask Erin/Dear Beth’ @askerindearbeth.bsky.social.
Episodes are posted every 2 weeks (ish).
focalplane.biologists.com/2026/02/16/a...
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
@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
Ep 23 - So what actually IS CellPainting anyway? You may have heard of it if you're say, a fan of the @drannecarpenter.bsky.social - @shantanu-singh.cc lab (and who isn't????), but what, you know, is it? Let @erinweisbart.bsky.social break it down for you!
youtu.be/9-d6DoHtgUY
Ep 22 - while we all love CellProfiler (right??), we know that often the challenging part is handling the "bookkeeping" to get your data into it in the first place. @erinweisbart.bsky.social and I do a quick overview, and then point to great longer-form materials. Welcome to AE/DB 2026!
The videos from this year's I2K are now online! Check out the Ask Erin / Dear Beth "Ask Us Anything" below, or the whole conference at www.i2kconference.org
Making these 24 (with bonuses) episodes might be the most fun thing I did in 2025 - see you with more AE/DB content in 2026!
Episode 21 - when we talk about doing image augmentations for deep learning, what do we MEAN? @erinweisbart.bsky.social uses CellProfiler to demonstrate exactly how we transform images to make neural networks more robust. PLUS (1/2)
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!
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!
Episode 18 - @erinweisbart.bsky.social and I hung out IRL at @sbi2.bsky.social, forgot to film TOGETHER, but did ask our friends hard-hitting interview questions. Silliness ensued!
Want to hang with us? We're doing a LIVE AMA next week at I2K - Wed Nov 19th, 1PM EST. Sign up at i2kconference.org !
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
Episode 17 - perhaps my favorite yet. How do you write a forum.image.sc post that will get you the answers you need without revealing information you don't want to tell? @erinweisbart.bsky.social and I go through what the experts need to know to help you. Post your sci q's today on forum.image.sc !
Episode 16 - Learn more about the Cell Painting Gallery, a free repository of nearly a petabyte of images and imaging data, curated by the incredibly talented @erinweisbart.bsky.social . Truly a goldmine for big-data lovers everywhere!
Episode 15 - do your images look, well, weird when you open them on your computer? Bad? Weird-and-bad? While we can't tell you EXACTLY what's going on, in this edition of Ask Erin/Dear Beth, @erinweisbart.bsky.social and I go over the most common "ugh, why does it look like THAT?" cases.
Episode 14 - In which @erinweisbart.bsky.social gives us a FANTASTIC tour through CellProfiler's illumination correction modules, how and when to use different kinds of illumination correction, and more. So so useful!
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
Episode 13 - so why is it so important to use the small brush in ilastik (ep 11)? How do random forests WORK, anyway? Join @erinweisbart.bsky.social and I as we explore using #marimo!
Looking for notebooks/pipelines/images, or want to submit a q? Check our site! ciminilab.github.io/AskErin_Dear...
Episode 12- my lucky number! Might become yours too if you have lots of cell outline images you need to make into masks - @erinweisbart.bsky.social shows you our plugin for this, along with SUCH a clever trick (that I never would have thought of) for cleaning up small and/or edge masks. Enjoy!
Episode 11 - In which @erinweisbart.bsky.social and I talk about just how much we love ilastik (@ilastik-team.bsky.social) and how it's great for so many problems! Also, that you should use a small brush.
Episode 10 - we've jumped an order of magnitude! Thanks for all the support, @erinweisbart.bsky.social and I totally appreciate it.
If you have artifact-free data, you can skip this one;
for us mere mortals, Erin talks about masks, alignment, and seeing how far from a mask an object is. So useful!
Episode 9 - maybe the #1 question we get on forum.image.sc is "how can I find cells and figure out what fraction are positive for marker X?". Since this is CellProfiler, we show you not 1 but 3 ways to do it, including a throwback to Ep 7. Let @erinweisbart.bsky.social and I help you get it done!
Episode 8 - CellProfiler does a lot, but could it do EVEN MORE? Hop on in to let @erinweisbart.bsky.social tell you all about CellProfiler plugins - where to find them, how to use them, and how they can add the Power Of Deep Learning to your local copy of CellProfiler!
