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!

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!

Episode 7 - want to add some sparkles (aka speckles) to your life? Check out @erinweisbart.bsky.social and my favorite tricks for modules and settings that make speckle finding a snap in CellProfiler on this week's episode of Ask Erin/Dear Beth!

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!

We decided to start with THE DEEP LORE - aka, how did Erin and I first meet and how did we begin on this wacky journey! If you want to know where the journey began, here's the opening chapter. (2/2)

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)

Episode 5 - sure, most cells have one nucleus, but what happens when they DON'T? @erinweisbart.bsky.social and I try to get to the bottom of what on earth you can do when your cells and nuclei just don't match up on the latest episode of "Ask Erin/Dear Beth"

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!

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

Got an idea for an episode or want to submit your most stubborn challenge? Let us know @ broad.io/AskErinDearB.... Thanks @erinweisbart.bsky.social for being my partner in pixels (and silliness). Link one more time is www.youtube.com/@AskErinDear... - we hope you enjoy and maybe even learn a bit!

We will have an emphasis on open-sourcing all the images and workflows/solutions that we make (as well as an emphasis on having lots of fun putting these solutions together). These materials can be found linked from our channel, as well as an our (WIP for now) website (below) (3/x)

Our first two episodes (on handling out of focus regions in images, as well as on how to download data from the IDR) are available now, with new episodes will drop ~every two weeks(ish)! While it will heavily feature #CellProfiler, we will use whatever tool is right for the challenge. (2/x)

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)