Ask Erin / Dear Beth
@askerindearbeth.bsky.social
The most sparkly biweekly bioimage analysis advice podcast you're likely to find! Episodes: https://www.youtube.com/@AskErinDearBeth; Materials: https://ciminilab.github.io/AskErin_DearBeth/ . Starring @erinweisbart.bsky.social and @bethcimini.bsky.social
Reposted by Ask Erin / Dear Beth
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!
February 2, 2026 at 4:21 PM
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!
Reposted by Ask Erin / Dear Beth
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
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
youtu.be
February 2, 2026 at 6:29 PM
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
Part 1/3 of a series on thresholding so keep an eye out for more w/ @bethcimini.bsky.social
youtu.be/ynrPqsOZVYE
Reposted by Ask Erin / Dear Beth
@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
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
youtu.be
January 26, 2026 at 6:15 PM
@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
h/t @drannecarpenter.bsky.social
#science #biology #cellpainting #microscopy #imageanalysis
Reposted by Ask Erin / Dear Beth
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
youtu.be/9-d6DoHtgUY
January 20, 2026 at 5:03 PM
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
youtu.be/9-d6DoHtgUY
Reposted by Ask Erin / Dear Beth
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!
January 5, 2026 at 5:21 PM
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!
Reposted by Ask Erin / Dear Beth
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!
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!
Image Analysis Ask Us Anything - A special LIVE Ask Erin/Dear Beth event!
YouTube video by I2K Conference
youtu.be
December 22, 2025 at 9:47 PM
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!
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!
Reposted by Ask Erin / Dear Beth
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)
December 22, 2025 at 9:47 PM
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)
Reposted by Ask Erin / Dear Beth
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!
December 8, 2025 at 6:55 PM
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!
Reposted by Ask Erin / Dear Beth
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!
November 24, 2025 at 10:51 PM
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!
Reposted by Ask Erin / Dear Beth
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 !
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 !
November 11, 2025 at 3:13 PM
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 !
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 !
Reposted by Ask Erin / Dear Beth
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
Reposted by Ask Erin / Dear Beth
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 !
October 27, 2025 at 6:20 PM
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 !
Reposted by Ask Erin / Dear Beth
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!
October 14, 2025 at 11:48 AM
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!
Reposted by Ask Erin / Dear Beth
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.
September 29, 2025 at 7:45 PM
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.
Reposted by Ask Erin / Dear Beth
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!
September 15, 2025 at 10:54 PM
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!
Reposted by Ask Erin / Dear Beth
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 Ask Erin / Dear Beth
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...
Looking for notebooks/pipelines/images, or want to submit a q? Check our site! ciminilab.github.io/AskErin_Dear...
September 2, 2025 at 12:20 PM
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...
Looking for notebooks/pipelines/images, or want to submit a q? Check our site! ciminilab.github.io/AskErin_Dear...
Reposted by Ask Erin / Dear Beth
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!
August 18, 2025 at 1:19 PM
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!
Reposted by Ask Erin / Dear Beth
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.
August 5, 2025 at 12:38 PM
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.
Reposted by Ask Erin / Dear Beth
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!
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!
July 22, 2025 at 4:08 PM
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!
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!
Reposted by Ask Erin / Dear Beth
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!
July 7, 2025 at 3:12 PM
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!
Reposted by Ask Erin / Dear Beth
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!
June 23, 2025 at 1:44 PM
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!
Reposted by Ask Erin / Dear Beth
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!
June 9, 2025 at 8:50 PM
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!
Reposted by 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
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
Reposted by Ask Erin / Dear Beth
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!