Ep 37 - part 2 in our series on collaboration! @erinweisbart.bsky.social talks @bethcimini.bsky.social through tools and tricks that can help make your collaborations smoother and more successful for everyone.

Working With Collaborators II - Tools for Collaborations - AskErinDearBeth Episode 37

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Ask Erin / Dear Beth@askerindearbeth.bsky.social · 2w ago

Episode 36 - better by the 3-dozen! It's another VIEWER QUESTION, which is always a delight. CellProfiler features come in all sorts of distribution types - normal, left-shifted, right-shifted, you name it. How do you handle that? @bethcimini.bsky.social and @erinweisbart.bsky.social try to answer!

Episode 36 - better by the 3-dozen! It's another VIEWER QUESTION, which is always a delight. CellProfiler features come in all sorts of distribution types - normal, left-shifted, right-shifted, you name it. How do you handle that? @bethcimini.bsky.social and @erinweisbart.bsky.social try to answer!

Cell Painting Feature Transformations - AskErinDearBeth Episode 36

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Ask Erin / Dear Beth@askerindearbeth.bsky.social · 4w ago

Episode 35! Being a bioimage analyst is ALL about collaboration, and no one is better at it than @erinweisbart.bsky.social . Listen to her and @bethcimini.bsky.social talk about how to set up your collaborations for success. More parts coming soon!

Episode 35! Being a bioimage analyst is ALL about collaboration, and no one is better at it than @erinweisbart.bsky.social . Listen to her and @bethcimini.bsky.social talk about how to set up your collaborations for success. More parts coming soon!

Working with Collaborators - Part I - AskErinDearBeth Episode 35

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Ask Erin / Dear Beth@askerindearbeth.bsky.social · last mo.

Ep 34! Our 2nd-ever VIEWER QUESTION, and we are still EXCITED about those! (You should ask us some!) How do we measure if our images are, y'know, good? Feels like it should be easy, but it isn't! @bethcimini.bsky.social and @erinweisbart.bsky.social go through the options, and why none is perfect:

Ep 34! Our 2nd-ever VIEWER QUESTION, and we are still EXCITED about those! (You should ask us some!) How do we measure if our images are, y'know, good? Feels like it should be easy, but it isn't! @bethcimini.bsky.social and @erinweisbart.bsky.social go through the options, and why none is perfect:

Interpreting CellProfiler's Image Quality Measurements - AskErinDearBeth Episode 34

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Ask Erin / Dear Beth@askerindearbeth.bsky.social · 2mo ago

Ep 33 - want to keep up on all the resources on Cell Painting? @erinweisbart.bsky.social has made a listing of the ones she has made (and those made by others, but she's made a lot of them!) and shares it in this week's episode with @bethcimini.bsky.social . Check out all the pretty colors here!

Ep 33 - want to keep up on all the resources on Cell Painting? @erinweisbart.bsky.social has made a listing of the ones she has made (and those made by others, but she's made a lot of them!) and shares it in this week's episode with @bethcimini.bsky.social . Check out all the pretty colors here!

Guide to Cell Painting for Biologists - AskErinDearBeth Episode 33

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Ask Erin / Dear Beth@askerindearbeth.bsky.social · 2mo ago

Ep 32 - a chat between @bethcimini.bsky.social and @erinweisbart.bsky.social about a vision for the future of microscopy data and AI - no surprise from us, we think the secret sauce is ALL THE METADATA. Learn why below!

Ep 32 - a chat between @bethcimini.bsky.social and @erinweisbart.bsky.social about a vision for the future of microscopy data and AI - no surprise from us, we think the secret sauce is ALL THE METADATA. Learn why below!

What Kinds of BioImaging Data Does AI Need? - AskErinDearBeth Episode 32

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Ask Erin / Dear Beth@askerindearbeth.bsky.social · 3mo ago

Ep 31- do you have cells (or other big objects) full of speckles (or other little objects)? Want to get rid of spots touching the cell edge? Let @erinweisbart.bsky.social and @bethcimini.bsky.social tell you how to make that happen in CellProfiler! (Not sure why we're making things LESS sparkly...)

Ep 31- do you have cells (or other big objects) full of speckles (or other little objects)? Want to get rid of spots touching the cell edge? Let @erinweisbart.bsky.social and @bethcimini.bsky.social tell you how to make that happen in CellProfiler! (Not sure why we're making things LESS sparkly...)

Filtering Objects that Touch the Cell Edge in CellProfiler - AskErinDearBeth Episode 31

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Ask Erin / Dear Beth@askerindearbeth.bsky.social · 3mo ago

Ep 30!!! Like Cell Painting, but miss specific stains? No reason you can't have your cake and image it too! Let @bethcimini.bsky.social and @erinweisbart.bsky.social tell you why nothing matters (and why that's actually AWESOME) when you're setting up Cell Painting.

Ep 30!!! Like Cell Painting, but miss specific stains? No reason you can't have your cake and image it too! Let @bethcimini.bsky.social and @erinweisbart.bsky.social tell you why nothing matters (and why that's actually AWESOME) when you're setting up Cell Painting.

Modifying the Cell Painting Assay - AskErinDearBeth Episode 30

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Ask Erin / Dear Beth@askerindearbeth.bsky.social · 4mo ago

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!

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!

Introduction to Pooled Cell Painting - AskErinDearBeth Episode 29

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Ask Erin / Dear Beth@askerindearbeth.bsky.social · 4mo ago

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 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!

Thresholding in CellProfiler Part 3: Correction Factor and Limits - AskErinDearBeth Episode 28

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Ask Erin / Dear Beth@askerindearbeth.bsky.social · 5mo ago

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 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!

Interpretable Deep Learning Features in Cell Painting: Anomaly Profiles - AskErinDearBeth Episode 27

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Ask Erin / Dear Beth@askerindearbeth.bsky.social · 5mo ago

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!

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!

Thresholding in CellProfiler Part 2: Picking the Right Algorithm - AskErinDearBeth Episode 26

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Ask Erin / Dear Beth@askerindearbeth.bsky.social · 6mo ago

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)

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)

Interpreting Cell Painting Features: Classic Cell Profiler Features - AskErinDearBeth Episode 25

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Beth Cimini 🔬💻📊@bethcimini.bsky.social · 6mo ago

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!

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!

Thresholding in CellProfiler Part 1: Adaptive Thresholding - AskErinDearBeth Episode 24

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Beth Cimini 🔬💻📊@bethcimini.bsky.social · 7mo ago

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

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

Thresholding in CellProfiler Part 1: Adaptive Thresholding - AskErinDearBeth Episode 24

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@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

Introduction to the Cell Painting Assay - AskErinDearBeth Episode 23

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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

Introduction to the Cell Painting Assay - AskErinDearBeth Episode 23

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Beth Cimini 🔬💻📊@bethcimini.bsky.social · 7mo ago

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!

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!

Overview of CellProfiler's Input Modules - AskErinDearBeth Episode 22

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Beth Cimini 🔬💻📊@bethcimini.bsky.social · 8mo ago

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)

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!

Image Analysis Ask Us Anything - A special LIVE Ask Erin/Dear Beth event!

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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)

Visualizing Common Deep Learning Image Augmentations - AskErinDearBeth Episode 21

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Beth Cimini 🔬💻📊@bethcimini.bsky.social · 8mo ago

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!

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!

Intro to the Bioimaging Guide - AskErinDearBeth Episode 20

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Beth Cimini 🔬💻📊@bethcimini.bsky.social · 8mo ago

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!

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!

Conferences We've Attended Recently - AskErinDearBeth Episode 19

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Beth Cimini 🔬💻📊@bethcimini.bsky.social · 9mo ago

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 !

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 !

Women on the Street Interviews: Hard Hitting Questions at SBI2 2025 - AskErinDearBeth Episode 18

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Beth Cimini 🔬💻📊@bethcimini.bsky.social · 9mo ago

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 !

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

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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 !

How to Write a Great Post on the Image.sc Forum - AskErinDearBeth Episode 17

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Beth Cimini 🔬💻📊@bethcimini.bsky.social · 10mo ago

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 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!

The Cell Painting Gallery, an Overview - AskErinDearBeth Episode 16

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Beth Cimini 🔬💻📊@bethcimini.bsky.social · 10mo ago

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 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.

Why Do My Scientific Images Look Ugly!? - AskErinDearBeth Episode 15

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Beth Cimini 🔬💻📊@bethcimini.bsky.social · 11mo ago

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!

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!

Illumination Correction in CellProfiler (Two Ways!) - AskErinDearBeth Episode 14

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Beth Cimini 🔬💻📊@bethcimini.bsky.social · 11mo ago

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...