Ask Erin/Dear Beth – an image analysis tips and tricks video podcast

Ask Erin/Dear Beth is an image analysis “video podcast” from Erin Weisbart and Beth Cimini of the Broad Institute Imaging Platform. Every 2 weeks, they hang out to answer real viewer questions about bioimage analysis, or just to talk about tips and tricks, old favorite resources, new favorite resources, or anything else related to image analysis. In honor of their 25th episode, they’re interviewing each other for FocalPlane. 

Beth: Who do you think should watch AE/DB?

Erin : Anyone with interest in image analysis! We initially thought it would be handy to build a catalogue of episodes answering common questions so that when folks in our lab are answering questions on the image.sc forum they could link to episodes. We’ve since found that most episodes have content helpful to folks with all levels of image analysis background – we try to break things down so a true novice can follow but I know that you and I have both learned tips from each other while recording!

Erin :What’s your favorite thing about recording Ask Erin Dear Beth?

Beth: Besides hanging out with you? Hanging out with you is a big part of it! But besides that, it’s feeling like we’re doing good by filling in gaps in people’s training knowledge – taking all the stuff that’s otherwise just “folk wisdom passed down image analyst to image analyst” and making it accessible to everyone. I mean, most image analysts I know (including us) LOVE to talk about this stuff, so it’s not hard to get this wisdom if you find the right person at the right time, but that’s not always possible or easy!

Beth: What do you think is the hardest part of learning about image analysis?

Erin :I think the hardest thing about learning image analysis is learning the line between science and art. For any image analysis workflow, pipeline, or task, there are many ways you can get to the same answer and some of learning to be a great image analyst is appropriately evaluating which is the best software given the constraints of my current technical skills, which is the best algorithm given the constraints of this batch of data, or which is the best segmentation I can achieve given the constraints of the biological question I’m trying to answer. Even you and I, who have very overlapping interests/skillsets/backgrounds, have surprised each other when recording episodes of AE/DB. We’ve both thought (and said!) “ooh, I wouldn’t have approached it this way but I see why you did.” I think it can be very uncomfortable for novices to not be able to learn the “best” way to do anything because there is no single “best” way.

Erin :What has surprised you most?

Beth: Two things: first of all, just the overall positive response, which has been a lovely surprise for something we thought would help our own team but weren’t sure would be useful to many other people. Secondly, how bad I am at predicting which episodes will be the most popular – obviously we think all our episodes are things that are valuable to know, but there are ones that I’m like “oh, really, that many people wanted content on _____? Amazing!” and ones where I’m like “hmmm, I swear we’ve gotten this question a LOT before, but the video isn’t really popping…”. I think the latter is at least partly that sometimes you don’t know the right term to search to actually find that there’re resources out there for it – which is still a problem we’re working on!

Beth:What do you hope the impact of AE/DB will be?

Erin : I think AE/DB is a great complement to our more formal educational oeuvre and I hope people can learn from us and engage with bioimage analysis in a way that is fun and casual. I initially pitched the idea thinking it would just be fun to have an excuse for the two of us to hang out, but I do think we’re already seeing an impact well beyond just us!

Erin :What’s your favorite episode?

Beth: I DO love our bonus episodes, but I think I’ll go with our episode on writing a forum post, because writing a forum post can be scary! Admitting in public that there’s stuff you don’t know can be hard! And it also can be hard to know what information someone helping you needs – info about your images, info about your computer, etc. If we ended up demystifying that process at all, I’ll feel really good about that.

Beth: How in practice do you put the episodes together?

Erin :You know the lead-up to recording – we’ve got a spreadsheet of ideas and a couple days before we record we’ll each claim a few episode ideas and pull together relevant images or a draft pipeline. Then we hop on a Zoom meeting and press record! After we’ve recorded, I use iMovie to crop the recording into episodes and add the intro/outro. I then generate subtitles using auto-subtitle and automatically clean them up using a bit of my own code (e.g. “CellProfiler” is auto-transcribed in all sorts of ways including self-profiler, spell profiler, so profiler, etc.) Then I upload them to our YouTube channel one at a time and do my best to add a helpful (and humorous) description and tags so that people can find our videos!

Catch new episodes of Ask Erin/Dear Beth every two weeks (ish) at www.youtube.com/@AskErinDearBeth . Got a question? Submit it at broad.io/AskErinDearBeth to possibly have your question featured on a future episode!

Neither Erin nor Beth are great at social media, but they do their best to post AEDB episodes to their Bluesky (https://bsky.app/profile/askerindearbeth.bsky.social) and LinkedIn (https://www.linkedin.com/company/ask-erin-dear-beth), so you can follow them there to catch new episodes too.

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