Beth Cimini 🔬💻📊
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bethcimini.bsky.social
Beth Cimini 🔬💻📊
@bethcimini.bsky.social
3.3K followers 3.3K following 1.3K posts
She/her. I turn pictures into numbers so others can turn them into medicine. Also I yell about politics a lot. See the fantastic things my team does at https://ciminilab.github.io/WeMakeStuff . Views my own, awesome science from my amazing team.
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bethcimini.bsky.social
Just 4 days until the start of I2K and its 33 totally free image analysis tutorials and events! Please share with your "home networks", especially early career researchers - the videos will be amazing and high-impact no matter how many people attend live, BUT (1/x)
A fluorescent embryo on black text, with the words Halfway to I2K: Virtual Tutorials on Image Analysis November 17-19, 2025 Virtual Conference for beginners to developers i2kconference.org Image Credit - "Sweet Embryo",Travis D. Carney, BINA Image Contest 2024
November 13, 2025 at 2:32 PM
bethcimini.bsky.social
November 7, 2025 at 12:16 AM
bethcimini.bsky.social
Always good to remember more people hate this administration than want it #nokings #boston
A peaceful crowd of many thousand people stand on the Boston Common.
October 18, 2025 at 5:44 PM
bethcimini.bsky.social
I expressed my dissatisfaction with not having a picture together since January and was rewarded
October 18, 2025 at 2:04 AM
bethcimini.bsky.social
Grateful that it's been exactly 10 years today since I last had to go on a first date; never would have guessed that a flight of beer and a trip to a bacon restaurant would turn into a lifelong best friend and partner, but grateful it did. Here's to 10 more!
A man and woman, both in dark hair and sunglasses, in a selfie in front of some trees in San Francisco's Golden Gate park in early 2016. A man and woman, both in dark hair and sunglasses, in a selfie in on a boat in San Diego in early 2025.
October 17, 2025 at 8:02 PM
bethcimini.bsky.social
Big news! Our week-long #bioimageanalysis bootcamp is BACK! Learn how to think about bioimage analysis like the pros do, learn what corrections you should (and shouldn't!) apply to your images, learn open source tools, and more. Apply NOW at broad.io/BAB3 for our January 2026 course!
A flyer for the Bioimage Analysis Beginnings Bootcamp - blue and white with a picture of cells on the top. It says "Learn core bioimage analysis skills using open-source tools for light microscopy. Open to participants at all skill levels." It also says it will be held a the Broad Institute, 415 Main Street, Cambridge MA USA, on Monday to Friday January 12th-16, 2026, from 9-5pm. Registration is $750 academic, $1250 industry, and applications are open at broad.io/BAB3
October 14, 2025 at 9:31 PM
bethcimini.bsky.social
Now that I can say it publicly - huge congratulations to @michelleitano.bsky.social , winner of this year's @bioimagingna.bsky.social Michael W Davidson award for "Community contributions, in any of the areas of Engagement, Education, Mentorship, and Standardization". So well deserved! #GBIxBINA2025
A black slide with the Bioimaging North America colorful logo in the top left, with the text "2025 Award Recipient - Michelle Itano, University of North Carolina, Chapel Hill". It has a picture of Michelle, as well as white text in a box- "Michelle embodies the various attributes that Michael Davidson was known for, and she is a beloved member of the imaging community who never hesitates to support it, or contribute to its growth.”
October 9, 2025 at 3:09 PM
bethcimini.bsky.social
But we're of course, at our heart, nerds, so we kicked everything off with a community survey, so we could create our community in a data-driven, intentional way. Almost 300 of you helped out -we couldn't have done it without you! (3/x)
A map of the world showing fractions of survey responses (most heavily concentrated in Europe, followed by the Americas), as well as gender , age, and career status breakdowns
July 10, 2025 at 10:23 PM
bethcimini.bsky.social
Feels like a 30 second ad that is this does numbers
{Two friends at a bar} - "Gotta pop to the bathroom" {friend hands purse} "Don't forget your ID" {cut to suburban house, 10 y.o. girl in soccer uniform by door} "Mom, I'm going to be late for the game" "There in a sec honey, can't find your gender certification" {cut to other suburban house, 40's guy 70's man+woman with coats on} Woman: "Off to vote" Young guy: {hands stack of papers} "Here's your birth certificate, marriage license to dad, dad's death certificate, marriage license to Jim, have fun!" {Text on background - "The party of freedom?"}
May 14, 2025 at 1:04 PM
bethcimini.bsky.social
BIG NEWS - for the first time ever, we're running a Bioimage Analysis Beginnings Bootcamp. Learn #bioimageanalysis from awesome folks, and gain familiarity with some new tools as well as how to pick the right tool in the first place. Aug 4th-8th - apply here (soon!) forms.gle/d2fCXsrWHVP8...
Ad for the Bioimage Analysis Beginnings Bootcamp at the Broad Institute. Where & When Broad Institute, 415 Main Street, Cambridge MA (in-person only) Monday–Friday, August 4–8, 20259:00 AM – 5:00 PM About the Bootcamp Learn core bioimage analysis skills using open-source tools for light microscopy in this hands-on, in-person course. The Bootcamp covers annotation, segmentation, and deep learning fundamentals. Fee: $600 (Academic/Non-Profit) | $1000 (Industry/For-Profit) For more information email ImagingAdmin@broadinstitute.org
May 1, 2025 at 9:22 PM
bethcimini.bsky.social
Proud to see so many people in #Boston #StandUpForScience
Hundreds of people rally, many with signs, under a patchy cloudy-and-blue sky on the Boston Common.
March 7, 2025 at 6:53 PM
bethcimini.bsky.social
An obvious advantage of live cell dyes is that they can be used, well, live - we looked at phenotypic activity and distinctiveness over time, and showed that it's probably possible to do live cell profiling followed by standard Cell Painting without perturbing the latter too much (5/x)
Colorful graphs of a violin plot on top and bubble chart below Colorful graphs of a violin plot on top and bubble chart below Two scatter plots, both showing strong linear correlation between the x and y axes
February 25, 2025 at 2:03 PM
bethcimini.bsky.social
Key takehome - for most compounds, most dye sets work well! This is especially true for phenotypic activity (distinct from DMSO) but also pretty true for phenotypic distinctiveness (distinct from other compounds). Results for each compound times each dye set in the supplement! (4/x)
Colorful graphs of a violin plot on top and bubble chart below Colorful graphs of a violin plot on top and bubble chart below
February 25, 2025 at 2:03 PM
bethcimini.bsky.social
Cell Painting is awesome! But what about other dyes? We tested standard image-based profiling approaches using some dye substitutions, including some pretty orthogonal dyes (other mito stains and/or phalloidin wavelengths), as well as live-cell dyes based on totally different chemistries (2/x)
Images of cells, with various compartments stained Images of cells, with various compartments stained - some cells have been treated with drugs and look sick
February 25, 2025 at 2:03 PM
bethcimini.bsky.social
Nice shout-out to #opensource #microscopy and #imageanalysis #bioimageanalysis software at #CZIImaging #ImagingTheFuture.
A slide titled "Supporting open source software and communities" showing logos and screenshots from scikit-image, napari, ImageJ, Fiji, CellProfiler, Piximi, and MicroManager
November 13, 2024 at 3:54 PM
bethcimini.bsky.social
It's great! I'm in heaven
A screenshot from deck.blue, showing side-by-side tracking of multiple feeds including "Home", "Bioimaging", "Science", "New PI", and "Mutuals"
November 11, 2024 at 6:53 PM
bethcimini.bsky.social
Is "Runs from top to bottom" clickable?
November 9, 2024 at 5:37 PM
bethcimini.bsky.social
I won't say too much here, because I'd love you to actually go read the paper (it's open access!), but briefly, we cover who bioimage analysts are, how we add value, how we can prove to our bosses we add value, and what we need from other groups/communities to thrive (4/x)
A figure with a line drawing of bioimage analyst in the center, showing 4 lists of major areas of competency in each corner,under the headings image analysis, implementation, project management, and education. A figure with an heading "Barriers to bioimage analysis", with a pink block headed "Personal" (with subheadings "Getting started" and "Career"), a yellow block headed "Scientific community" (with subheadings "Peer pressure", "Governance principles", and "Moral incentive"), and a blue block headed "Structural" (with subheadings "Publishing", and "Funding). A figure titled "Working with your friendly local bioimage analyst", with a medium-sized red circle titled DON'Ts and a large green circle titled DOs. Items under DON'Ts include "Wait until the end to reach out", "Assume analysts know your experimental details", "Overlook interdisciplinary connections", and "Dismiss the role of specialists"; items under DOs include "Reach out early and often", "Plan ahead", "Verify data quality", "Stay up to date", and "Respect expertise". A figure titled "What can we do? What do we need?". It has a large block titled "Bioimage analysis community", which under "Short-term goals" has headings "Define standards", "Catalog resources", and "Adopt best practices" and under "Long-term goals" has headings "Disseminate standards", "How-to guides", and "Training". In a smaller block titled "Policy makers and funders" there are headings "Provide dedicated funding", "Support publications", and "Recognize non-standard scientific contributions".
October 30, 2024 at 2:23 PM
bethcimini.bsky.social
I won't say too much here, because I'd love you to actually go read the paper (it's open access!), but briefly, we cover who bioimage analysts are, how we add value, how we can prove to our bosses we add value, and what we need from other groups/communities to thrive (4/x)
November 10, 2024 at 5:52 PM
bethcimini.bsky.social
Virtual I2K starts TOMORROW, Monday the 28th! 34 FREE sessions, 900+ registrants so far. Learn more about favorite #bioimageanalysistools or find your next fav! <a href="http://i2kconference.org/virtual" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">http://i2kconference.org/virtual

Please also help our community improve by filling out our survey -...
November 12, 2024 at 10:24 AM
bethcimini.bsky.social
Virtual I2K starts TOMORROW, Monday the 28th! 34 FREE sessions, 900+ registrants so far. Learn more about favorite #bioimageanalysis tools or find your next favorite! i2kconference.org/virtual

Please also help our community improve by filling out our survey - forum.image.sc/t/2024-image...
A green and magenta fluorescence microscopy image of kelp blades, next to text saying "Virtual I2K2024: Online Tutorials on Image Analysis. October 28-30, 2024. Virtual Conference for beginners to developers. i2kconference.org for more info .
October 27, 2024 at 9:48 AM
bethcimini.bsky.social
FAIR reuse of FAIR slides at #i2k2024 @ctrue.bsky.social @joshmoore.bsky.social
Josh Moore presenting Curtis Rueden's call for action to be a FAIR community
October 25, 2024 at 10:13 AM
bethcimini.bsky.social
Blown away by the initial talks by @ctrue.bsky.social and Hari Shroff at #i2k2024 . Amazing inspiration of how we can build the best, most inclusive tools, and what discovery we empower when we do!
Curtis Rueden showing a slide that calls on research software engineers to create FAIR tools that work together, and to use each other's tools when possible rather than empire building. Hari Shroff on stage at I2K, introducing the ideas of why studying embryology is important (and hard!)
October 23, 2024 at 8:31 AM
bethcimini.bsky.social
#i2k2024
The image.sc main screen being presented at I2K The GloBIAS.org bioimage analyst database being shown at I2K The 2020 gather town image.sc Island being presented at I2K The 2018 I2K poster, being presented at I2K 2024
October 23, 2024 at 7:55 AM
bethcimini.bsky.social
#i2k2024 let's go! Can't wait!
Florian Jug onstage, showing several black and white photos of conference organizers and sponsors Human Technopole, Bioimaging North America, and Zeiss
October 23, 2024 at 7:37 AM