iiinova — where your digital self keeps evolving

Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 26/06/2026

ONLY the latent spaces that had the nuc/membrane images, not just transcripts! Adding transcripts to transcripts doesn't help, only new info does. This makes total sense! There's much more we want to do/are doing here, but wanted to share it now because one of the most exciting bits to us …(7/x)

A set of bar graphs for homogeneity scores - TC on the left is outperformed by TC+LS2, TC+LS3, TC+LS4, and TC+LS5. TC+LS1 is a bit lower, and TC+CPsm and TC+CPlg are basically invisible.

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 26/06/2026

What could we DO with these fun new latent spaces? We were bummed but not shocked to see we were not outperforming ST alone, but found it super interesting that the latent space data was better than the CellProfiler measurements @emiglietta.bsky.social was kind enough to put together. (5/x)

A 3x3 series of brightly colored UMAPs displaying clusters of various cell types. The top left UMAP (of transcript counts) is nicely structured, the next 5 (all labeled as LS 1-5 for latent spaces) are kind of structured but more mixed, and the bottom two are annotated CP (for CellProfiler) and are totally mixed garbage.

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 26/06/2026

Levin, aided by local DL expert @gnodar.bsky.social, designed several variational autoencoders (VAEs), incorporating the transcripts, nuclear image, cell membrane image, or some combo. Figuring out the joint representations took some doing, but eventually we got some models that worked nicely (4/x)

A diagram of a variational autoencoder, with input images on the left, a latent space in the middle, and reconstructed images on the right. 5 different sets of input images are shown, labeled VAE 1-5.

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 08/05/2026

Today I learned that the team at #Nextflow must be fans of The Wire, given the auto-generated name my workflow just got

Console text reading "Launching `./main.nf` [drunk_mcnulty]

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 19/04/2026

Want to present a poster, talk, or workshop at this year's Images 2 Knowledge (I2K) meeting - Sep 27 - October 2nd in Madison, WI? Please fill out the form by Thursday - we really want to highlight your contributions! airtable.com/appPes56Tahc...

A cow behind some buildings overlooking a lake - top banner says "I2KxBINA 2026 Community Congress", while bottom banner says "Cultivating the Multiscale Imaging Frontier"

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 12/04/2026

Decided today at QI was for making dumb microscopy memes. Make sure to do your pilots before you do your final experiment!

A meme that says at the top "Quantification without pilots", and at the bottom "not even once". In the middle is a circle with 4 wedges, one each for sample preparation, image acquisition, image analysis, and data interpretation. Arrows indicate the workflow should go in both directions, not just one!

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 01/04/2026

Your April 1st gift from the CellProfiler team - adjustable table fonts :).

A software screenshot of a window displaying a table of numeric data. The table uses the font Comic Sans.

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 20/03/2026

Our Bioimage Analysis Beginnings Bootcamp is back and better than ever! Delighted to offer some fee support this time, thanks to the generous sponsorship of @bioimagingna.bsky.social . Apply now to join us June 1st to 5th to level up your skills! Learn more at cimini-lab.broadinstitute.org/bootcamp

An advertisement for the Bioimage Analysis Beginnings Bootcamp, in blue and white text and abstract shapes on top of pictures of cells.
Learn core bioimage analysis skills using open-source tools for light microscopy. Open to participants at all skill levels.
Registrations open through April 10
Sponsored by BioImaging North America
Where & When
Broad Institute, 415 Main Street, Cambridge, MA (in-person only)
Monday–Friday, June 1–5, 2026 9:00 AM – 5:00 PM
Register at broad.io/BAB3
Fee: $750 (Academic/Non-Profit)
$1250 (Industry/For-Profit)

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 17/02/2026

Extra special bonus - video of Erin and I in the same place! It does happen!

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 16/02/2026

Chocolate peanut butter brownies, but make them *sparkly*.

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 05/01/2026

The 7 street rotary in East Longmeadow, MA - all 7 main streets of town come into a single intersection!

A Google Maps overhead view of seven streets converging to a central circle, like some horrible wheel of doom with 7 spokes coming form a central circle at seemingly random angles.

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 13/11/2025

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

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 18/10/2025

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.

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 18/10/2025

I expressed my dissatisfaction with not having a picture together since January and was rewarded

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 17/10/2025

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.

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 14/10/2025

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

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 09/10/2025

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

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 10/07/2025

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)

$A map of the world showing fractions of survey responses (most heavily concentrated in Europe, followed by the Americas), as well as gender , age, and career status breakdowns$

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 14/05/2025

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?"}

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 01/05/2025

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

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 25/02/2025

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

Two scatter plots, both showing strong linear correlation between the x and y axes

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 25/02/2025

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)

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 25/02/2025

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

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 09/11/2024

Is "Runs from top to bottom" clickable?

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 30/10/2024

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".

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 30/10/2024

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 27/10/2024

Virtual I2K starts TOMORROW, Monday the 28th! 34 FREE sessions, 900+ registrants so far. Learn more about favorite #bioimageanalysistools or find your next fav! i2kconference.org/virtual Please also help our community improve by filling out our survey -...

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 27/10/2024

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 .

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 23/10/2024

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!)

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 08/10/2024

#bioimageanalysis friends, the deadline to submit your tutorial to the FREE Virtual I2K meeting is tomorrow- head to www.i2kconference.org/virtual to learn more. Help learners all over the world discover your tool/workflow! Please RT and spread the word for trainers and...

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 08/10/2024

#bioimageanalysis friends, the deadline to submit your tutorial to the FREE Virtual I2K meeting is tomorrow- head over to www.i2kconference.org/virtual to learn more. Help learners all over the world discover your tool or workflow! Please repost and spread the word for trainers and learners both!

Poster with a green and magenta image of kelp advertising "Virtual I2K 2024: online tutorials on image analysis, October 28-30 2024"

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 24/09/2024

@shatavishadg, @emiglietta1, @Le__Liu, Rajavi Shah, and Kamal Hamid. You're all amazing colleagues and helpers of the community. broad.io/CiminiLabMakesStuff

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 24/09/2024

I regret that I never got to meet him. Being named @BioimagingNA's inaugural Michael Davidson Award winner is therefore an incredibly moving and humbling experience - that's an outstanding class of humans to be put into. I'm so grateful to the community... (2/x)

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 24/09/2024

David Stirling, Nasim Jamali, Pearl Ryder, Alice Lucas, Barbara Diaz-Rohrer, Rebecca Senft, Callum Tromans-Coia, Mario Costa Cruz, Levin Moser, Andréa Papaleo, Suganya Sivagurunathan, Paula Llanos, Shatavisha Dasgupta, Esteban Miglietta, Le Liu, Rajavi Shah, and Kamal Hamid (7/x)

A group of 18 people smiling in a restaurant. A sign on the back wall reads "I don't know where I'm going but I can promise it won't be boring".

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 24/09/2024

Being named @bioimagingna.bsky.social's inaugural Michael Davidson Award winner is therefore an incredibly moving and humbling experience - that's an outstanding class of humans to be put into. I'm so grateful to the community, and thankful for everyone's kind words, but ... (2/x)

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 18/09/2024

Bluesky now has over 10 million users, and I was #383,684!

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 02/09/2024

Current Methods in Cell Biology, let's goooooo! #EMBOCellBiology

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 16/05/2024

We wanted to find out what works for THEM, so we asked them anonymously to rate and rank the parts of the program - we found most things work pretty well, but opinions vary widely per person on what is most and least important (5/x)

Relative scores (left) and rankings (right) of the value of 12 aspects of the training program to the participant's training experience. Aspects include: having an official training curriculum, running workshops, working with the image.sc forum, working on individual analysis projects, writing code, working on data-science-heavy-projects, writing papers, training with/from permanent staff members (image analyst/software engineers), training with/from other postdoc program members, interaction with collaborators, explicit and/or implicit training on project management skills, and explicit and/or implicit training on communication skills. Scores were on a scale of 1-7; rankings were performed 1st-12th with no possibility of ties.
Left graph shows mean scores of 5-7 of 7 for almost all aspects, right graph shows huge variability in importances with all but one aspect having at least one top-3 rank and at least one bottom-3 rank.

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