Beth Cimini 🔬💻📊

@bethcimini.bsky.social

3511 Followers 3489 Following

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.

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.
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.
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.
McNulty and Bunk in The Wire share a bottle of whiskey poured into paper cups
Console text reading "Launching `./main.nf` [drunk_mcnulty]
A cow behind some buildings overlooking a lake - top banner says "I2KxBINA 2026 Community Congress", while bottom banner says "Cultivating the Multiscale Imaging Frontier"
The ImageJ logo, with "In ImageJ" in bold black text above and "we trust" below.
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!
A tall bearded man with a hat and glasses stands beneath a slide at the front of a room with some chairs. The slide shows images going into some cartoon pipes, with a CellProfiler logo at the top right. He's doing a very good job explaining the concepts!
A software screenshot of a window displaying a table of numeric data. The table uses the font Comic Sans.
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)
Two women in selfie mode, talking- one is taller with pink hair, one is shorter with brown hair.
A short video showing a close up of a pan of dessert. The dessert is covered in holographic chocolate shards, which move around in the light when the pan is moved.
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.
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
Taylor Swift drinks a glass of wine in black and white, text shows the lyric "I had a marvelous time ruining everything"
A peaceful crowd of many thousand people stand on the Boston Common.
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 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
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.”
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
{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?"}
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
Hundreds of people rally, many with signs, under a patchy cloudy-and-blue sky on the Boston Common.
Colorful graphs of a violin plot on top and bubble chart below
Colorful graphs of a violin plot on top and bubble chart below
Images of cells, with various compartments stained
A slide titled "Supporting open source software and communities" showing logos and screenshots from scikit-image, napari, ImageJ, Fiji, CellProfiler, Piximi, and MicroManager
A screenshot from deck.blue, showing side-by-side tracking of multiple feeds including "Home", "Bioimaging", "Science", "New PI", and "Mutuals"
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 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 .
Josh Moore presenting Curtis Rueden's call for action to be a FAIR community
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.
The image.sc main screen being presented at I2K
Florian Jug onstage, showing several black and white photos of conference organizers and sponsors Human Technopole, Bioimaging North America, and Zeiss
Poster with a green and magenta image of kelp advertising "Virtual I2K 2024: online tutorials on image analysis, October 28-30 2024"
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".
A certificate for the Michael W Davidson Memorial Award, awarded to Beth Cimini. A pin with the Bioimaging North America logo sits on top, and surrounding both are a black scarf covered with fluorescent images taken by Mike Davidson.
Bluesky now has over 10 million users, and I was #383,684!
A sign with the EMBL logo
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.
Community impact: collaborated with dozens of labs, first- or co-first authored 9 publications (871 citations), middle authorship on 9 more publications; a companion website has received >4,000 visitors and has been translated into 3 languages. 29 workshops, reaching >1200 participants either in person or on Zoom, writing and/or translating 8 CellProfiler tutorial exercises. 17 tutorial videos with >38,000 collective views, 17 blog posts which received >16,000 page views. They conducted 118 office hours and posted collectively >2,100 times on the Scientific Community Image Forum (forum.image.sc).
A triangular glass award saying "ABRF Alan B Smith Mentor of the Year Award presented to: Beth Cimini, April 2024"
A cycle of bioimaging steps, starting at "Sample Preparation", then "Image Acquistion", "Image Analysis", and "Data Interpretation", then returning to "Sample Preparation". A line marked "Feedback" shows each step feeding back onto the previous one, and between each step, questions that link it to the next step are listed.