Jun 12
In neuronal benchmarks, applying CellProfiler, Cytoself, and Paired Cell Inpainting to CellAligner-mapped images rather than to the original images improved the ability of these methods to distinguish ground-truth localization patterns by more than two-fold.
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📂 Open CellProfiler workflows turn #GI biopsy images into single-cell data, enabling reproducible quantification of disease-relevant stress markers in #IBD and supporting translational research
🔗 ow.ly/rNar50Z4vqC
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Apr 6
CellProfiler was my first intro to your work, and I have used it a number of times over the years.
Congratulations on the new chapter, looking forward to the amazing things you do next.
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Feb 7
finally, a way to show CellProfiler results that isn't a PCA
Feb 7
A crazy mental trick is to map complex concepts onto regions the brain is “primed” for (Chernoff).
The most hilarious example I’ve seen is…multivariate portfolio data on cartoon fish.
Analysts would thus look for the "weird fish" in the aquarium.
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Jan 20
using the full power of gemini and claude code to figure out how to make the metadata for this cellprofiler pipeline
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Also, grateful to Dr. Sahoo, who let @meghal_desai and me assist him with an editorial for #CMGH . This editorial highlights two amazing CellProfiler pipelines for studying stress granules. pubmed.ncbi.nlm.nih.gov/4138…
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28 Nov 2025
Thrilled to see Dr. Kevin Eliceiri and Dr. Beth Cimini awarded an NIGMS R24 grant! 🚀
A major boost for the future of open-source image analysis tools like Fiji, ImageJ & CellProfiler.
buff.ly/1LBphLf
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29 Oct 2025
Today, napari users can’t fully leverage Xarray’s labeled metadata, as slider names, units & dimensions often get out of sync. That’s changing, as napari, Xarray & CellProfiler devs begin a collab to build true metadata-aware visualization across sciences
earthmover.io/blog/scientifi…
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12 Oct 2025
This preprint calls for scientific review, but here’s my takeaway: look closely at your cells (in CellProfiler). If you notice subtle differences, you may have uncovered a phenotype! Massive imaging isn’t just for pretty screensavers, it’s real data waiting to be explored!
10 Oct 2025
15 years in the making, we confirmed that mitochondria -the powerhouse of the cell- have an unusual localization in patients who experience psychosis (including schizophrenia and bipolar disorders). You’ll never guess what kind of patient cells we used to make this discovery...🧵
ALT mitochondria are more compact near the nucleus in cells from patients with bipolar disorder as compared to controls in these images. Control patients' mitochondria are more evenly dispersed towards the cell edges
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📚 Kick off the SBI2 Annual Meeting with our Educational Sessions!
📅 October 27th, 2025
➡️ Using Deep Learning tools for segmentation in CellProfiler -
Instructors: Beth Cimini, Erin Weisbart
➡️ Nextflow for Bioimaging
Instructor: Ken Brewer, PhD
sbi2.org/conference/
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6 Aug 2025
Ensuring reproducibility in GUI-based bio-image analysis tools can be tricky. In her blogpost, @maralampert highlights features in Napari, Fiji, QuPath, Galaxy, CellProfiler and JIPipe that support workflow saving and sharing.
focalplane.biologists.com/20…
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11 Jun 2025
i have to double check this vibe-coded CellProfiler result, but taking a closer look at the mitochondria segmentation (cyan), looks like some cool cross-cell networks
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10 Jun 2025
The work turned out to be as open source as possible, all models were made in @FreeCADNews , microscope images were processed in @napari_imaging, ImageJ and @CellProfiler.
7/n
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7 May 2025
yeah, and i kind of prefer the cellprofiler features being released instead of embeddings or something
trying to see if i can pull a thread on mitochondrial dynamics with the heart muscle cell x the mito inhibitors they have
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22 Apr 2025
👉🏼 Attention #LABICommunity
Tomorrow, April 23, is the last day to apply for the free online Latin American CellProfiler Workshop!
A great opportunity to dive into image analysis using CellProfiler.
🔗 broad.io/latam_workshop2025
10 Apr 2025
🚨Latin American Workshop Series🚨
The @CiminiLab from @broadinstitute and @COBA_NIH will host a free, hands-on image analysis workshops for LATAM... in SPANISH🇪🇸 and PORTUGUESE🇧🇷!!!🎉🎊
broad.io/latam_workshop2025
Deadline: April 23rd, 2025
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10 Apr 2025
Label-free droplet image analysis with Cellprofiler biorxiv.org/content/10.1101/… #biorxiv_bioinfo
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10 Apr 2025
🚨Workshop Latinoamericano de CellProfiler🚨
El @CiminiLab del @broadinstitute, junto a @COBA_NIH están organizando un Workshop Introductorio a CellProfiler para Latinoamérica gratuito, online y en ESPAÑOL🇪🇸/PORTUGUÉS 🇧🇷!!🎉🎊
broad.io/latam_workshop2025
Fecha límite: 23/4/2025
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10 Apr 2025
I owe so much to the dedicated scientists at @RecursionPharma and SyzOnc, and throughout the pharma industry, for adopting our tech and proving its worth!
Bravo to the scientists and engineers in my lab over the past two decades who helped build @CellProfiler and Cell Painting!
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