Good ML code comes from people who fundamentally believe that ML is a trickster god and wants them to fail

TrackMate v8 - segmentation editor and Python CLI integration TrackMate v8: 2D Segmentation Editor & Python CLI Integration Hi everyone, I am excited to announce TrackMate v8, a major update introducing key improvements for both end-users and developers. Mai...

New release of the TrackMate single particle tracking plugin for ImageJ by @jytinevez.bsky.social looks amazing! forum.image.sc/t/trackmate-...
Loads of new features, most excitingly to me deep learning segmentation algorithms including Omnipose (for cells), and Spotiflow (for spots) #bioimaging

A holiday demonstration of the different penetration depths of red and blue light into tissue.

#optics

Thank you editors for improving the readability of our paper by removing acronyms. Now we grow our cluster of differentiation 4+ Forkhead box 3+ cells in Roswell Park Memorial Institute media with phorbol 12-myristate 13-acetate.

TIL, RPMI media is actually Roswell Park Memorial Institute media

We present Olmo 3, our next family of fully open, leading language models.
This family of 7B and 32B models represents:

1. The best 32B base model.
2. The best 7B Western thinking & instruct models.
3. The first 32B (or larger) fully open reasoning model.

@ninaluong.bsky.social is really upping her costume game this year. And she can still work in it!

When #halloween meets #FluorescenceFriday 🎃

🎃A fluorescent turmeric jack-o'-lantern!🎃
I filled a flat-bottom flask with turmeric extract. Jordan Tanen drew the face.🖊️ #FluorescenceFriday #SciArt #SciComm #RealTimeChem #ChemArt

The #OME-Zarr RFC-5 proposal allows you to transform multiple images into the same coordinateSystem. Trying this out with napari at github.com/will-moore/n.... Cool that you can offset T-dimension as well as XYZ!

🎃Welcome to my fluorescent pumpkin patch!🎃
Jack-O-Lanterns are pipette tips filled with 😈 lucifer yellow, fluorescein, or rhodamine 101.🎃
🌝 #FluorescenceFriday #PipetteArt #SciArt #ChemArt #SciComm #HappyHalloween #Halloween 🎃

New #NeurIPS2025 paper: how should we evaluate machine learning models without a large, labeled dataset? We introduce Semi-Supervised Model Evaluation (SSME), which uses labeled and unlabeled data to estimate performance! We find SSME is far more accurate than standard methods.

Going through some Erdős problems that Mark Sellke and Mehtaab Sawhney found had already been solved using GPT5 pro for search. More precisely, these were listed as open, but solutions to them already existed in the literature, but not recognized as such. Quite remarkable.

One example: [+]

For this #FluorescenceFriday 🔬
a cryosection of a dissected zebrafish gill, stained with phalloidin (orange) and DAPI (blue-ish).

#Zebrafish #DevBio #Microscopy

what do you mean i have to submit an abstract now for a presentation in april?

A chicken neural crest explant with neural crest marker sox9 in green, e-cadherin in orange, filamentous actin in magenta, and nuclei in gray.

Today for #FluorescenceFriday I’m sharing a 👻Halloween-themed🎃 neural crest explant “web of cells” from Julia Godinez, a 4th year @ucdavis.bsky.social graduate student in the lab. She is studying mechanisms driving conserved and divergent cranial neural crest migration and differentiation. #DevBio

As part of our monthly meeting, we do a run-down of all* the new #bioimageanalysis tools that have been published in the last couple of weeks on BioRxiv**, so I thought I'd start sharing here as well.

*I will miss some, apologies if I miss your paper

Stages of CV research work

1. Denial
2. Anger
3. Bargaining
4. Depression
5. Manual data labeling
6. ???
7. PROFIT

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

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!

I found these immune cells just finished mitosis but their midbody is still yet to be resolved. How cool? If you zoom in to the midbody, you can see its classical shape just like in the textbooks. I love these little details.

The future of High-Content Imaging has arrived.

-> Ultra-fast 3D imaging of multi-well plates at high resolution using an air objective!

See previous posts and the new miOPM preprint for details: doi.org/10.1101/2025...

Threw away the pellet

#SpatialOmics

MCMICRO
Multiple Choice Microscopy pipeline
mcmicro.org

Multi-channel whole-slide images▶️
Single-cell data + Spatial Feature Tables

Multimodal (CyCIF CODEX mIHC) registration + HE IMC MIBI

#NatMethods 2022
www.nature.com/articles/s41...

The connectome of the entire male Drosophila central nervous system is out!! Acquired using FIB-SEM @ 8x8x8nm, we aligned 7.5 mio 2D images aligned into one seamless 3D volume, which was used to segment & proofread neurons and synapses. @hhmijanelia.bsky.social

www.biorxiv.org/content/10.1...

Happy #FluorescenceFriday! Our #CellLineOfTheWeek is Nucleoporin Nup153! 🧫

Our stem cell lines and plasmids, illuminating specific cell structures, are available for just the cost of shipping to support scientific discovery.

📦 Distributed by @coriellinstitute.bsky.social & @addgene.bsky.social

α-spectrin (red), lipid droplets (green), and nuclei (blue) are shown in adipocytes. Scale bar is 20 μm.

For #FluorescenceFriday, α-spectrin (red) and lipid droplets (green) are shown in adipocytes 🔬 #Microscopy #CellBiology

After many years of hm-ing and haw-ing about why some of the fusion proteins I’ve cloned showed cytoplasmic background I’ve finally found the culprit

Rainbow shading of a confocal micrograph of a developing mouse neural tube. The protein actin is stained and colored in rainbow to indicate depth in the section.

Happy #FluorescenceFriday! This is a maximum intensity projection of depth shaded actin (🌈) in a section from an E9.5 🐭 neural tube (NT). 🔬 by postdoc @christinaadaly.bsky.social 👩‍🔬 🧪 Image shows the floor plate and lumen of the developing NT.

#SciArt #DevBio #DevNeuro

🎃💀Boys & girls of every age. Wouldn't you like to see something strange?💀🎃
🖌️🎨I painted Jack Skellington with E. coli expressing the small Ultra-Red Fluorescent Protein (smURFP).🧬🦠🧫
#TheNightmareBeforeChristmas #JackSkellington #SciArt #AgarArt #SciComm

Keynote at #COLM2025: Nicholas Carlini from Anthropic

"Are language models worth it?"

Explains that the prior decade of his work on adversarial images, while it taught us a lot, isn't very applied; it's unlikely anyone is actually altering images of cats in scary ways.

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.”

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