Kyle Harrington

Highly recommended!

Four representative slices of cryo-tomograms showing annotated organelles.

New on the CryoET Data Portal: ~27,000 tomograms of affinity-captured lysosomes from HEK293T cells across 4 physiological states. Includes raw data, AreTomo3 reconstructions & Membrain-Seg annotations. Openly available for reuse!

cryoetdataportal.czscience.com/depositions/...

Magnetically sensitive proteins could lead to new imaging tools and remote-controlled drugs New study shows how engineered proteins can be tracked with an MRI-like approach

Here's the other one:

www.science.org/content/arti...

‘Remote controlled’ proteins illuminate living cells The discovery that some fluorescent proteins are sensitive to magnets could lead to the development of switchable drugs and biosensors.

Thanks, Rita! I was pretty darn happy that the journalists at Nature (and Science) were kind enough to write up the story of Maria's discoveries.

I appreciate y'all, it really helps our mission.

www.nature.com/articles/d41...

BIG FIGHT AT POLAND’S WROCLAW ZOO!!!

This one was quite the journey! The paper describing the #ChlamyDataset is finally out and on the cover of Mol Cell!

This beautiful rendering made by co-author @jessheebner.bsky.social and Holly Peterson shows an instance of mitochondrial fission found in the dataset 😍

[Maybe long thread ahead]

Great sentiments here, but the semantics aren't safe quite yet. Models like the ESM family are scientific LLMs that are not chat bots, and the prevalent VAE models in scientific research are gen AI (also not chat bots).

GitHub - czimaginginstitute/zarr-particle-tools: Particle extraction and reconstruction from OME-Zarr tilt series. Particle extraction and reconstruction from OME-Zarr tilt series. - czimaginginstitute/zarr-particle-tools

Hi #teamtomo! Want to use OME-Zarr for your tilt series but can't integrate it with your existing sub-tomogram averaging pipelines?

Try zarr-particle-tools - RELION-style extraction & reconstruction built for OME-Zarr-based workflows!

📦 pip install zarr-particle-tools
🔗 github.com/czimagingins...

I love the name!!! Looking forward to checking out🍦

Rerun with increased neighbor detection radius

This is awesome! Way to go William!!!

#geff v1 is released! 🎉 GEFF is a zarr-based Graph Exchange File Format with special support for tracking applications in Python and Java. Thank you to all the amazing developers who contributed at the Janelia 2025 Trackathon! liveimagetrackingtools.org/geff/

Howdy #arxiv folks, could someone please endorse my colleague Ambrose Carr on q-bio.QM for a preprint? Endorsement code O488JD

thank you!

—

What about looking at the one person you're trying to make laugh via DM

Save the date! The @pasteur.fr Pasteur course on image analysis is announced:

It will happen from the 1st of June to the 5th 2026.

This year there will be only one track: the Early Career Investigator track (beginners). 👇

A realistic phantom dataset for benchmarking cryo-ET data annotation - Nature Methods A standardized, realistic phantom dataset consisting of ground-truth annotations for six diverse molecular species is provided as a community resource for cryo-electron-tomography algorithm benchmarki...

A standardized, realistic phantom dataset consisting of ground-truth annotations for 6 diverse complexes serves as a community resource for benchmarking cryo-ET algorithms.

www.nature.com/articles/s41...

Caroline Hemphill also wrote up a great blog post about the competition: www.czbiohub.org/life-science...

A realistic phantom dataset for benchmarking cryo-ET data annotation - Nature Methods A standardized, realistic phantom dataset consisting of ground-truth annotations for six diverse molecular species is provided as a community resource for cryo-electron-tomography algorithm benchmarki...

Better ML for cryo-ET starts with better benchmarks.

We built a phantom cryo-ET dataset (~500 tomograms) + hosted a Kaggle challenge.

The result: community models beat expert tools.

Read more in the @natmethods.nature.com article that just came out:
🔗 doi.org/10.1038/s415...

Is that an anvil?

It's hard to express how much gratitude I have to everyone involved in the journey, both mine and @napari.org's, that has led to this point. #EurekaPrizes A small attempt below: 👇

🚀The napari team is excited to announce our brand new development roadmap — a community-informed vision for the future of napari!

🔍Read the blog to learn about our process and priorities:
napari.org/island-dispa...

🗺️OR check out the roadmap itself on napari.org:
napari.org/stable/roadm...

If you post the frames in a thread then we can try scrolling really fast

Polarity-JaM: an image analysis toolbox for cell polarity, junction and morphology quantification - Nature Communications Studying cell polarity is often limited by the complexity and variety of image data. Polarity-JaM is a software suite streamlining cell polarity analysis with easy-to-use tools and interfaces demonstr...

when you discover new tools and ideas via biorixv, sometimes you don't even notice when it is published, some great stuff here :
www.nature.com/articles/s41...

bsky.app/profile/wais...

There is a @napari.org hackathon at GloBIAS!

Be there or be square (or whatever layer type you'd like)

TFW you discover the internet in the conference venue isn't stable enough for a Google Slides presentation with videos 😅 luckily with >24hr warning

a woman in a hat is crying and says " i 've traveled a good many miles to get here " Alt: Charlotte from the Sanditon TV series, emotionally exclaiming, "I've traveled a good many miles to get here!"

And it's finally here! napari 0.6.0 is out on PyPI and conda-forge! 🥳 We've had a few threads about this release already but let's recap with some highlights: 🧵

We have a suite for studying cell polarity in Python polarityjam.readthedocs.io feel free to post an issue if you need any more functionality