📣 Tracking cells through time – including divisions – is a core problem in live-imaging microscopy. We built HOCT, an edge-centric Transformer that hits state-of-the-art on the Cell Tracking Challenge without a pretrained image encoder. Work led by @jookuma.bsky.social arxiv.org/abs/2607.11754 🧪🔬💻

🚨Open call to the Cell Tracking crowd out there🚨! Loïc's team at @biohub.org opened our Kaggle Challenge for 3D cell tracking, with $60k of prize money💰. Spread the news, delve into our gigabytes of imaging (zarr3) and cell tracking (geff) data of developing zebrafish embryos, and start tracking 🤩

Loïc A. Royer 💻🔬🧪@loicaroyer.bsky.social · 2mo ago

1/ 🧬🔬 How does one cell become an entire animal? We can now film it in 3D 🐟, but turning those movies into accurate cell tracks is brutally hard. Enter our new #Kaggle challenge: $60K prize pool, to help crack 3D+time cell tracking at scale! 🧵👇 www.kaggle.com/competitions... @biohub.org

Want to build some of the most advanced light-sheet microscopes in the world to watch life assemble itself cell by cell? The Royer Lab @ Biohub is hiring an Optical Engineer (Advanced Light Sheet Microscopy). 🧪🔬💻🔧 #Hardware + #Python + Advanced #Optics job-boards.greenhouse.io/biohub/jobs/...

Optical Engineer, Advanced Light Sheet Microscopy

San Francisco, CA (Hybrid)

job-boards.greenhouse.io

What a luxury to travel to #bps2026 by bike this year 🚲, locally in SF! I will be presenting the work from the Royer lab (@biohub.org) on Monday, 1:30 pm, in the Biophysics 101 session 🐠🔬. Followed by a poster ...

Join us for the AI Applications in Biology Symposium at @biohub.org! A full day of talks on ML for structural biology, imaging, single-molecule & multimodal/omics data 🗓️ Feb. 20, 2026 (1 day before BPS) 📍San Francisco 🔗 shorturl.at/uQerL Attend in-person or virtual. Submit abstracts by Jan. 20!

Ultrack on the cover of Nature Methods! Thanks @alexandredizeux.bsky.social for helping us with the beautiful cover art! 😍

Nature Methods@natmethods.nature.com · 10mo ago

Our November issue is now live! 🎉 www.nature.com/nmeth/volume... On the cover, cell tracking in a developing zebrafish embryo visualized using Ultrack. Cover by Alexandre Dizieux, Jordão Bragantini, Loic Royer, Merlin Lange, CZ Biohub. Paper here: www.nature.com/articles/s41...

Apparently, 🐟 cells are not at all different from herds of 🦓! Great use of #inTRACKtive on very different types of data. Thanks Niko, for trying it out and getting it working already 'during’ my talk 😮

Niko Sirmpilatze@nikosirmpilatze.com · 9mo ago

Great track visualisation tool by @teunhuijben.bsky.social and colleagues. Over lunch we discovered that inTRACKtive can handle herds of zebras almost as well as groups of migrating cells.

Second speaker is @teunhuijben.bsky.social from @loicaroyer.bsky.social group at @czbiohub.bsky.social #CBIAS2025 Tracking is hard because segmentation is hard, especially in whole zebra fish embryos: Ultrack can help github.com/royerlab/ult...

Our very own @teunhuijben.bsky.social from the @loicaroyer.bsky.social lab at the Biohub gave a brilliant overview of their journey to improve tracking and visualisation (and our lives in general 😝) at #CBIAS2025 👩🏻‍💻🔬👩🏻‍🔬 #tracking #interdisciplinary #bioimageanalysis

Happy to be in London for #CBIAS2025! Looking forward to two days of image analysis, and presenting #inTRACKtive and #Ultrack tomorrow 🔬😊

Crick BioImage Analysis Symposium@cbias.bsky.social · 9mo ago

And we’re off. #CBIAS2025 6th Edition, first outside of the Crick but impressed by the localities at @wellcomecollection.bsky.social @david-j-barry.bsky.social welcoming the community

Had a great time in Janelia this summer developing #geff with this amazing group of cell tracking enthousiasts and software engineers! #geff is a file format for tracking data allowing universal cross-tool communication for a wealth of tracking tools, amongst others our #ultrack and #inTRACKtive 🚀

Morgan Schwartz@msschwartz21.bsky.social · 11mo ago

#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/

🍾What a day 🥳 Two papers of the Royer lab in Nature Methods today, including #inTRACKtive! Check out Loïc's thread below for the details ⬇️ Over the next days, I will share the exciting new features we have added since the original preprint. Stay tuned!

Loïc A. Royer 💻🔬🧪@loicaroyer.bsky.social · last yr.

🧬🔬🧪 🎉 Our team at @czbiohub is thrilled to share TWO companion papers out today in @NatureMethods! 📦 Ultrack — robust, scalable nD cell tracking 🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration Let’s dive in! 👇 www.nature.com/articles/s41... www.nature.com/articles/s41...

Saying goodbye to beautiful @hhmijanelia.bsky.social, after an intense two weeks trackhathon. Organized by legends Caroline Malin-Mayor and Morgan Schwartz in the @janfunkey.bsky.social. It has been awesome and productive. Thank you!!

Enjoying two weeks of cell tracking tools, file formats, and collaboration, all at the beautiful Janelia Research Campus. What a place! 🤩🔬🧪 @hhmijanelia.bsky.social

Microscopy Nodes is now up on bioRxiv! 🚀 This is a Blender extension that seamlessly integrates and visualizes 3D microscopy data (TIF & @zarr.dev). High-quality volume rendering for anyone, in both EM and fluorescence, regardless of computational expertise! 🔬 www.biorxiv.org/content/10.1...

Little Nanobiology reunion in San Diego. Great to see multiple professors/alumni at the Cell Bio conference! 🙌 @tudelft.bsky.social #nanobiology #ASCB24 #CellBio2024

Liedewij Laan@liedewijlaan.bsky.social · 2y ago

Nanobiology Rocks! #ASCB2024

Happy to be in sunny☀️San Diego for ASCB Cell Bio! Tomorrow I will present #Ultrack and #inTRACKtive (poster B513) at 11:15 am. Swing by the CZI+@czbiohub.bsky.social booth (#119) for live demos of these tools + #napari & #zebrahub 🐠 Looking forward to connect!🤩🧪🔬 #CellBio2024 #ASCB24 #celltracking

Join us next Friday at UC San Diego for a day full of microscopy 💡🔬, mass spec, and AI! Shout out to @manorlaboratory.bsky.social for putting this together! I will present our recent work on cell tracking algorithms and visualization with #Ultrack and #inTRACKtive🧪 #CellBio2024

Uri Manor@manorlaboratory.bsky.social · 2y ago

Re-upping this - please register if you're in San Diego this Friday and want to hear about the latest advances in cryoEM/cryoET, mass spec, live imaging, and AI! tinyurl.com/ASCBSANDBOX

We modified our STED🔬to make it more efficient ('smart') to acquire high-resolution data of small and rare objects in a 3D cell volume. This enabled collecting a large amount of data in a fully automated fashion. With that, we visualized the ulra-structure a small nuclear body, the paraspeckle👇🏻(1/3)

PSFs are just Gaussians, right?? Not when your fluorophore💡is close to a nanoparticle 🟠! Excited to share our recent ACS Nano paper 🥳 in which we present a novel PSF-fitting approach for localization microscopy near nanoparticles. pubs.acs.org/doi/full/10.... Main findings below in🧵[1/10]

Indeed! Hello everyone!

🚀Thrilled to announce #inTRACKtive: a web-based tool for exploring massive cell-tracking datasets, no software installation required! Open your browser and dive into terabytes of developmental biology data 🐭🪰🪱🪲🐠 Preprint: biorxiv.org/content/10.1... Repository: github.com/royerlab/inT... 🧵1/n

I will be reposting a few threads from the 🐦 app to populate my profile and share the science we are doing :)

#HiSciSky, time for an introduction! I work with Loïc Royer at the CZ Biohub in San Francisco. My work focuses on image analysis, light-sheet microscopy, and AI. I did my PhD in SMLM, so expect a mix of localization microscopy, cell tracking, light-sheet movies, data viz, and super-resolution!💡🧪🔬

inTRACKtive - A Web-Based Tool for Interactive Cell Tracking Visualization https://www.biorxiv.org/content/10.1101/2024.10.18.618998v1

inTRACKtive - A Web-Based Tool for Interactive Cell Tracking Visualization https://www.biorxiv.org/content/10.1101/2024.10.18.618998v1

We introduce inTRACKtive, an innovative web-based tool for interactive visualization and sharing of

biorxiv.org