🧬🔬🧪 🎉 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! 👇 (LINKS BELOW)

@czbiohub @cziscience "Readcube" links for easy access and reading: Ultrack: https://t.co/jJxmwNJaEM Intracktive:

🙏 Last but not least, this work was funded by @czbiohub.bsky.social @cziscience.bsky.social , and by our founders and funders: Priscilla Chan and Mark Zuckerberg, Merci!

🤝 And collaborators: @adrianjacobo Akilandeswari Balasubramanian, @Tiger_Lao @edhirata @mattersoflight @lammerdinglab Richa Agrawal, Alexandre X. Falcao @AlexandreDizeux Andrew Sweet and @aganders3 @cziscience

💙 All of this would not have been possible without the awesome team @czbiohub : @jookuma @ilan_theodoro @teunhuijben @hoover_zhao, @shengxiao_, @merlinlange Shruthi VijayKumar

📄 Ultrack in Nature Methods: https://t.co/kmsS8iAuRU 🌐 inTRACKtive in Nature Methods: https://t.co/dqokOqVne2 📦 Code: https://t.co/hChONWkXtI https://t.co/S3jOMcPEU8 🧬 Zoo:

🚀 Explore the Virtual Embryo Zoo! Built with Intracktive! Six tracked embryos across species: zebrafish, Drosophila, mouse, C. elegans, ascidian, Tribolium. View online, download data, use in teaching or analysis. 👉 https://t.co/ruF8VtAaLT

Now what do you do with all those tracks? Say hello to inTRACKtive: 🧬 Navigate complex lineages 🔍 Select cells, trace ancestry 🎨 Color by gene, lineage, division 🔗 Share with a link No installs. Just your browser. https://t.co/S3jOMcPEU8 Led by @teunhuijben.bsky.social

🔥 In one test (500-frame light-sheet dataset), Ultrack reduced manual corrections by >2× ! Built to work with tools like Cellpose, Stardist, Ilastik. Open-source, napari-compatible, GPU-accelerated. awesome data from @adrianjacobo.bsky.social !

💡Ultrack is a robust tracking framework based on multi-hypothesis segmentation & integer linear programming. Scales to full embryos, and supports multicolor, 2D/3D, HPC workflows. More here: https://t.co/hChONWkXtI A tour de force by @jookuma.bsky.social

We built these tools because modern light-sheet microscopy generates massive datasets—millions of cells, terabytes of data, hours of embryonic development. 🧠 But data is only half the story. We need to track, explore, and share. That’s where Ultrack and inTRACKtive come in.

https://t.co/kmsS8iAuRU https://t.co/dqokOqVne2

Honored that our work @czbiohub on https://t.co/Ymb0B8SRIU has been recognised! And in particular, the *disease* angle is really dear to me as it shows that the work we have done is relevant to folks that work closely with disease models. 'Be useful' is my new motto :-)

🎊 Thrilled to share that @ZDMSociety has recognized @LoicARoyer/#CZBiohubSF with its Junior Faculty Award for Excellence. He was honored for Zebrahub, a state-of-the-art cell atlas that gives an unprecedented view of developmental biology. Learn more 🔗 https://t.co/6ZznujqNyg

Just pushed a 'hot fix' version (2025.6.25.2) of Omega (#napari_chatgpt #OmegaAgent) that addresses some issues introduced by the ever-changing model lists from #OpenAI. https://t.co/9MiyG3Ls8U

This is the closest I will probably ever get of the original ‘napari’ 😄 To be exact: 1940.421 km away✈️ @napari_imaging

I just asked #Claude 3.7 to make a web version of the 'Global Thermonuclear War' game from the classic #WarGames movie from the 80s. And it is not too bad!! Except for its skills at drawing continents... Game play could be more engaging too... haha. https://t.co/iFcG4PDIUW

Note: You can really think of our 'Scientist' positions as well-paid, well-resourced 'PostDocs on Steroids'. We do Science, we write papers, and we do so hyper-collaboratively.

🧪 Exciting opportunity! Join the Royer/Jacobo labs @CZBiohub SF! We're seeking a Spatial Molecular Cartography Scientist to push the limits of 3D transcriptomics in zebrafish. Expertise in HCR/FISH techniques wanted! Help us map gene expression at unprecedented detail.