Loïc A. Royer 💻🔬🧪

Hello little one!
🤖
#nvidia

ICYMI!
🚀 NEW PANEL ANNOUNCEMENT: Agentic Workflows in Bioinformatics at scverse 2025! 🚀
We're thrilled to introduce an exciting panel discussion at the upcoming scverse Conference 2025!

More information in 🧵

#scverse2025 #Bioinformatics #AgenticAI #Conference

You are going to have a blast!!

Join us as we explore emerging trends in agentic AI applications across bioinformatics workflows.

✨ Featured Panelists:
Kexin Huang - Stanford University
Vega Shah, PhD - NVIDIA
Loic Royer - Chan Zuckerberg Biohub Network
Jonah Cool - Anthropic

🚀 NEW PANEL ANNOUNCEMENT: Agentic Workflows in Bioinformatics at scverse 2025! 🚀
We're thrilled to introduce an exciting panel discussion at the upcoming scverse Conference 2025!

More information in 🧵

#scverse2025 #Bioinformatics #AgenticAI #Conference

We miss you Merlin!
I wish you the best in your new adventure!

Update I'm back in France 🇫🇷! Joining Inserm to build a multi-omics team on retinal development, at the nexus of live imaging, omics & human embryology.

Huge thanks to CZ Biohub SF folks, esp. my mentor, friend & science soulmate @loicaroyer.bsky.social for the amazing time. More cool science soon🧪

On the neighbor's roof, not listening to his dad asking him to come back...

Today’s office…

Ultrack: pushing the limits of cell tracking across biological scales Nature Methods - Ultrack leverages candidate segmentations from multiple algorithms and temporal consistency across time points for robust, long-term 3D segmentation in challenging samples such as...

"Readcube" links for easy access and reading:
Ultrack: rdcu.be/eCfAu
Intracktive: rdcu.be/eCfyc

🙏 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.bsky.social, Akilandeswari Balasubramanian, Tiger Lao, @edhirata.bsky.social @mattersoflight.bsky.social , @lammerdinglab.bsky.social Richa Agrawal, Alexandre X. Falcao @alexandredizeux.bsky.social Andrew Sweet and @aganders3.bsky.social @cziscience.bsky.social

💙 All of this would not have been possible without the awesome team @czbiohub.bsky.social : @jookuma.bsky.social @ilan-theodoro.bsky.social @teunhuijben.bsky.social @hoover_zhao, @shengxiao_, @merlinlange.bsky.social Shruthi VijayKumar

📄 Ultrack in Nature Methods: www.nature.com/articles/s41...

🌐 inTRACKtive in Nature Methods: www.nature.com/articles/s41...

📦 Code:
github.com/royerlab/ult...

github.com/royerlab/inT...

🧬 Zoo: embryozoo.org

🚀 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.
👉 embryozoo.org

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.
github.com/royerlab/inT...
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.
It reduces errors dramatically, scales to full embryos, and supports multicolor, 2D/3D, HPC workflows.
More here: github.com/royerlab/ult...
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.

🧬🔬🧪 🎉 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...

This was magical — @loicaroyer.bsky.social live on piano @mpi-cbg.de. Made my day! It’s always amazing to learn about unexpected talents apart from the amazing science.

Day four of #LISH25 begins with a powerful presentation by @loicaroyer.bsky.social on digitizing zebrafish development, combining light-sheet and single-cell data. Loïc took the #walk-up song to another level, improvising on the piano as his massive fish development visualisation played. Beautiful.

comparison table for v2 and v3

Production has started for a new #Snoutscope objective, AMS-AGY v3. It has significantly larger FOV and some other tweaks from v1 and v2. Currently accepting pre-orders. The price will need to increase modestly after deliveries start late October.

Just pushed a 'hot fix' version (2025.6.25.2) of Omega (napari_chatgpt) that addresses some issues introduced by the ever-changing model lists from #OpenAI.
pypi.org/project/napa...

Claude can be brutal sometimes...

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

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.

claude.ai/public/artif...

According to ChatGPT image generation, this is my 'Spirit Animal'. 😆

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.

This role sits at the intersection of molecular biology, advanced microscopy, and computational analysis.
Ideal candidates have a recent PhD and strong expertise in FISH techniques, RNA handling, and probe design. Join us in creating comprehensive spatial maps of developing vertebrate organisms!