Loïc A. Royer 💻🔬🧪
@loicaroyer.bsky.social
Director of Imaging AI & Sr. Group Leader @czbiohub SF. Researcher at the meeting point of #AI, #Microscopy, and #Biology using #zebrafish as model — co-creator of @napari_imaging and #Omega. #devbio #zebrahub #deeplearning #lightsheet #Imaging #dataviz
Mind-bender: The observable universe has ~10^80 atoms. But even a simple 1000×1000 black‑and‑white image has 2^{1,000,000} ≈ 10^{301,030} possibilities — and 24‑bit color explodes to ~10^{7,224,720}. The space of (small) images dwarfs the cosmos. 🔬🧪💻
November 13, 2025 at 2:31 AM
Mind-bender: The observable universe has ~10^80 atoms. But even a simple 1000×1000 black‑and‑white image has 2^{1,000,000} ≈ 10^{301,030} possibilities — and 24‑bit color explodes to ~10^{7,224,720}. The space of (small) images dwarfs the cosmos. 🔬🧪💻
October 24, 2025 at 9:34 PM
Today’s office…
September 16, 2025 at 11:57 PM
Today’s office…
🚀 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
Six tracked embryos across species: zebrafish, Drosophila, mouse, C. elegans, ascidian, Tribolium.
View online, download data, use in teaching or analysis.
👉 embryozoo.org
August 25, 2025 at 9:06 AM
🚀 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
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
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
August 25, 2025 at 9:06 AM
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
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 !
Built to work with tools like Cellpose, Stardist, Ilastik.
Open-source, napari-compatible, GPU-accelerated.
awesome data from @adrianjacobo.bsky.social !
August 25, 2025 at 9:06 AM
🔥 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 !
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
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
August 25, 2025 at 9:06 AM
💡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
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.
🧠 But data is only half the story. We need to track, explore, and share.
That’s where Ultrack and inTRACKtive come in.
August 25, 2025 at 9:06 AM
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.
🧠 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...
📦 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...
August 25, 2025 at 9:06 AM
🧬🔬🧪 🎉 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...
📦 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...
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...
pypi.org/project/napa...
June 26, 2025 at 12:48 AM
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...
pypi.org/project/napa...
Claude can be brutal sometimes...
June 24, 2025 at 10:27 PM
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
@napari.org
June 18, 2025 at 7:33 PM
This is the closest I will probably ever get of the original ‘napari’ 😄 To be exact: 1940.421 km away✈️
@napari.org
@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...
claude.ai/public/artif...
April 29, 2025 at 10:18 PM
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...
claude.ai/public/artif...
According to ChatGPT image generation, this is my 'Spirit Animal'. 😆
April 24, 2025 at 4:17 AM
According to ChatGPT image generation, this is my 'Spirit Animal'. 😆
Things are getting a bit out of control...
April 3, 2025 at 7:05 AM
Things are getting a bit out of control...
Humanity, I think we are going to be fine... (for some time)
March 10, 2025 at 2:33 AM
Humanity, I think we are going to be fine... (for some time)
Exciting opportunity at @CZBiohub SF! Join us as an Optical Scientist developing cutting-edge light-sheet microscopy to map vertebrate development. PhD in Optics/EE/Physics preferred. #ScienceJobs #Microscopy #BioImaging 🧪🔬💻
job-boards.greenhouse.io/chanzuckerbe...
job-boards.greenhouse.io/chanzuckerbe...
March 6, 2025 at 1:12 AM
Exciting opportunity at @CZBiohub SF! Join us as an Optical Scientist developing cutting-edge light-sheet microscopy to map vertebrate development. PhD in Optics/EE/Physics preferred. #ScienceJobs #Microscopy #BioImaging 🧪🔬💻
job-boards.greenhouse.io/chanzuckerbe...
job-boards.greenhouse.io/chanzuckerbe...
We have serious hackers at the hub! Here is Andy Zhou, Genomics Hacker extraordinaire, with his near-neural computer interface (commonly referred as keyboard)
February 7, 2025 at 11:52 PM
We have serious hackers at the hub! Here is Andy Zhou, Genomics Hacker extraordinaire, with his near-neural computer interface (commonly referred as keyboard)
At the @czbiohub even our computer workstations are
#zebrafish fanatics! (This is not a flux capacitor, but the CPU cooling system of @ilan_theodoro’s computer 🤣)
#zebrafish fanatics! (This is not a flux capacitor, but the CPU cooling system of @ilan_theodoro’s computer 🤣)
January 9, 2025 at 5:30 PM
At the @czbiohub even our computer workstations are
#zebrafish fanatics! (This is not a flux capacitor, but the CPU cooling system of @ilan_theodoro’s computer 🤣)
#zebrafish fanatics! (This is not a flux capacitor, but the CPU cooling system of @ilan_theodoro’s computer 🤣)
At the @czbiohub.bsky.social even our computer workstations are #zebrafish fanatics! (This is not a flux capacitor, but the CPU cooling system of @ilan_theodoro’s computer 🤣)
January 9, 2025 at 5:26 PM
At the @czbiohub.bsky.social even our computer workstations are #zebrafish fanatics! (This is not a flux capacitor, but the CPU cooling system of @ilan_theodoro’s computer 🤣)
Karl the Fog has taken over the lower parts of the city! Potrero hill is like an island above the clouds, beautifull! #SanFrancisco
December 18, 2024 at 3:37 PM
Karl the Fog has taken over the lower parts of the city! Potrero hill is like an island above the clouds, beautifull! #SanFrancisco
The birth of fruit fly's central nervous system imaged with multicolor #adaptive #lightsheet microscopy. The microscope self-aligns to a signal that appears during imaging.
www.nature.com/articles/nbt...
www.nature.com/articles/nbt...
December 11, 2024 at 8:32 PM
The birth of fruit fly's central nervous system imaged with multicolor #adaptive #lightsheet microscopy. The microscope self-aligns to a signal that appears during imaging.
www.nature.com/articles/nbt...
www.nature.com/articles/nbt...
When I go to a concert, I always geek out on the sound consoles and the wizards that control them…
December 11, 2024 at 3:38 AM
When I go to a concert, I always geek out on the sound consoles and the wizards that control them…