I found a Loic in Paris! Always great to catch up with my friend and mentor @loicaroyer.bsky.social, after 2hours of conversations I'm back in the lab full of motivation and fresh thoughts.
Loïc A. Royer 💻🔬🧪
@loicaroyer.bsky.social
Sr. Director of Imaging AI @biohub. 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
📣 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 🧪🔬💻
1/ 🧬🧪 New preprint! Do you actually need a biology-specific foundation model to predict how cells respond to perturbations? Surprising answer: a general-purpose tabular model - never trained on a single cell - matches or beats the specialists. 🧵 📄 doi.org/10.64898/2026.06.28.735106 @biohub
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
🧬 🧪Our RNA velocity benchmark is out in PLOS Comp Biol We tested 5 methods on mouse & zebrafish data. They often disagree (just 1/100 driver genes shared 😬). A hypothesis tool, not ground truth. Open access 👉 doi.org/10.1371/jour... Led by the brilliant Sarah Ancheta (not on bsky)
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
"Do not ask what comes next; ask what must not be left undone."
"We present DanioDecima, a zebrafish-specific model leveraging transfer learning from human and mouse-trained models to predict tissue- and cell-type-specific gene expression during zebrafish embryogenesis." New work from @loicaroyer.bsky.social that's sure to (Danio)decimate the competition 🐟
bioRxivpreprint@biorxivpreprint.bsky.social · 2mo agoDanioDecima: A DNA sequence-to-function model of zebrafish embryogenesis https://www.biorxiv.org/content/10.64898/2026.05.29.728876v1
#Lightsheet imaging of early #zebrafish development. Credit to @loicaroyer.bsky.social. #ZebrafishZunday 🧪
"No one is remembered for the hills they climbed, but for the mountain they dared scale."
“If it is not nearly impossible, it is not worth it”
We are all super happy and proud to see our work on the function and evolution of the #cephalic #furrow published in @nature.com. Let me say a few things about the background and history of this work on the #Evolution_of_Morphogenesis (1/12)
#UMAP in VR for #3DThursday! In this zebrafish embryogenesis dataset, RNA-seq + ATAC-seq across 94k+ cells reveal changing regulatory programs over time. 🥼 Yang-Joon Kim, Loic Royer @loicaroyer.bsky.social , Matthias Haury 📝 www.biorxiv.org/content/10.1... 🏛️ Biohub @biohub.org 🎬 #syGlass v2.6.0
1/ 🚀 Excited to release: napari-mcp - agentic control of napari from any MCP-capable AI assistant! Use it for interactive image processing, analysis, and visualisation! Really cool project from @ilan-theodoro.bsky.social from my team! #napari #bioimageanalysis #MCP @biohub
Excited to share our new paper (CVPR 2026 🚀): "MuViT: Multi-Resolution Vision Transformers for Learning Across Scales in Microscopy" which enables local predictions to use global context. Great work led by @albertdm.bsky.social & another fun collab w @gioelelamanno.bsky.social! @scadsai.bsky.social
Our symposium on ‘AI applications in Biology’ is about to start in 30 minutes! Great lineup of speakers for what promises to be a fantastic meeting! 🧪
1/ 🚀🧪🤖 Big update for #Omega — the LLM-powered autonomous agent for bioimage analysis in @napari.org ! Custom LLM endpoints, layer actions, plugin extensibility, agentic widget maker, modernized UI, & 30+ fixes. Here's what's new in version *2026.2.8.2*:
📡🧵 Excited to release an updated version of our preprint: Zebrahub-Multiome: Uncovering Gene Regulatory Network Dynamics During Zebrafish Embryogenesis 🧪🧬🖥️🐠 doi.org/10.1101/2024... A tour-de-force by @yangjoonkim with an unexpected discovery!
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!
Sometimes you have to push your favourite AI model beyond its comfort zone, encourage it, and show support. 😂 💻
Very interesting @latent.space Podcast with Mark and Priscilla! Our cell tracking data is spinning on a screen in the background... www.latent.space/p/biohub
Building open AI to cure or prevent all disease by 2110 (w/ Mark Zuckerberg and Priscilla Chan)
The CZI has acquired EvoScale, established the first 10,000 GPU cluster for bio research, open sourced the largest atlas of human cell types, and gone all in on AI x Bio for its 2nd decade.
latent.space
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
