Loïc A. Royer 💻🔬🧪

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! 🧪

There was an issue with version 2026.2.8.2, I deleted it and created a new one: 026.2.9

Thanks, Zebrafish Rocks! It is not new, but it has been massively improved with new features and many bug fixes! 😀

12/ I would like to thank @anthropic.com for making Claude Code. CC did most of the maintenance work to 'fix' Omega. It even addressed the issues directly, fixing the code, adding comments, closing issues, reviewing image.sc, and further fixing issues and implementing new requested features! nuts!

GitHub - royerlab/napari-chatgpt: A napari plugin to process and analyse images with chatGPT! A napari plugin to process and analyse images with chatGPT! - royerlab/napari-chatgpt

11/ 🔬🧪 Try it today! pip install napari-chatgpt — GitHub: github.com/royerlab/napari-chatgpt — Paper: doi.org/10.1038/s41592-024-02310-w #Omega #napari #AI #BioImageAnalysis

10/ And remember! An often overlooked feature of Omega is its integrated code editor! All code generated by Omega is saved for you to edit, improve, and reuse later!

9/ 🛡️ 30+ bug fixes & security hardening: Qt thread safety segfaults, Windows Unicode errors, macOS shutdown hangs, shell injection prevention, and infinite loop guards. #Omega is now much more robust across all platforms!/home/royer/workspace/python/napari-chatgpt/screenshots/card_bug_fixes.png

8/ 🧰 More tools & better napari integration: FileDownload, PipInstall (with user permission!), web search, exception catcher. Plus sample data in the napari File menu so you can start experimenting with #Omega immediately.

7/ ✨ Modernized chat UI: dark theme, message bubbles, thinking animations, collapsible tool output, responsive layout, and a live session token counter. Removed 176K lines of vendored CSS for a clean, fast experience.

6/ 🤖 Agentic widget maker! #Omega now uses a sub-agent to generate napari/magicgui widgets. If the code fails, it reads the error and self-corrects — up to 3 attempts. Smarter code generation, fewer failures!

5/ ⚡ New: Layer Actions! Ask #Omega to create custom right-click context menu items & keyboard shortcuts for napari layers. Say 'make an action that applies a Gaussian blur' and it appears in your context menu, ready to use on any layer!

4/ 🧩 New: NapariPluginTool! #Omega can now discover & use ANY installed napari plugin. Plus, 3rd-party devs can extend Omega with custom tools via Python entry points — just add an entry in your pyproject.toml!

3/ 🔧 Bring your own LLMs! Connect Ollama, Azure, vLLM, or any OpenAI-compatible endpoint via ~/.omega/config.yaml. Got a GitHub token? #Omega auto-detects it and unlocks free GitHub Models. Frontier to local — your choice!

2/ 🔗 Multi-provider LLM support for the very latest frontier models! #Omega now works with OpenAI, Anthropic (Claude), & Google Gemini via the LiteMind library. No more vendor lock-in. You can even set separate models for conversation & coding tasks!

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*:

Peak 3D UMAP - Zebrahub 640K genomic regions, pseudobulked over celltypes and timepoints

It is just standard UMAP. You can use the UMAP algorithm (unrelated to 'force directed' graph layout) to project in any number of dimensions, actually. I am obsessed with 3D UMAPs because they are extremely informative, especially compared to 2D UMAPs. Check:
zebrahub.sf.czbiohub.org/umap/peak_um...

23/ 🐠 Dive into the depths of zebrafish development with Zebrahub-Multiome! #DevelopmentalBiology #SingleCell #Multiomics #Zebrafish

22/ 💬 We want your feedback! We expect and hope for a robust and enthusiastic discussion with the community and welcome feedback, ideas, and suggestions! Reach out at yang-joon.kim@czbiohub.org, merlin.lange@czbiohub.org and loic.royer@czbiohub.org

21/ We are deeply grateful to CZB SF founders Priscilla Chan and Mark Zuckerberg for their generous support, which made this research possible.

20/ ..., @hoover_zhao, @kyleawayan, Amanda Seng, @mikeborjatweets, Sheryl Paul, Honey Mekonen, Ritwicq Arjyal, Angela Detweiler, Norma Neff, @shenbaba, @Merlin_Lange, collaborators, all San Francisco biohubbers!

19/ 🤝 This work would not have been possible without the great work and help of the whole team: @yangjoonkim, @Shruthi94Vijay, Benjamin Iovino, @ale_agranados, @Sarah_E_Ancheta, @MaxFlorainFrank, ...

18/ 🔍 Zebrahub-multiome resource offers insights into zebrafish development, from gene regulation to cell fate decisions. Perfect for developmental biologists, geneticists, and computational biologists!

17/ 🎯 Lastly, Explore #zebrafish 's regulatory landscape of 640K+ chromatin accessibility peaks organized by cell-type and temporal patterns. Each cluster annotated using LLM with motif enrichment, developmental dynamics, and biological context. zebrahub.sf.czbiohub.org/slt?name=mul...

16/ Fourth, run silico perturbations to test TF knockouts and predict effects on cell fate decisions.
Currently focused on NMP lineages, mesoderm vs. neuroectoderm trajectories.
zebrahub.sf.czbiohub.org/slt?name=mul...

15/ 🕸️ Third, explore time- and cell-type-resolved gene regulatory networks. Watch regulatory modules activate as development progresses, from shared early programs to lineage-specific circuits.
zebrahub.sf.czbiohub.org/slt?name=mul...

14/ 🧬 Second, Explore genes cluster by their chromatin accessibility and expression patterns across development.
Discover coordinated regulatory programs, identify co-regulated genes, and track temporal waves of activation.
zebrahub.sf.czbiohub.org/slt?name=mul...

13/ 📊 Start with CZ CELLxGENE: Find your genes Browse RNA-seq, ATAC-seq, or joint embeddings.
Perform differential expression analysis directly in your browser.
Identify genes of interest across cell types and developmental stages.
zebrahub.sf.czbiohub.org/epigenomics

12/ We also made a massive update on our web portal to enable interactive exploration of the datasets, including our RNA+ATACseq cell-based 3D UMAPs. zebrahub.sf.czbiohub.org/epigenomics

11/ 🧪 … and again, a similar structure in human from the dataset of Argelaguet et al. BioRxiv 2022, quite strikingly similar to the one for zebrafish, actually! We are working on 'aligning' these structures and understanding their relationship.

10/ You might wonder if this mysterious continuous hierarchical organisation is a zebrafish or technological oddity specific to our model or experimental protocols. We checked, and we find a similar structure in a mouse dataset from Domcke et al. Science, 2022