We are thrilled to announce the inaugural Stanford Virtual Embryo Challenge at NeurIPS 2026 @StanfordAILab @NeurIPSConf , in collaboration with Laude Institute @LaudeInstitute , UCSD, and Harvard! Join us in building AI models that predict how life takes shape, across space, scale, time, and perturbation: virtualembryo.ai/challenge. We welcome participants from academia and industry, independent researchers, and even AI agent scientists!!! Our vision is inspired by and complementary to the virtual-cell efforts championed by @arcinstitute . But life is more than a collection of individual cells. Why Virtual Embryos? See below 🧵👇

Introducing Pantheon Fleet, building on PantheonOS, a distributed, open-source drop-in for Claude Science + GPT Rosalind. Claude Science @claudeai GPT Rosalind @OpenAI made AI research accessible. But your data, compute, and workflows still live on someone else's platform. Today we're launching Pantheon Fleet: one command to orchestrate every resource you own—laptop, HPC cluster, cloud GPUs, private infrastructure—privacy preserved by default. But there are more: Pantheon-Store: 2,300+ skills, agents, and scientific teams. Pantheon auto-picks the right ones for every task. Pantheon-Evolve: improves ML algorithms on its own—already beating human baselines on single-cell batch correction. Real discoveries: asymmetric gene-expression gradients in mouse embryos, congenital disease genes in the human heart. Full stack: Web, Desktop, CLI, Jupyter, Pantheon Claw. Your data. Your compute. Your models. Your science.

Introducing PantheonOS Live View PantheonOS agents can now open popular interactive scientific viewers, including 3D Spatial Viewer with WebGL, Viv (spatial imaging), Vitessce (single cell & spatial omics), IGV (genomics browser), and Mol* (3D molecular structures), directly on your data, explore data interactively with your agent, and generate publication-grade figures, all live in your browser. This transforms the agent experience from static reports into an interactive, visual workflow where you can inspect data, explore results, and follow analyses as they happen. Alongside Live View, the PantheonOS online platform has received a major upgrade, delivering substantially improved stability and reliability for long-horizon analyses, together with more than 4× faster execution speeds than previous releases.

PantheonOS allows any biologist to perform complex data analyses of emerging single cell, multi-omics and spatial transcriptomics datasets end to end through AI agent and human collaboration. We are releasing six replays of use cases trajectories. Each "trajectory" is a complete end-to-end run, from prompt to analysis, to figures, and finally to report, and in fully inspectable and reproducible manner. See the six user cases in our PantheonOS Gallery: 1. 3D mouse embryo analysis: Tangram deconvolution and PyVista-based 3D visualization of E6 mouse embryo spatial transcriptomics data 2. 3D human fetal heart analysis: Spatial mapping of heart disease gene patterns using MERFISH data 3. Multi-omics spatial integration: Single cell multi-omics-to-spatial mapping with MOSCOT optimal transport 4. Gene panel design: 1000-plex immune-oncology MERFISH gene panel optimization 5. Cell segmentation benchmarking: Comparative evaluation of Cellpose-SAM, InstanSeg, StarDist, and other tools 6. Spatial disease biology: Ligand–receptor analysis of disease-associated tissue microenvironments We would love to hear how you can use PantheonOS for your research! Got an interesting agent run of your own and want to share? In the Pantheon UI, click Export Bundle (top-right of any chat) to package the full trajectory — chat history, code, figures, report — then submit it here:

PantheonOS Now Tackles Gene Panel Design Gene panel selection represents a critical bottleneck in spatial and single-cell genomics, where suboptimal choices compromise cell-type resolution and experimental validity. Pantheon automates this end-to-end via multi-agent workflow orchestration. A leader agent orchestrates the full pipeline, delegating to specialized analyzers that dynamically route tools and benchmark strategies in real time — enabling long-horizon, autonomous discovery. What can Pantheon do? 🧬 Multi-strategy gene selection — orchestrating parallel selection strategies to synthesize a single optimized panel. 📊 Clustering-aware optimization and biological grounding — directly maximizing ARI/NMI metrics while grounding decisions in domain knowledge, for panels that are both statistically and biologically meaningful. 📄 Self-documenting, reproducible runs — generating live notebooks, agent traces, and automated PDF reports with zero manual intervention. Unless you want to interact with it! Benchmarked on pan-cancer immuno-oncology with @Vizgen, PantheonOS achieves superior overlap with expert-curated panels while outperforming classical baselines on clustering metrics. Built on PantheonOS — the first evolvable, multi-agent operating system for biological discovery. Genomics is the beginning; the architecture goes beyond, and PantheonOS is fine-tunable for domain-specific scientific research. 📄 Preprint: biorxiv.org/content/10.64898… 🌐 Website: pantheonos.stanford.edu Thank you to Erwin and @Nanguage for this incredible opportunity, and to @JiangHe_PhD , Lorenz Rongioni and the entire Vizgen @vizgen_inc team for the amazing collaboration. More to come soon!

Big news: Our Virtual Embryo project has been selected as a Laude Institute Moonshots Seed Grant winner — chosen from 125 proposals evaluated by 600+ leading researchers. I’m deeply honored to be recognized alongside a remarkable community that includes Fields Medalists like Terence Tao, Nobel laureates like Michael Kremer, Turing Award winners like Raj Reddy, and creators of transformative tools such as Jupyter Notebook. We are now building (1) the largest time-resolved organism-level 3D perturbation atlas of mouse embryogenesis; (2) what could become the first digital twin of mammalian embryogenesis — a predictive model of development designed to uncover the mechanisms of congenital disease and ultimately help ensure that every newborn has the healthiest possible start in life. If this vision excites you, come build with us — alongside Emily Fox, James Zou (@james_y_zou), and Marinka Zitnik (@marinkazitnik). Thank you to @LaudeInstitute for believing in this vision. We also welcome industrial and philanthropic partners who want to help shape the future of developmental biology and human health.

We're excited to release Pantheon-Claw: a multi-channel IM gateway that brings PantheonOS's agentic AI capabilities to the messaging apps you use every day. Supported Channels (7): Telegram · Discord · Slack · WeChat · Feishu · QQ · iMessage What can you do? 📱 Chat from your phone: Send tasks to your AI agent while on the go. Ask it to download data, run analyses, generate plots — all from a text message. 🖼️ Rich media support: Send files and images to the agent, receive generated plots and reports back. 👥 Group collaboration: Mention @PantheonClaw in Slack or Discord. The agent identifies speakers and maintains shared context across the team. 🔧 Easy setup: Built-in step-by-step configuration guides for each platform. Collapsible instructions cover bot creation, permissions, and token setup — no extra docs needed. Built on PantheonOS, our fully open-source agentic platform for computational biology and beyond.

Introducing PantheonOS-Desktop — the easiest way to accelerate biomedical discovery via local AI agent platform. No pip. No conda. No CLI. Just install → open → load data → start analyzing → gain biological insights → export notebooks, reports and more! But this isn’t just about simplicity, PantheonOS: 🔐 Privacy-first — your data never leaves your machine ⚡ Zero environment setup — no dependency headaches 🧠 Built-in Agents + 1300+ bio-AI skills out of the box 🧪 Designed for automatic, interactive, and evolvable data science discoveries From raw data → biological insight → organized reports in minutes. Fully open-source. Fully local.