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!

U-Probe: universal agentic probe design for imaging-based spatial-omics biorxiv.org/content/10.64898… #biorxiv_bioinfo

U-Probe is a great example of what agentic systems can enable in biology. Built on PantheonOS, it turns probe design — traditionally expert-driven and protocol-specific — into a programmable, agent-assisted workflow. Excited to see this direction emerging. 🧬

Introducing U-Probe — the first agent-assisted platform for FISH probe design. 🧬 Probe design today is still fragmented and expert-heavy: different tools for different protocols, manual parameter tuning, and limited support for new probe designs. U-Probe addresses this by: • Supporting diverse protocols (MERFISH, seqFISH, DNA-FISH, etc.) • Enabling custom probe architectures via a programmable framework • Using AI agents to assist with panel design and parameter selection ⚙️ Built on the @PantheonOS evolvable multi-agent framework → from experimental goal to synthesis-ready probes

PantheonOS will serve as the agent interface layer in this effort, helping connect agents with predictive model and multimodal embryogenesis data. Excited to be part of the digital twin of embryogenesis and advancing the future of developmental biology and human health! 🚀🧬

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.

PantheonOS v0.5.1 is out. Highlights: • PantheonClaw gateway integration • Free OAuth via Codex CLI & Gemini CLI • LiteLLM removed → native SDK adapters • Intelligent context optimization autocompact Release notes: pantheonos.stanford.edu/blog… #AI #Agents #OpenSource

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.

From raw data → biological insight → organized reports in minutes. Fully open-source. Fully local! 🎇

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.

PantheonOS: An Evolvable Multi-Agent Framework for Automatic Genomics Discovery biorxiv.org/content/10.64898…

I believe this is an important update, and I hope to build Pantheon-Store into a vibrant Biomedical AI community!🔥

Come and try Pantheon-Store! Aiming to build an Agent community for the biomedical field! 💫💫💫 app.pantheonos.stanford.edu/…

It's really cool! Please check our manuscript! 😎

We are thrilled to share our preprint (tinyurl.com/3mtbtcwu) on PantheonOS, the first evolvable, privacy-preserving multi-agent operating system for automatic genomics discovery. 📄 Preprint: tinyurl.com/3mtbtcwu 🤖 Open-source App (free to all users): app.pantheonos.stanford.edu 🌐 More: pantheonos.stanford.edu PantheonOS unites LLM-powered agents, reinforcement learning, and agentic code evolution to push beyond routine analysis — evolving state-of-the-art algorithms to super-human performance. 🧬 Evolved batch correction (Harmony, Scanorama, BBKNN) and Reinforcement learning or RL agumented algorithms 🧠 RL–augmented gene panel design 🧭 Intelligent routing across 22 virtual cell foundation models 🧫 Autonomous discovery from newly generated 3D early mouse embryo data 🫀 Integrated human fetal heart multi-omics with 3D whole-heart spatial data From uncovering asymmetric Cer1–Nodal inhibition in early mouse embryos to mapping spatial disease programs in the human heart, PantheonOS demonstrates a future where AI agents don’t just analyze biology — they drive discovery. This is a step toward self-evolving AI systems that accelerate science itself and push human civilization toward the singularity. This work is built over 2 years by an incredible team (Weize @Nanguage who led this project, and also to Erwin, Zhongquan @BAKEZQ, Chris @chriswzou , Zehua @starlitnightly, Yifan @YifanLu2024 , Xuehai, Zhongquan, and Miao, Cinlong's wetlab support and the entire Qiu lab. We are grateful for all our funders and industrial collaborators: @Lenovo @vizgen_inc We are excited to scale this work further and welcome philanthropic, industrial, and venture support. We invite the community (pantheonos.stanford.edu/ecos…) to contribute, extend, and collectively reimagine the future of automated biological discovery. 🌐 More details below:

The first truly expert-level solution. Surpassing all existing automatic annotation methods. ✔️ Detecting and validating marker genes ✔️ Interpreting clusters through chat ✔️ Finalizing cell type with supporting evidence youtube.com/watch?v=Ox4xePjc…

🚀 Introducing PantheonOS (pantheonOS.stanford.edu): A Fully Open-Source Agent OS for Science PantheonOS began as a research project in my Stanford lab and has since evolved into a vision to redefine data science in the era of AI—starting with computational biology, especially single-cell and spatial genomics. PantheonOS is a general agent platform built from the ground up. It is arguably the first distributed agent framework designed for scientific data analysis. 🔑 Key Features 1. Multi-Agent Collaboration – Built-in paradigms for distributed, cross-machine cooperation among agents and toolsets. 2. Native Toolset Support – Python, R, Julia, LaTeX, and more—designed for real scientific workflows. 3. Modular & Extensible – Developer-friendly design with shallow wrappers, plus LLM-driven toolset generation. 4. Evolvable Agents – Capable of evolving large-scale code projects to achieve superhuman performance (e.g., evolving upon the original Harmony [I Korsunsky, 2019, Nature Biotechnology] and Scanorama [BL Hie, 2019, Nature Biotechnology] implementations), and even evolving the system itself to adapt to new fields. 🎉 Stepwise Release Strategy We’re releasing PantheonOS in stages: Pantheon-CLI (today!), followed by Pantheon-Lab, Pantheon-Notebook, Pantheon-Slack, and more. 🌟 Pantheon-CLI Highlights - We're not just building another CLI tool. We're defining how scientists will interact with data in the AI era. - Open, Powerful, Python-First – The first fully open-source, endlessly extendable scientific “vibe analysis” framework. - Mixed Programming Magic – Combine Python, natural language, R, or Julia—seamlessly in the same environment. - PhD-Level Assistant – A command-line agent for complex real-world genomics and beyond, handling workflows at the PhD level. - Privacy by Design – Run entirely offline with local LLMs—your data never leaves your computer. ✅ Proven Applications (10 Demonstrations) Computational biology: 1. ATAC-seq: From raw reads to peak matrix 2. RNA-seq: From raw reads to expression matrix 3. Complex single-cell workflows (PhD-level) 4. Hybrid natural language R for Seurat annotation 5. Learning from web tutorials invoking single-cell foundation models 6. Cell segmentation on 10x Genomics HD Visium data And beyond: 7. Mixed Python & R programming examples 8. Molecular docking & structural analysis 9. Exploratory factor analysis for behavioral survey data 10. Customer segmentation & finance analytics 🌐 Learn More & Get Started Website: pantheonOS.stanford.edu Pantheon-CLI Documentation: pantheon-cli-docs.netlify.ap… GitHub Repo: github.com/aristoteleo/panth… 💬 Join our community: PantheonOS Slack: pantheonos.slack.com/ssb/red… PantheonOS Discord: discord.com/invite/74yzAGYW