CellPilot

output.mp4

CellPilot is a serverless, AI-powered desktop application for chat-based single-cell and spatial transcriptomics analysis. It runs entirely on your local machine. No server or data upload required.

Supported data types: scRNA-seq · scATAC-seq · Multiome · Spatial (Visium, Visium HD, Xenium, MERFISH, CosMx)

AI backends: Local models via WebLLM or Ollama · OpenAI · Anthropic Claude · Google Gemini · Groq · OpenRouter

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For non-developers

Download the pre-built desktop app at cellpilot.humphreyslab.com

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agent_select_region.mp4

For developers

Requirements

• Node.js 18+ and npm
• (macOS only, for packaging) Xcode Command Line Tools

Install

npm install

Run in development mode

npm run electron-dev

This starts the React dev server and Electron together. Hot-reload is enabled for the frontend.

Run production build locally

npm run build
npm run electron

agent.mp4

Package as a desktop app

macOS (Apple Silicon):

npm run dist:mac-arm

macOS (Intel):

npm run dist:mac-intel

Windows:

npm run electron-pack-win

Linux:

npm run electron-pack-linux

Output goes to dist/. macOS builds require an Apple Developer certificate and notarization credentials — set APPLE_KEYCHAIN_PROFILE and fill in the identity field in package.json before building.

Tech stack

• Frontend: React 18, Deck.gl, OpenSeadragon
• Desktop shell: Electron
• Analysis engine: WebAssembly (scran.js, bakana, custom WASM modules)
• AI: WebLLM (in-browser local LLMs), Ollama (local server), or any OpenAI-compatible API

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