Calcium imaging analysis tools
CaLab is a suite of browser-based tools for calcium imaging analysis. The tools run entirely in the browser — no installation, no server, no data upload. Load your fluorescence traces, tune deconvolution parameters with real-time visual feedback, and export the results.
The flagship app, CaTune, lets you interactively adjust deconvolution parameters (rise time, decay time, sparsity) while watching the solver update in real time. The deconvolution engine is a FISTA solver written in Rust and compiled to WebAssembly, running in Web Workers for parallel multi-cell processing.
A companion Python package (calab) provides the same deconvolution algorithm in Python, with data exchange utilities for round-tripping parameters between the browser tools and analysis scripts. An optional community sharing feature (powered by Supabase) lets users share and browse deconvolution parameters across datasets and indicators.
- Open CaTune in your browser
- Try the built-in demo data to explore the interface
- Drag and drop your own
.npyor.npzfile containing calcium traces - Adjust parameters with the sliders and observe real-time deconvolution
- Export your tuned parameters as JSON for use in analysis pipelines
pip install calabThe calab Python package is the Python entrypoint to CaLab. It runs the same FISTA deconvolution algorithm in Python, and provides utilities for exchanging data with the web apps — load CaTune export JSON files, prepare traces for the browser tool, and run batch deconvolution with tuned parameters.
Note: The Python package is under active development — major updates are planned.
See python/README.md for full API documentation.
| App | Description | Status |
|---|---|---|
| CaTune | Interactive calcium deconvolution parameter tuning | Stable |
.
├── apps/
│ ├── catune/ # SolidJS SPA — deconvolution parameter tuning
│ └── carank/ # SolidJS SPA — trace quality ranking
├── packages/
│ ├── core/ # @calab/core — shared types, pure math, WASM adapter
│ ├── compute/ # @calab/compute — worker pool, warm-start cache
│ ├── io/ # @calab/io — file parsers, validation, export
│ ├── community/ # @calab/community — Supabase DAL, submission logic
│ ├── tutorials/ # @calab/tutorials — tutorial types, progress persistence
│ └── ui/ # @calab/ui — shared layout components
├── crates/
│ └── solver/ # Rust FISTA solver crate (compiled to WASM + PyO3)
├── python/ # Python companion package
├── docs/ # Documentation
├── scripts/ # Build and deploy scripts
└── supabase/ # Supabase config
| Package | Description |
|---|---|
@calab/core |
Shared types, pure utilities, domain math, WASM adapter |
@calab/compute |
Generic worker pool, warm-start caching, kernel math, downsampling |
@calab/io |
File parsers (.npy/.npz), data validation, cell ranking, JSON export |
@calab/community |
Supabase data access layer for community parameter sharing |
@calab/tutorials |
Tutorial type definitions, progress persistence (localStorage) |
@calab/ui |
Shared SolidJS layout components (DashboardShell, panels, cards) |
- Node.js 22 (LTS) — use
.nvmrc:nvm use - Rust stable + wasm-pack — only needed if modifying the solver
- Python >= 3.10 — only needed for the Python package
git clone https://github.com/miniscope/CaLab.git
cd CaLab
nvm use
npm install
npm run dev| Script | Description |
|---|---|
npm run dev |
Start CaTune dev server |
npm run build |
Build WASM + all apps |
npm run build:pages |
Build + combine dist for GitHub Pages |
npm run build:wasm |
Compile Rust solver to WASM |
npm run test |
Run Vitest tests across all workspaces |
npm run lint |
Run ESLint |
npm run typecheck |
Run TypeScript type checking |
npm run format |
Format all files with Prettier |
See docs/CONTRIBUTING.md for the full development guide.
- Architecture — module layout, dependency DAG, state management, boundaries
- Contributing — setup, scripts, code style, CI
- Changelog — release history
- New App Guide — adding a new app to the monorepo
- CaTune — CaTune app documentation
- WASM Solver — Rust FISTA solver documentation
- Python Package — Python companion package
- Frontend: SolidJS + TypeScript + Vite
- Solver: Rust + wasm-pack (WebAssembly)
- Charts: uPlot
- Community: Supabase (optional)
- Styling: Pure CSS with custom properties
The monorepo uses a single v* tag for all web apps and packages (e.g., v2.0.4). The Python package has a separate py/v* tag series. See the Changelog for release history.
MIT — Copyright (c) 2025 Daniel Aharoni
Contributions are welcome! See docs/CONTRIBUTING.md for setup instructions, code style guidelines, and the CI pipeline. Bug reports and feature requests can be filed via GitHub Issues.