Quick Start

This guide gets you started with PyAMA using the React + Electron client and the pyama API server.

1. Start the PyAMA API Server

# From the repository root
uv run pyama serve
# Default port: 8765. Use --dev for fake tasks and reload.

2. Launch the React Desktop Client

# In a second terminal
cd pyama-react
bun install
bun run dev

The Electron app opens and connects to the local API (http://localhost:8765). Set PYAMA_API_URL to override.

3. Create and Run a Processing Task

  1. Open the Processing page

  2. Select your microscopy input file (ND2/CZI)

  3. Configure channels and features (PC: area, aspect_ratio; FL: intensity_total)

  4. Select an output directory

  5. Start the task and monitor progress in the task list

4. Review Outputs

Typical outputs in the output directory:

  • raw.zarr – raw frames + segmentation/tracking/background arrays

  • crops.zarr – per-cell crop tensors

  • traces/position_{id}.csv – per-position traces

5. Optional CLI Workflow

# Generate config and run pipeline
uv run pyama processing config --input data.nd2 --output config.yaml
uv run pyama processing execute --input data.nd2 --config config.yaml --output ./out

# Merge traces and generate plots
uv run pyama processing merge --input ./out/traces --samples samples.yaml --output ./out
uv run pyama analysis plot --input ./out/traces_merged --output ./out/plots

Next Steps