# 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

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

## 2. Launch the React Desktop Client

```bash
# 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

```bash
# 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

- See the [Installation Guide](installation.md)
- Read the [User Guide](../user-guide/)
- Check [Reference Documentation](../reference/)