# PyAMA Documentation

PyAMA is a modular Python application for microscopy image analysis. It consists of:

- **pyama**: Core processing library (CLI and FastAPI server) with orchestrated pipelines, analysis, and visualization endpoints
- **pyama-react**: React + Electron desktop client (TanStack Router, React Query) with Processing, Visualization, Analysis, and Chat
- Command-line tools for config generation, pipeline execution, merge, and analysis plots

```{toctree}
:caption: Getting Started
:maxdepth: 2

getting-started/installation.md
getting-started/quickstart.md
```

```{toctree}
:caption: User Guide
:maxdepth: 2

user-guide/processing-tab.md
user-guide/visualization-tab.md
user-guide/analysis-tab.md
user-guide/merge-workflow.md
```

```{toctree}
:caption: Packages
:maxdepth: 1

packages/pyama.md
packages/pyama-acdc.md
```

```{toctree}
:caption: Reference
:maxdepth: 1

reference/workflow-pipeline.md
reference/api-reference.md
reference/plugins.md
```

```{toctree}
:caption: Development
:maxdepth: 1

development/contributing.md
development/testing-protocol.md
```

```{toctree}
:caption: Publications
:maxdepth: 1

publications/dpg2026/abstract.md
publications/dpg2026/poster.md
```