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

Getting Started

• Installation
  • Prerequisites
  • Install with UV (Recommended)
  • Install with pip
  • Verify Installation
  • Development Dependencies
  • Docker (API Server)
  • Troubleshooting
• Quick Start
  • 1. Start the PyAMA API Server
  • 2. Launch the React Desktop Client
  • 3. Create and Run a Processing Task
  • 4. Review Outputs
  • 5. Optional CLI Workflow
  • Next Steps

User Guide

• Processing Tab
  • Workflow Overview
  • Step-by-Step Guide
  • Output Structure
  • Tips and Tricks
  • Common Issues
  • Next Steps
• Visualization Tab
  • Prerequisites
  • Workflow Overview
  • Step-by-Step Guide
  • Output Structure
  • Tips
  • Troubleshooting
  • Next Steps
• Analysis Tab
  • Prerequisites
  • Workflow Overview
  • Step-by-Step Guide
  • Models
  • Data Flow
  • Tips
  • Troubleshooting
  • Next Steps
• Merge Workflow
  • When to Use Merge
  • Overview
  • Step-by-Step Guide
  • Advanced Usage
  • YAML File Format
  • Best Practices
  • Troubleshooting
  • Next Steps

Packages

• pyama
• PyAMA-ACDC

Reference

• Workflow Pipeline Reference
• API Reference
• Plugin System

Development

• Contributing to PyAMA
• Testing Protocol

Publications

• Abstract: Quantifying Live Single-Cell Array Benefits with the PyAMA Refresh (DPG 2026)
• PyAMA Live Single-Cell Array Imaging Refresh (DPG 2026 Poster)