Getting Started

  • Installation
    • Prerequisites
    • Install with UV (Recommended)
    • Install with pip
    • Verify Installation
    • Development Dependencies
    • Docker (API Server)
      • Volume Mounts
      • GPU Support
    • Troubleshooting
      • Python Version
      • UV Installation
      • Web Frontend Dependencies
  • 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
      • 1. Load Microscopy File
      • 2. Configure Channels
      • 3. Set Output Folder
      • 4. Configure Parameters (Optional)
      • 5. Run Workflow
      • 6. Assign FOVs to Samples (for Multiple Samples)
      • 7. Merge Processing Results
    • Output Structure
    • Tips and Tricks
    • Common Issues
    • Next Steps
  • Visualization Tab
    • Prerequisites
    • Workflow Overview
    • Step-by-Step Guide
      • 1. Set Workspace (Landing Page)
      • 2. Select Position and Channel
      • 3. View Crops and Traces
    • Output Structure
    • Tips
    • Troubleshooting
    • Next Steps
  • Analysis Tab
    • Prerequisites
    • Workflow Overview
    • Step-by-Step Guide
      • 1. Analysis Setup
      • 2. Compare View
      • 3. Fit View
      • 4. Results View
    • Models
    • Data Flow
    • Tips
    • Troubleshooting
    • Next Steps
  • Merge Workflow
    • When to Use Merge
    • Overview
    • Step-by-Step Guide
      • 1. Assign FOVs to Samples
      • 2. Save Sample Configuration
      • 3. Configure Merge Settings
      • 4. Run Merge
      • 5. Verify Results
    • Advanced Usage
      • Using Inspected Data
      • Batch Processing Multiple Experiments
      • FOV Verification
    • YAML File Format
    • Best Practices
      • Sample Naming
      • FOV Assignment
      • File Organization
    • Troubleshooting
      • Common Errors
      • Recovery Strategies
    • Next Steps

Packages

  • pyama
    • Installation
      • Docker
    • Main Components
      • I/O Utilities (pyama.io)
      • Processing Pipeline (pyama.apps.processing)
      • Merge Processing (pyama.apps.processing.merge)
      • Analysis (pyama.apps.analysis)
      • Feature Extraction (pyama.apps.processing.extract)
    • API Server (pyama.api.server)
    • Key Data Structures
      • MicroscopyMetadata (pyama.types.microscopy)
      • ProcessingConfig (pyama.types.pipeline)
    • Extending pyama
      • Adding Custom Features
      • Adding Custom Models
    • API Reference (Key Functions)
    • Examples
    • Integration
  • PyAMA-ACDC
    • Purpose
    • Installation
    • Architecture
    • Usage in Cell-ACDC
      • Basic Integration
      • Advanced Integration
    • Workflow Integration
      • PyAMA Workflow Steps in Cell-ACDC Context
      • File Integration
    • Configuration
      • Cell-ACDC Plugin Registration
      • Integration Points
    • API Reference
      • Main Classes
      • Utility Functions
    • Migration Path
      • From Cell-ACDC to PyAMA
      • Hybrid Workflows
    • Examples
      • Basic Usage Example
      • Data Integration Example
    • Development
      • Building the Plugin
      • Testing Integration
      • Debug Mode
    • Troubleshooting
      • Common Issues
      • Debug Information
    • Best Practices
      • Data Organization
      • Workflow Integration
      • Performance
    • Future Enhancements
    • Resources

Reference

  • Workflow Pipeline Reference
    • Overview
    • Input Requirements
      • Microscopy Data
      • Channel Configuration
      • Processing Context
    • Workflow Steps
      • Step 1: CopyingService
        • Input
        • Processing Algorithm
        • Output Format
        • Implementation Notes
      • Step 2: SegmentationService
        • Input
        • LOG-STD Algorithm
        • Output
        • Algorithm Characteristics
      • Step 3: TrackingService
        • Input
        • IoU-based Hungarian Assignment Algorithm
        • Output
        • Implementation Details
      • Step 4: BackgroundEstimationService
        • Input
        • IoU-based Hungarian Assignment Algorithm
        • Output
        • Implementation Details
        • Tiled Interpolation Algorithm
        • Output
        • Algorithm Notes
      • Step 5: CroppingService
        • Input
        • Processing Algorithm
        • Output Format
        • Implementation Notes
      • Step 6: ExtractionService
        • Input
        • Feature Extraction Algorithm
        • Quality Filtering
        • Output Format
      • Step 7: CachingService
        • Input
        • Processing Algorithm
        • Output Format
        • Implementation Notes
    • Output Structure
    • Batch Processing Implementation
      • Thread Pool Executor Pattern
      • Memory Management
      • Cancellation Support
    • Data Type Specifications
      • Image Arrays (Zarr Format)
      • CSV Schemas
    • Algorithm Parameters
      • Segmentation Parameters
      • Tracking Parameters
      • Extraction Parameters
    • Performance Characteristics
      • Memory Usage
      • Processing Speed
      • Optimization Strategies
    • Extension Points
      • Custom Features
      • Alternative Algorithms
      • Integration Hooks
    • Implementation Guidelines
      • Plugin Development
      • Quality Assurance
  • API Reference
    • Server Endpoints
    • Base URLs
    • Authentication
    • MCP Integration
      • Connection
      • Available MCP Tools
        • load_microscopy
        • get_processing_config_schema
        • create_processing_task
        • list_tasks
        • get_task
        • cancel_task
      • MCP Client Configuration
      • Example MCP Workflow
    • REST API
    • General Response Format
      • Success Response
      • Error Response
    • Processing Endpoints
      • Load Microscopy Metadata
        • Request Body
        • Response
        • Example
      • Get Available Features
        • Response
      • Start Processing Workflow
        • Request Body
        • Response
        • Data Models
      • Get Workflow Status
        • Response
        • Status Values
      • Cancel Workflow
        • Response
      • Get Workflow Results
        • Response
      • Merge Processing Results
        • Request Body
        • Response
    • File Explorer Endpoints
      • List Directory Contents
        • Request Body
        • Response
      • Search Files
        • Request Body
        • Response
      • Get File Information
        • Request Body
        • Response
      • Get Recent Files
        • Query Parameters
        • Response
    • Analysis Endpoints
      • Get Available Models
        • Response
      • Load Trace Data
        • Request Body
        • Response
      • Start Fitting Analysis
        • Request Body
        • Response
      • Get Fitting Status
        • Response
      • Cancel Fitting
        • Response
      • Get Fitting Results
        • Response
    • System Endpoints
      • Health Check
        • Response
      • System Metrics
        • Response
      • Active Jobs List
        • Response
    • Error Codes
    • Usage Examples
      • Python Client Library
      • JavaScript/TypeScript Client
  • Plugin System
    • Overview
    • Plugin Directory Structure
    • Example Plugins
      • Available Examples
    • Feature Plugins
      • Creating a Phase Contrast Feature
      • Creating a Fluorescence Feature
    • Model Plugins
      • Creating a Custom Analysis Model
    • Installation Methods
      • Method 1: Manual Installation (Recommended)
      • Method 2: Batch Installation Script
    • Using Plugins
      • Feature Plugins
      • Model Plugins
    • Plugin Development Guidelines
      • General Practices
      • Feature Development
      • Model Development
    • Testing Plugins
      • Local Testing
      • Client UI Testing Workflow
      • Integration Testing
    • troubleshooting
      • Common Issues
      • Debugging Tips
    • Best Practices
      • Performance
      • Compatibility
      • Documentation
      • Distribution

Development

  • Contributing to PyAMA
    • Development Environment
      • Prerequisites
      • Setup
      • Recommended VS Code Extensions
    • Coding Guidelines
      • Style Guide
      • Type Hints
      • Import Organization
      • Docstring Format
      • Frontend State/Events (React)
    • Testing Guidelines
      • Test Structure
      • Visual Testing Rules
      • Running Tests
    • Documentation Guidelines
      • Code Documentation
      • README Files
      • Changes Documentation
    • Git Workflow
      • Branch Structure
      • Commit Messages
      • Development Workflow
      • Pull Request Process
    • Code Quality
      • Linting and Formatting
      • Pre-commit Hooks (Optional)
      • Code Review Focus Areas
    • Package-specific Guidelines
      • pyama
      • pyama-react
    • Performance Considerations
      • Memory Management
      • Threading
      • Vectorization
    • Release Process
      • Version Management
      • Release Checklist
      • Publishing
    • Getting Help
      • Resources
      • Asking Good Questions
    • Recognition
  • Testing Protocol
    • Overview
    • Test Organization
    • Running Tests
      • All Tests
      • Specific Categories
    • Visual Testing Guidelines
      • Plot Generation
      • Test Requirements
    • PyAMA-React Client Testing Protocol
      • Manual Testing Checklist
    • Integration Testing
      • Workflow Integration
      • API Integration
    • Performance Testing
      • Memory Usage
      • Processing Speed
    • Data Validation
      • Synthetic Data Generation
      • CSV Validation
    • Continuous Integration
      • GitHub Actions Workflow
      • Test Categories in CI
    • Test Data Management
      • Synthetic Test Data
      • Real Test Data
      • Test Artifacts
    • Debugging Tests
      • Debug Mode
      • Test Output
      • Common Issues
    • Contributing to Tests
    • Test Metrics and Targets
      • Coverage Targets
      • Performance Targets
      • Quality Targets

Publications

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