Welcome to OpenHCS Documentation

OpenHCS is a bioimage analysis platform for high-content screening datasets. It provides unified access to Python image processing libraries with automatic GPU acceleration and memory management for large-scale microscopy data analysis.

For Biologists

Want to get started with using OpenHCS without dealing with technical details? Check out OpenHCS for Biologists.

Overview

OpenHCS addresses the computational challenges of high-content screening by providing:

Unified interface to major Python image processing libraries (scikit-image, CuCIM, pyclesperanto)
Automatic GPU acceleration with seamless memory type conversion
Scalable processing for datasets ranging from single images to 100GB+ experiments
Microscope format compatibility supporting multiple vendor platforms

Quick Start

# Install OpenHCS with desktop GUI
pip install "openhcs[gui]"
openhcs-gui

# Or install with terminal interface (for remote/SSH use)
pip install "openhcs[tui]"
openhcs-tui

For complete installation and basic examples, see Introduction to OpenHCS.

Core Capabilities

Library Integration: Seamless access to scikit-image, CuCIM, and pyclesperanto through unified 3D array interface
GPU Acceleration: Automatic memory type conversion between NumPy, CuPy, PyTorch, and pyclesperanto arrays
Scalable Processing: Parallel execution across wells and sites with intelligent memory management
Format Compatibility: Support for multiple microscope platforms including ImageXpress and Opera Phenix
Storage Flexibility: Virtual file system with memory, disk, and compressed Zarr backends
Real-Time Visualization: Automatic napari streaming with materialization-aware filtering for monitoring pipeline progress
Analysis Functions: Specialized tools for cell counting, neurite tracing, and morphological analysis

Documentation Structure

New to OpenHCS? Follow this learning path:

Getting Started: Introduction to OpenHCS - Installation and basic examples
Core Concepts: Core Concepts - Understanding pipelines, steps, and data organization
Function Library: Function Library - Available processing functions and backends
User Guide: User Guide - Detailed usage patterns and workflows
Integration Guides: Integration Guides - System integration and advanced topics