User Guide

Under Construction

The user guide is currently being rewritten to reflect the latest OpenHCS architecture and workflows.

Note

Interface Options: OpenHCS provides both a PyQt6 desktop GUI (recommended for local use) and a Textual TUI (for remote/SSH environments). Most documentation applies to both interfaces.

For immediate help, use these resources:

• Complete OpenHCS Examples - Complete examples and code patterns

• API Reference - API reference with working examples

• Core Concepts - Core concepts and architecture

• Introduction to OpenHCS - Basic installation and setup

Available Guides:

• Creating Custom Functions - Creating custom processing functions in the GUI

• Custom Function Management - End-to-end custom function management flow

• Real-Time Visualization with Napari and Fiji - Real-time visualization with napari streaming

• Code/UI Bidirectional Editing - Bidirectional editing between TUI and Python code

• Automatic Dtype Conversion - Automatic data type conversion for GPU libraries

• CPU-Only Mode - CPU-only mode for CI testing and deployment

• Analysis Consolidation Guide - Automatic analysis result consolidation

• Experimental Layout Configuration - Excel-based experimental design and well-to-condition mapping

• Log Viewer - Advanced log viewing with async loading and server discovery

• LLM Pipeline Generation - LLM-assisted pipeline generation with Ollama

Environment Configuration:

• CPU-Only Mode - Configure OpenHCS for CPU-only environments

Experimental Design:

• Experimental Layout Configuration - Define complex experimental layouts with biological replicates

Data Management:

• Analysis Consolidation Guide - Consolidate multi-well analysis results

What’s Coming:

• Interface Workflow Guide - Complete tutorial for both GUI and TUI interfaces

• Script Generation Guide - How OpenHCS generates self-contained scripts

• Integration Patterns - Real-world usage examples and best practices

• Performance Optimization - GPU acceleration and large dataset handling

• Troubleshooting Guide - Common issues and debugging approaches

Current Status:

The existing user guide sections contain outdated references and examples. We’re rewriting them to match the current OpenHCS architecture and provide accurate, practical guidance.

Need Help Now?

1. Start with the example script - openhcs/debug/example_export.py

2. Check the API documentation - All examples are tested and working

3. Review the concepts - Core architecture explanations are accurate

4. Ask questions - The development team is responsive to user needs

Timeline:

• Phase 1: Complete example integration ✅ Done

• Phase 2: Interface workflow documentation 🚧 In Progress

• Phase 3: Practical integration examples 📋 Planned

• Phase 4: Performance and troubleshooting guides 📋 Planned