Core Concepts

This section provides a comprehensive overview of OpenHCS’s core concepts and architecture. These pages serve as a context primer for both scientists with domain knowledge and developers with CS backgrounds, focusing on building intuition about why OpenHCS exists and what it enables.

Getting Started: If you’re new to OpenHCS, we recommend reading these pages in order. Each concept builds on the previous ones to give you a complete understanding of the system.

Target Audience: These pages are designed for both non-CS scientists needing to understand OpenHCS fundamentals and developers without domain knowledge who need scientific context.

Understanding the Domain

Start here to understand the scientific problems that OpenHCS solves.

• Domain Fundamentals
  • The High-Content Screening Challenge
  • Microscope Format Chaos
  • Computational Bottlenecks
  • Reproducibility and Collaboration Challenges
  • Why Traditional Tools Fall Short
  • The OpenHCS Solution Approach

Core Building Blocks

The fundamental concepts that define how OpenHCS works.

• Pipelines and Steps
• Function Patterns
• Data Dimensions
• Component System

Processing System

Understanding what functions are available and how data is stored.

• Function Library
• Storage System
• DtypeConfig System

Practical Guidance

Mental models and patterns for effective usage.

• Building Intuition

Additional Reference

Additional documentation for advanced users and developers.

• Module Structure
  • Overview
  • Basic Module Concepts
  • OpenHCS Module Structure
  • Key Modules and Their Purpose
  • Initialization Discipline
  • Public API
  • Doctrinal Compliance
  • Best Practices