Overview and Key Components

This section explains the core concepts of microscopy image stitching and how EZStitcher handles them.

• Basic Microscopy Concepts
  • Introduction to Microscopy Image Stitching
  • Key Microscopy Concepts
• Architecture Overview
  • Pipeline Architecture
  • Core Components
  • Key Component Relationships
  • Workflow Composition and Modularity
  • Typical Processing Flow
• PipelineOrchestrator
  • Role and Responsibilities
  • Creating an Orchestrator
  • Plate-Specific Services
  • Running Pipelines
  • Orchestrator-Pipeline Relationship
• Pipeline
  • Overview
  • Creating a Pipeline
  • Pipeline Parameters
  • Running a Pipeline
  • Pipeline Context
  • Multithreaded Processing
  • Directory Resolution
  • Saving and Loading Pipelines
  • Best Practices
  • Pipeline Factory Integration
• Pipeline Factory
  • Overview
  • Pipeline Structure
  • Parameters
  • Step Types
  • Examples
  • Factory Pipelines vs. Custom Pipelines
• Step
  • Overview
  • Creating a Basic Step
  • Step Parameters
  • Processing Arguments
  • Step Initialization Best Practices
  • Variable Components
  • Group By
  • Best Practices
• Function Handling
  • Function Patterns Overview
  • When to Use Each Pattern
  • The stack() Utility Function
  • Advanced Patterns
  • Best Practices
• ProcessingContext
  • Overview
  • Creating a Context
  • Accessing Context Attributes
  • Accessing the Orchestrator
• Directory Structure
  • Overview
  • Basic Directory Concepts
  • Default Directory Structure
  • Directory Resolution
  • Example Directory Flow
  • Step Initialization Best Practices
  • Custom Directory Structures
  • Customizing ImageStitchingStep Directories
  • When to Specify Directories Explicitly
  • Configuring Directory Suffixes
  • Best Practices