Welcome to EZStitcher’s Documentation

EZStitcher is a Python package for stitching microscopy images with support for Z-stacks, multi-channel fluorescence, and advanced focus detection.

Getting Started Quickly

The fastest way to get started with EZStitcher is to use stitch_plate:

from ezstitcher import stitch_plate

# Stitch a plate with a single function call
stitch_plate("path/to/microscopy/data")

For a complete guide including installation and examples, see Getting Started with EZStitcher.

Key Features

• Simplified Interface for Non-Coders: Process and stitch images with minimal code using stitch_plate

• Multi-channel fluorescence support: Process and stitch multiple fluorescence channels

• Z-stack handling: Process 3D image stacks with various projection methods

• Advanced focus detection: Find the best focused plane in Z-stacks

• Flexible preprocessing: Apply custom preprocessing to images

• Multiple microscope support: Works with ImageXpress and Opera Phenix microscopes

• Automatic detection: Automatically detect microscope type and image organization

• Object-oriented API: Clean, modular design for easy customization

Key Resources

• Getting Started with EZStitcher - Install EZStitcher and run your first pipeline in minutes

• Basic Usage - Learn about the simplified interface for non-coders

• Architecture Overview - Learn about EZStitcher’s architecture

• Intermediate Usage - Create custom pipelines with steps

• Best Practices - Learn best practices for using EZStitcher

Getting Started

• Getting Started with EZStitcher
  • Installation
  • Quick Start
  • Common Options
  • Next Steps

User Guide

• Introduction
  • What is EZStitcher?
  • Why EZStitcher?
  • Key Features
  • Supported Microscope Types
  • Next Steps
• Basic Usage
  • Three-Tier Approach
  • Getting Started with EZStitcher
  • Key Parameters
  • Z-Stack Processing
  • More Control
  • Troubleshooting
  • Understanding Key Concepts
  • When You Need More Control
• Intermediate Usage
  • Understanding the EZ Module Under the Hood
  • Reimplementing EZ Module Functionality
  • Simple Examples of Custom Pipelines
  • When to Move to Advanced Usage
• Advanced Usage
  • Understanding Pre-defined Steps
  • 1. Creating custom processing functions
  • 2. Building an advanced custom pipeline
  • 3. Channel‑aware processing with group_by='channel'
  • 4. Conditional processing based on context
  • 5. Multithreading for large plates
  • 6. Adding a new microscope handler
• Best Practices
  • EZ Module in one minute
  • Pipeline Best Practices
  • Directory Management Best Practices
  • Step Configuration and Usage Best Practices
  • Function Handling Best Practices
  • Custom Pipeline Best Practices
  • Need more depth?
• Integrating EZStitcher with Other Tools
  • 1. BaSiCPy + N2V2 denoising
  • 2. ROI extraction via template matching (Multi-Template-Matching)
  • Navigation

Core Concepts

• 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

API Reference

• API Reference
  • Core Components
  • Interfaces and Configuration
  • Microscope Implementations

Development

• Development
  • Architecture Overview
  • Extending EZStitcher
  • Testing
  • Contributing

Appendices

• Appendices
  • Glossary
  • File Formats
  • Microscope Formats

Indices and tables

• Index

• Module Index

• Search Page