Introduction

What is EZStitcher?

EZStitcher is a Python library designed to simplify the processing and stitching of microscopy images. It provides a flexible pipeline architecture that allows researchers to easily process large microscopy datasets, create composite images, flatten Z-stacks, and stitch tiled images together.

Why EZStitcher?

Modern microscopy generates complex datasets with multiple channels, Z-stacks, and tiled images. While powerful stitching tools exist, they often require significant programming expertise or lack support for advanced workflows. EZStitcher bridges this gap by:

• Providing an intuitive interface for non-programmers

• Maintaining the flexibility needed by advanced users

• Automating common microscopy workflows

• Reducing processing errors through standardized pipelines

• Building on the robust Ashlar stitching engine

Key Features

• Basic Usage: Process and stitch images with minimal code using the EZ module

• Pipeline: Organize processing steps in a logical sequence

• Directory Structure: Protect original data while maintaining organized outputs

• Function Handling: Apply various processing functions in different patterns

• Microscope Formats: Work with data from different microscope types

• PipelineOrchestrator: Process multiple wells in parallel for faster results

For a detailed understanding of how these components work together, see Architecture Overview.

Supported Microscope Types

EZStitcher currently supports multiple microscope types, including ImageXpress and Opera Phenix. For detailed information about supported microscope types, including file formats, naming conventions, and directory structures, see Microscope Formats and Comparison of Microscope Formats.

Support for additional microscope types can be added by implementing the appropriate interfaces. See the Extending EZStitcher guide for details.

Next Steps

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

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

• Intermediate Usage - Create custom pipelines with steps

• Best Practices - Learn best practices for using EZStitcher