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Introduction
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What is EZStitcher?
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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?
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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
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* :doc:`../user_guide/basic_usage`: Process and stitch images with minimal code using the EZ module
* :doc:`../concepts/pipeline`: Organize processing steps in a logical sequence
* :doc:`../concepts/directory_structure`: Protect original data while maintaining organized outputs
* :doc:`../concepts/function_handling`: Apply various processing functions in different patterns
* :doc:`../appendices/microscope_formats`: Work with data from different microscope types
* :doc:`../concepts/pipeline_orchestrator`: Process multiple wells in parallel for faster results

For a detailed understanding of how these components work together, see :doc:`../concepts/architecture_overview`.

Supported Microscope Types
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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 :ref:`microscope-formats` and :ref:`microscope-comparison`.

Support for additional microscope types can be added by implementing the appropriate interfaces. See the :doc:`../development/extending` guide for details.

Next Steps
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* :doc:`../getting_started/getting_started` - Install EZStitcher and run your first pipeline
* :doc:`basic_usage` - Learn about the simplified interface for non-coders
* :doc:`intermediate_usage` - Create custom pipelines with steps
* :doc:`best_practices` - Learn best practices for using EZStitcher