.gitignore
.readthedocs.yml
README.md
my_use.py
pytest.ini
requirements.txt
setup.py
docs/requirements.txt
docs/source/conf.py
docs/source/index.rst
docs/source/api/config.rst
docs/source/api/file_system_manager.rst
docs/source/api/focus_analyzer.rst
docs/source/api/image_locator.rst
docs/source/api/image_processing.rst
docs/source/api/image_processing_operations.rst
docs/source/api/image_processor.rst
docs/source/api/index.rst
docs/source/api/microscope_interfaces.rst
docs/source/api/microscopes.rst
docs/source/api/pipeline.rst
docs/source/api/pipeline_orchestrator.rst
docs/source/api/steps.rst
docs/source/api/stitcher.rst
docs/source/appendices/file_formats.rst
docs/source/appendices/glossary.rst
docs/source/appendices/index.rst
docs/source/appendices/microscope_formats.rst
docs/source/concepts/architecture_overview.rst
docs/source/concepts/basic_microscopy.rst
docs/source/concepts/directory_structure.rst
docs/source/concepts/function_handling.rst
docs/source/concepts/index.rst
docs/source/concepts/pipeline.rst
docs/source/concepts/pipeline_orchestrator.rst
docs/source/concepts/processing_context.rst
docs/source/concepts/specialized_steps.rst
docs/source/concepts/step.rst
docs/source/development/architecture.rst
docs/source/development/contributing.rst
docs/source/development/extending.rst
docs/source/development/index.rst
docs/source/development/testing.rst
docs/source/getting_started/installation.rst
docs/source/user_guide/advanced_usage.rst
docs/source/user_guide/basic_usage.rst
docs/source/user_guide/best_practices.rst
docs/source/user_guide/index.rst
docs/source/user_guide/integration.rst
docs/source/user_guide/intermediate_usage.rst
docs/source/user_guide/introduction.rst
ezstitcher/__init__.py
ezstitcher/__main__.py
ezstitcher.egg-info/PKG-INFO
ezstitcher.egg-info/SOURCES.txt
ezstitcher.egg-info/dependency_links.txt
ezstitcher.egg-info/requires.txt
ezstitcher.egg-info/top_level.txt
ezstitcher/core/__init__.py
ezstitcher/core/config.py
ezstitcher/core/file_system_manager.py
ezstitcher/core/focus_analyzer.py
ezstitcher/core/image_locator.py
ezstitcher/core/image_processor.py
ezstitcher/core/main.py
ezstitcher/core/microscope_interfaces.py
ezstitcher/core/opera_phenix_xml_parser.py
ezstitcher/core/pipeline.py
ezstitcher/core/pipeline_orchestrator.py
ezstitcher/core/steps.py
ezstitcher/core/stitcher.py
ezstitcher/core/utils.py
ezstitcher/microscopes/__init__.py
ezstitcher/microscopes/imagexpress.py
ezstitcher/microscopes/opera_phenix.py
ezstitcher/tests/__init__.py
ezstitcher/tests/generators/__init__.py
ezstitcher/tests/generators/generate_synthetic_data.py
tests/README.md
tests/conftest.py
tests/test_function_tuples.py
tests/test_opera_phenix_field_remapping.py
tests/integration/__init__.py
tests/integration/test_pipeline_orchestrator.py
tests/unit/test_pipeline.py
tests/unit/test_prepare_patterns_and_functions.py
tests/unit/test_step_processing_args.py