├── .gitignore ├── CITATION.cff ├── LICENSE ├── MANIFEST.in ├── README.md ├── config_examples ├── config_1.yaml ├── config_2.yaml ├── config_3.yaml └── config_with_all_info.yaml ├── environment.yaml ├── microaligner ├── __init__.py ├── __main__.py ├── feature_reg │ ├── __init__.py │ ├── feature_detection.py │ ├── feature_registrator.py │ └── tile_registration.py ├── optflow_reg │ ├── __init__.py │ ├── flow_calc.py │ ├── optflow_registrator.py │ └── warper.py ├── pipeline_modules │ ├── __init__.py │ ├── config_reader.py │ ├── metadata_handling.py │ ├── ome_meta_processing.py │ └── stack_builder.py └── shared_modules │ ├── __init__.py │ ├── dtype_aliases.py │ ├── img_checks.py │ ├── similarity_scoring.py │ ├── slicer.py │ ├── stitcher.py │ └── utils.py └── setup.py /.gitignore: -------------------------------------------------------------------------------- 1 | __pycache__ 2 | .idea 3 | microaligner.egg-info 4 | dist 5 | build 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