├── .github └── workflows │ ├── docs_build_and_deploy.yml │ └── test_and_deploy.yml ├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── MANIFEST.in ├── README.md ├── brainglobe_template_builder ├── __init__.py ├── io.py ├── napari │ ├── __init__.py │ ├── _reader.py │ ├── _widget.py │ ├── align_widget.py │ ├── mask_widget.py │ ├── napari.yaml │ ├── reorient_widget.py │ └── save_widget.py ├── plots.py ├── postproc │ └── annotation_filter.py ├── preproc │ ├── __init__.py │ ├── alignment.py │ ├── brightness.py │ ├── cropping.py │ ├── masking.py │ ├── preproc_config.py │ ├── preprocess.py │ ├── splitting.py │ ├── standardise.py │ ├── transform_utils.py │ └── wingdisc_utils.py └── validate.py ├── cruft.json ├── data ├── SWC_BlackCap_use-for-template.csv └── SWC_brain-list_for-atlases_2024-04-15.csv ├── docs ├── Makefile ├── make.bat ├── requirements.txt └── source │ ├── conf.py │ └── index.rst ├── environment.yaml ├── examples ├── blackcap │ ├── 1_source_images.py │ ├── 2_prep_lowres.py │ ├── 3_prep_highres.py │ ├── 4_build_template.sh │ ├── 5_post_build.py │ └── 6_post_annotation.py ├── drosophila │ └── preprocessing_wing-disc.py ├── molerat │ ├── 1_downsample_source_images.py │ ├── 2_molerat_prep_lowres.py │ ├── 3_molerat_prep_highres.py │ └── 4_build_template.sh ├── slurm │ ├── batch_across_average_types.sh │ ├── batch_across_templates.sh │ ├── build_template.sh │ ├── build_template_molerat.sh │ └── post_build.sh └── tadpole │ ├── 1_downsample_source_images.py │ ├── 2_prep_lowres.py │ └── 3_build_template.sh ├── pyproject.toml └── tests ├── __init__.py ├── conftest.py ├── fetch_test_data.py ├── test_integration └── __init__.py └── test_unit ├── __init__.py ├── test_brightness.py ├── test_cropping.py ├── test_plots.py ├── test_preprocess.py ├── test_standardise.py ├── test_transform_utils.py └── test_validate.py /.github/workflows/docs_build_and_deploy.yml: -------------------------------------------------------------------------------- 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