.gitignore
.pre-commit-config.yaml
AGENTS.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
tox.ini
.github/PULL_REQUEST_TEMPLATE.md
.github/dependabot.yml
.github/ISSUE_TEMPLATE/bug_report.yml
.github/ISSUE_TEMPLATE/documentation.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/ISSUE_TEMPLATE/task.md
.github/workflows/test_and_deploy.yml
.napari-hub/DESCRIPTION.md
.napari-hub/config.yml
docs/images/meiotic_nuclei_segmentation_model_v1.png
docs/images/plot_example.svg
docs/images/stitched_image_example.png
src/carltonlab_napari_tools/__init__.py
src/carltonlab_napari_tools/_model_directories.py
src/carltonlab_napari_tools/_model_download.py
src/carltonlab_napari_tools/_multigonad_project.py
src/carltonlab_napari_tools/_protocols.py
src/carltonlab_napari_tools/_sbs_lock_manager.py
src/carltonlab_napari_tools/_shared_variables.py
src/carltonlab_napari_tools/_shared_widgets.py
src/carltonlab_napari_tools/_tile_utils.py
src/carltonlab_napari_tools/_utils.py
src/carltonlab_napari_tools/_version.py
src/carltonlab_napari_tools/_viewer_utils.py
src/carltonlab_napari_tools/_widget.py
src/carltonlab_napari_tools/napari.yaml
src/carltonlab_napari_tools.egg-info/PKG-INFO
src/carltonlab_napari_tools.egg-info/SOURCES.txt
src/carltonlab_napari_tools.egg-info/dependency_links.txt
src/carltonlab_napari_tools.egg-info/entry_points.txt
src/carltonlab_napari_tools.egg-info/requires.txt
src/carltonlab_napari_tools.egg-info/scm_file_list.json
src/carltonlab_napari_tools.egg-info/scm_version.json
src/carltonlab_napari_tools.egg-info/top_level.txt
src/carltonlab_napari_tools/assets/icons/.gitkeep
src/carltonlab_napari_tools/assets/icons/add_dir.svg
src/carltonlab_napari_tools/assets/icons/add_file.svg
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src/carltonlab_napari_tools/assets/icons/zarr_file.svg
src/carltonlab_napari_tools/automatic_foci_count/__init__.py
src/carltonlab_napari_tools/automatic_foci_count/_auto_foci_count.py
src/carltonlab_napari_tools/automatic_foci_count/_auto_settings.py
src/carltonlab_napari_tools/automatic_foci_count/_nuclei_features.py
src/carltonlab_napari_tools/channel_extraction/__init__.py
src/carltonlab_napari_tools/channel_extraction/_channel_extraction.py
src/carltonlab_napari_tools/foci_count_widgets/__init__.py
src/carltonlab_napari_tools/foci_count_widgets/_auto_foci_count_widget.py
src/carltonlab_napari_tools/foci_count_widgets/_auto_settings_widget.py
src/carltonlab_napari_tools/foci_count_widgets/_foci_count_project.config
src/carltonlab_napari_tools/foci_count_widgets/_foci_count_widget.py
src/carltonlab_napari_tools/foci_count_widgets/_generate_plots_widget.py
src/carltonlab_napari_tools/foci_count_widgets/_pick_nuclei_widget.py
src/carltonlab_napari_tools/foci_count_widgets/_plot_manager.py
src/carltonlab_napari_tools/foci_count_widgets/_sbs_flags_manager.py
src/carltonlab_napari_tools/foci_count_widgets/_score_nuclei_widget.py
src/carltonlab_napari_tools/foci_count_widgets/_stitch_widget.py
src/carltonlab_napari_tools/general_widgets/_file_saver_widget.py
src/carltonlab_napari_tools/general_widgets/_project_list_widget.py
src/carltonlab_napari_tools/general_widgets/_set_contrast_widget.py
src/carltonlab_napari_tools/image_processing/__init__.py
src/carltonlab_napari_tools/image_processing/_sbs_cropping.py
src/carltonlab_napari_tools/image_resolver/__init__.py
src/carltonlab_napari_tools/image_resolver/_image_resolver.py
src/carltonlab_napari_tools/image_stitching/__init__.py
src/carltonlab_napari_tools/image_stitching/_image_stitching.py
src/carltonlab_napari_tools/image_stitching/_stitching_options_widget.py
src/carltonlab_napari_tools/resources/THIRD_PARTY_NOTICES.md
src/carltonlab_napari_tools/resources/_clsa_project.config
src/carltonlab_napari_tools/resources/clsa_structure.json
src/carltonlab_napari_tools/resources/clsp_structure.json
src/carltonlab_napari_tools/segmentation/__init__.py
src/carltonlab_napari_tools/segmentation/_model_directories_widget.py
src/carltonlab_napari_tools/segmentation/_segmentation.py
src/carltonlab_napari_tools/segmentation/models.config
src/carltonlab_napari_tools/spline_manager/_spline_manager.py
src/carltonlab_napari_tools/stitched_regions_widgets/_stitched_regions_widget.py
tests/__init__.py
tests/test_auto_foci_count.py
tests/test_auto_settings.py
tests/test_model_directories.py
tests/test_multigonad_project.py
tests/test_nuclei_features.py
tests/test_sbs_lock_manager.py
tests/test_tile_utils.py
tests/test_utils.py