.coveragerc
.gitignore
.pre-commit-config.yaml
CODE_OF_CONDUCT.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
tox.ini
uv.lock
.github/workflows/build_docs.yml
.github/workflows/preview_metadata.yml
.github/workflows/test_and_deploy.yml
.napari/DESCRIPTION.md
.napari/config.yml
conda/napari_CellSeg3D_ARM64.yml
docs/TODO.md
docs/_config.yml
docs/_toc.yml
docs/references.bib
docs/welcome.rst
docs/_templates/custom-class-template.rst
docs/_templates/custom-module-template.rst
docs/source/code/api.rst
docs/source/guides/cropping_module_guide.rst
docs/source/guides/custom_model_template.rst
docs/source/guides/detailed_walkthrough.rst
docs/source/guides/inference_module_guide.rst
docs/source/guides/installation_guide.rst
docs/source/guides/metrics_module_guide.rst
docs/source/guides/review_module_guide.rst
docs/source/guides/training_module_guide.rst
docs/source/guides/training_wnet.rst
docs/source/guides/utils_module_guide.rst
docs/source/images/Review_Parameters.png
docs/source/images/WNet_architecture.svg
docs/source/images/converted_labels.png
docs/source/images/cropping_process_example.png
docs/source/images/inference_plugin_layout.png
docs/source/images/inference_results_example.png
docs/source/images/init_image_labels.png
docs/source/images/plot_example_metrics.png
docs/source/images/plots_train.png
docs/source/images/plugin_crop.png
docs/source/images/plugin_inference.png
docs/source/images/plugin_menu.png
docs/source/images/plugin_review.png
docs/source/images/plugin_train.png
docs/source/images/plugin_welcome.png
docs/source/images/review_process_example.png
docs/source/images/stat_plots.png
docs/source/images/training_tab_1.png
docs/source/images/training_tab_2.png
docs/source/images/training_tab_3.png
docs/source/images/training_tab_4.png
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examples/README.md
examples/c5image.tif
examples/test_very_small.tif
napari_cellseg3d/__init__.py
napari_cellseg3d/_version.py
napari_cellseg3d/config.py
napari_cellseg3d/interface.py
napari_cellseg3d/napari.yaml
napari_cellseg3d/plugins.py
napari_cellseg3d/setup.py
napari_cellseg3d/utils.py
napari_cellseg3d.egg-info/PKG-INFO
napari_cellseg3d.egg-info/SOURCES.txt
napari_cellseg3d.egg-info/dependency_links.txt
napari_cellseg3d.egg-info/entry_points.txt
napari_cellseg3d.egg-info/requires.txt
napari_cellseg3d.egg-info/top_level.txt
napari_cellseg3d/_tests/__init__.py
napari_cellseg3d/_tests/fixtures.py
napari_cellseg3d/_tests/test_base_plugin.py
napari_cellseg3d/_tests/test_dock_widget.py
napari_cellseg3d/_tests/test_helper.py
napari_cellseg3d/_tests/test_inference.py
napari_cellseg3d/_tests/test_interface.py
napari_cellseg3d/_tests/test_labels_correction.py
napari_cellseg3d/_tests/test_model_framework.py
napari_cellseg3d/_tests/test_models.py
napari_cellseg3d/_tests/test_plugin_inference.py
napari_cellseg3d/_tests/test_plugin_training.py
napari_cellseg3d/_tests/test_plugin_utils.py
napari_cellseg3d/_tests/test_plugins.py
napari_cellseg3d/_tests/test_review.py
napari_cellseg3d/_tests/test_training.py
napari_cellseg3d/_tests/test_utils.py
napari_cellseg3d/_tests/test_weight_download.py
napari_cellseg3d/_tests/test_wnet_training.py
napari_cellseg3d/_tests/res/test.png
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napari_cellseg3d/_tests/res/wnet_test/lab/test.tif
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napari_cellseg3d/code_models/__init__.py
napari_cellseg3d/code_models/crf.py
napari_cellseg3d/code_models/instance_segmentation.py
napari_cellseg3d/code_models/model_framework.py
napari_cellseg3d/code_models/worker_inference.py
napari_cellseg3d/code_models/worker_training.py
napari_cellseg3d/code_models/workers_utils.py
napari_cellseg3d/code_models/models/TEMPLATE_model.py
napari_cellseg3d/code_models/models/__init__.py
napari_cellseg3d/code_models/models/model_SegResNet.py
napari_cellseg3d/code_models/models/model_SwinUNetR.py
napari_cellseg3d/code_models/models/model_TRAILMAP.py
napari_cellseg3d/code_models/models/model_TRAILMAP_MS.py
napari_cellseg3d/code_models/models/model_VNet.py
napari_cellseg3d/code_models/models/model_WNet.py
napari_cellseg3d/code_models/models/model_test.py
napari_cellseg3d/code_models/models/pretrained/__init__.py
napari_cellseg3d/code_models/models/pretrained/pretrained_model_urls.json
napari_cellseg3d/code_models/models/unet/__init__.py
napari_cellseg3d/code_models/models/unet/buildingblocks.py
napari_cellseg3d/code_models/models/unet/model.py
napari_cellseg3d/code_models/models/wnet/__init__.py
napari_cellseg3d/code_models/models/wnet/model.py
napari_cellseg3d/code_models/models/wnet/soft_Ncuts.py
napari_cellseg3d/code_plugins/__init__.py
napari_cellseg3d/code_plugins/plugin_base.py
napari_cellseg3d/code_plugins/plugin_convert.py
napari_cellseg3d/code_plugins/plugin_crf.py
napari_cellseg3d/code_plugins/plugin_crop.py
napari_cellseg3d/code_plugins/plugin_helper.py
napari_cellseg3d/code_plugins/plugin_metrics.py
napari_cellseg3d/code_plugins/plugin_model_inference.py
napari_cellseg3d/code_plugins/plugin_model_training.py
napari_cellseg3d/code_plugins/plugin_review.py
napari_cellseg3d/code_plugins/plugin_review_dock.py
napari_cellseg3d/code_plugins/plugin_utilities.py
napari_cellseg3d/dev_scripts/__init__.py
napari_cellseg3d/dev_scripts/artefact_labeling.py
napari_cellseg3d/dev_scripts/classifier_test.ipynb
napari_cellseg3d/dev_scripts/colab_training.py
napari_cellseg3d/dev_scripts/correct_labels.py
napari_cellseg3d/dev_scripts/crop_data.py
napari_cellseg3d/dev_scripts/evaluate_labels.py
napari_cellseg3d/dev_scripts/remote_inference.py
napari_cellseg3d/dev_scripts/remote_training.py
napari_cellseg3d/dev_scripts/sliding_window_voronoi.py
napari_cellseg3d/dev_scripts/test_new_evaluation.ipynb
napari_cellseg3d/dev_scripts/thread_test.py
napari_cellseg3d/dev_scripts/whole_brain_utils.py
napari_cellseg3d/res/__init__.py
napari_cellseg3d/res/logo_alpha.png
notebooks/Colab_WNet3D_training.ipynb
notebooks/Colab_inference_demo.ipynb
notebooks/assess_instance.ipynb
notebooks/label_stats_csv_plot.ipynb
notebooks/labels_plot.ipynb
notebooks/plots_data.csv
notebooks/plots_data2.csv
notebooks/view_wnet.ipynb