├── .github └── workflows │ └── test_and_deploy.yml ├── .gitignore ├── .napari └── config.yml ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── CITATION.cff ├── LICENSE ├── MANIFEST.in ├── README.md ├── codecov.yml ├── docs ├── _config.yml ├── _toc.yml ├── api.rst ├── clusters-plotter-demo.gif ├── contributing │ ├── documentation.md │ └── new_algorithm.md ├── examples │ ├── imgs │ │ ├── sample_data_bbbc1.gif │ │ ├── sample_data_cells3d.gif │ │ ├── sample_data_skan_skeleton.gif │ │ └── sample_data_tgmm.gif │ └── sample_data.md ├── intro.md ├── logo.png ├── references.bib ├── requirements.txt └── usage │ ├── clustering_widget.md │ ├── dimensionality_reduction_widget.md │ ├── imgs │ ├── Zeichnung.svg │ ├── categorical_features.png │ ├── clustering_overview1.png │ ├── clustering_overview1_annotated.png │ ├── clustering_overview2.png │ ├── clustering_overview3.png │ ├── clustering_visualization1.png │ ├── copy_export_objects_function.gif │ ├── dimensionality_reduction_overview1.png │ ├── dimensionality_reduction_overview1_annotated.png │ ├── dimensionality_reduction_overview2.png │ ├── dimensionality_reduction_visualize1.png │ ├── dimensionality_reduction_visualize2.png │ ├── feature_immediacy3.gif │ ├── features_immediacy1.gif │ ├── features_immediacy2.gif │ ├── layer_demo_tracks.gif │ ├── plotter_overview1.png │ ├── plotter_overview1_annotated.png │ ├── plotter_overview2.png │ ├── plotter_overview3.png │ ├── plotter_overview3_annotated.png │ ├── selecting_cluster_id.png │ ├── selecting_features1.gif │ ├── selecting_layers1.png │ ├── selecting_layers1_annotated.png │ ├── selecting_layers2.png │ ├── selecting_layers3.gif │ ├── selecting_layers4.png │ ├── selecting_layers4_annotated.png │ └── selecting_layers5.png │ ├── overview.md │ └── plotter_widget.md ├── notebooks ├── demo_biological_data.ipynb ├── demo_cluster_export.ipynb ├── demo_new_plotter.ipynb ├── demo_new_reduction.ipynb └── demo_shapes_clustering.ipynb ├── pyproject.toml ├── src └── napari_clusters_plotter │ ├── __init__.py │ ├── _algorithm_widget.py │ ├── _algorithms.py │ ├── _dim_reduction_and_clustering.py │ ├── _new_plotter_widget.py │ ├── _sample_data.py │ ├── _tests │ ├── __init__.py │ ├── test_dimensionality_reduction.py │ ├── test_layers.py │ ├── test_plotter.py │ └── test_sample_data.py │ ├── _utilities.py │ ├── napari.yaml │ ├── plotter_inputs.ui │ └── sample_data │ ├── BBBC007_v1_images │ ├── A9 │ │ ├── A9 p10d.tif │ │ ├── A9 p10d_features.csv │ │ ├── A9 p10d_labels.tif │ │ ├── A9 p5d.tif │ │ ├── A9 p5d_features.csv │ │ ├── A9 p5d_labels.tif │ │ ├── A9 p7d.tif │ │ ├── A9 p7d_features.csv │ │ ├── A9 p7d_labels.tif │ │ ├── A9 p9d.tif │ │ ├── A9 p9d_features.csv │ │ └── A9 p9d_labels.tif │ ├── data_source.txt │ ├── f96 (17) │ │ ├── 17P1_POS0006_D_1UL.tif │ │ ├── 17P1_POS0006_D_1UL_features.csv │ │ ├── 17P1_POS0006_D_1UL_labels.tif │ │ ├── 17P1_POS0007_D_1UL.tif │ │ ├── 17P1_POS0007_D_1UL_features.csv │ │ ├── 17P1_POS0007_D_1UL_labels.tif │ │ ├── 17P1_POS0011_D_1UL.tif │ │ ├── 17P1_POS0011_D_1UL_features.csv │ │ ├── 17P1_POS0011_D_1UL_labels.tif │ │ ├── 17P1_POS0013_D_1UL.tif │ │ ├── 17P1_POS0013_D_1UL_features.csv │ │ ├── 17P1_POS0013_D_1UL_labels.tif │ │ ├── 17P1_POS0014_D_1UL.tif │ │ ├── 17P1_POS0014_D_1UL_features.csv │ │ └── 17P1_POS0014_D_1UL_labels.tif │ └── f9620 │ │ ├── 20P1_POS0002_D_1UL_labels.tif │ │ ├── 20P1_POS0005_D_1UL.tif │ │ ├── 20P1_POS0005_D_1UL_features.csv │ │ ├── 20P1_POS0005_D_1UL_labels.tif │ │ ├── 20P1_POS0007_D_1UL.tif │ │ ├── 20P1_POS0007_D_1UL_features.csv │ │ ├── 20P1_POS0007_D_1UL_labels.tif │ │ ├── 20P1_POS0008_D_1UL.tif │ │ ├── 20P1_POS0008_D_1UL_features.csv │ │ ├── 20P1_POS0008_D_1UL_labels.tif │ │ ├── 20P1_POS0010_D_1UL.tif │ │ ├── 20P1_POS0010_D_1UL_features.csv │ │ ├── 20P1_POS0010_D_1UL_labels.tif │ │ ├── 20P1_POS0011_D_1UL.tif │ │ ├── 20P1_POS0011_D_1UL_features.csv │ │ └── 20P1_POS0011_D_1UL_labels.tif │ ├── cells3d │ ├── faces.txt │ ├── nucleus.tif │ ├── signature.csv │ └── vertices.txt │ ├── compression_vectors │ ├── data_source.txt │ └── granular_compression_test.csv │ ├── shapes_skeleton │ ├── all_paths.csv │ ├── blobs.tif │ └── skeleton_features.csv │ └── tracking_data │ ├── LICENSE │ ├── README.md │ ├── tgmm-mini-spot.csv │ ├── tgmm-mini-tracks-layer-data.csv │ ├── tgmm-mini.csv │ └── tgmm-mini.tif └── tox.ini /.github/workflows/test_and_deploy.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BiAPoL/napari-clusters-plotter/HEAD/.github/workflows/test_and_deploy.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BiAPoL/napari-clusters-plotter/HEAD/.gitignore -------------------------------------------------------------------------------- /.napari/config.yml: 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