├── .DS_Store ├── .idea ├── .gitignore ├── Spacell.iml ├── inspectionProfiles │ └── profiles_settings.xml ├── misc.xml ├── modules.xml └── vcs.xml ├── LICENSE ├── README.md ├── SpaCell.egg-info ├── PKG-INFO ├── SOURCES.txt ├── dependency_links.txt └── top_level.txt ├── SpaCell ├── .DS_Store ├── __init__.py ├── __pycache__ │ ├── config.cpython-37.pyc │ ├── dataset_management.cpython-37.pyc │ ├── model.cpython-37.pyc │ └── utils.cpython-37.pyc ├── config.py ├── count_matrix_normalization.py ├── dataset_management.py ├── image_normalization.py ├── model.py ├── spacell_classification.py ├── spacell_clustering.py ├── spacell_validation.py └── utils.py ├── dataset ├── .DS_Store ├── cm │ ├── .DS_Store │ ├── CN51_C2_2_stdata_aligned_counts_IDs.txt │ ├── CN52_C2_2_stdata_aligned_counts_IDs.txt │ ├── CN62_E2_stdata_aligned_counts_IDs.txt │ ├── CN63_E2_stdata_aligned_counts_IDs.txt │ ├── CN64_C1_stdata_aligned_counts_IDs.txt │ ├── CN67_E2_stdata_aligned_counts_IDs.txt │ ├── CN79_D1_stdata_aligned_counts_IDs.txt │ ├── CN80_E1_stdata_aligned_counts_IDs.txt │ ├── CN81_E1_stdata_aligned_counts_IDs.txt │ ├── CN94_D1_stdata_aligned_counts_IDs.txt │ ├── CN94_D2_stdata_aligned_counts_IDs.txt │ ├── L6CN51_E1_2_stdata_aligned_counts_IDs.txt │ ├── L6CN51_E2_2_stdata_aligned_counts_IDs.txt │ ├── L7CN84_E1_stdata_aligned_counts_IDs.txt │ └── L7CN85_E1_stdata_aligned_counts_IDs.txt ├── image │ ├── .DS_Store │ ├── CN51_C2_HE.jpg │ ├── CN52_C2_HE.jpg │ ├── CN62_E2_HE.jpg │ ├── CN63_E2_HE.jpg │ ├── CN64_C1_HE.jpg │ ├── CN67_E2_HE.jpg │ ├── CN79_D1_HE.jpg │ ├── CN80_E1_HE.jpg │ ├── CN81_C2_HE.jpg │ ├── CN81_E1_HE.jpg │ ├── CN94_D1_HE.jpg │ ├── CN94_D2_HE.jpg │ ├── L6CN51_E1_HE.jpg │ ├── L7CN84_E1_HE.jpg │ └── L7CN85_E1_HE.jpg ├── metadata │ └── mouse_sample_names_sra.tsv └── validation │ ├── .DS_Store │ ├── annotation.png │ ├── cluster_predictions.tsv │ ├── expected_output │ ├── .DS_Store │ ├── contour_overlay_image_10x.jpeg │ ├── contour_spot_overlay_image_10x.pdf │ ├── registration_correlation_coefficient_plot.pdf │ ├── registration_overlay_image_10x.jpeg │ └── roc_curve.pdf │ ├── output │ └── .DS_Store │ ├── transformation_matrix.txt │ └── wsi_10x_downscale.jpeg ├── dist └── SpaCell-0.0.1.tar.gz ├── figure ├── .DS_Store ├── README.md ├── age_confusion_matrix_combine.png ├── age_roc_combine.png ├── clustering_1.png ├── clustering_2.png ├── clustering_3.png └── logo.png ├── requirements.yml ├── setup.py └── tutorial ├── Tutorial_Spacell_ALS.ipynb └── Tutorial_Spacell_validation.ipynb /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BiomedicalMachineLearning/Spacell/HEAD/.DS_Store -------------------------------------------------------------------------------- /.idea/.gitignore: -------------------------------------------------------------------------------- 1 | 2 | # Default ignored files 3 | /workspace.xml 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