├── .github ├── dependabot.yml ├── release-drafter-config.yml ├── scripts │ └── get_example_dataset.py └── workflows │ ├── build.yml │ ├── ci.yml │ ├── release-drafter.yml │ ├── release.yml │ └── test.yml ├── .gitignore ├── .readthedocs.yml ├── LICENSE ├── README.md ├── conftest.py ├── docs ├── Makefile ├── _images │ ├── anndata_schema.png │ ├── ark_processing.png │ ├── docker_preferences.png │ ├── mantis_feature_file.png │ ├── mantis_feature_view.png │ └── mantis_loading.png ├── _rtd │ ├── contributing.md │ ├── data_types.md │ ├── development.md │ ├── faq.md │ ├── landing.md │ └── pipeline.md ├── _static │ └── .gitkeep ├── _templates │ └── .gitkeep ├── conf.py ├── index.rst ├── make.bat └── rtd-requirements.txt ├── environment.yml ├── hatch.toml ├── pyproject.toml ├── src └── ark │ ├── __init__.py │ ├── analysis │ ├── __init__.py │ ├── cell_neighborhood_stats.py │ ├── dimensionality_reduction.py │ ├── neighborhood_analysis.py │ ├── spatial_analysis_utils.py │ └── visualize.py │ ├── phenotyping │ ├── __init__.py │ ├── cell_cluster_utils.py │ ├── cell_meta_clustering.py │ ├── cell_som_clustering.py │ ├── cluster_helpers.py │ ├── pixel_cluster_utils.py │ ├── pixel_meta_clustering.py │ ├── pixel_som_clustering.py │ ├── pixie_preprocessing.py │ ├── post_cluster_utils.py │ └── weighted_channel_comp.py │ ├── segmentation │ ├── __init__.py │ ├── ez_seg │ │ ├── __init__.py │ │ ├── composites.py │ │ ├── ez_object_segmentation.py │ │ ├── ez_seg_display.py │ │ ├── ez_seg_utils.py │ │ └── merge_masks.py │ ├── fiber_segmentation.py │ ├── marker_quantification.py │ ├── regionprops_extraction.py │ ├── segmentation_utils.py │ └── signal_extraction.py │ ├── settings.py │ ├── spLDA │ ├── __init__.py │ └── processing.py │ └── utils │ ├── __init__.py │ ├── data_utils.py │ ├── deepcell_service_utils.py │ ├── example_dataset.py │ ├── masking_utils.py │ ├── metacluster_remap_gui │ ├── __init__.py │ ├── colormap_helper.py │ ├── file_reader.py │ ├── metaclusterdata.py │ ├── metaclustergui.py │ ├── throttle.py │ └── zscore_norm.py │ ├── plot_utils.py │ └── spatial_lda_utils.py ├── start_jupyter.sh ├── templates ├── 1_Segment_Image_Data.ipynb ├── 2_Pixie_Cluster_Pixels.ipynb ├── 3_Pixie_Cluster_Cells.ipynb ├── 4_Post_Clustering.ipynb ├── Calculate_Mixing_Scores.ipynb ├── Generalized_Masking.ipynb ├── Image_Stitching.ipynb ├── LDA_Preprocessing.ipynb ├── LDA_Training_and_Inference.ipynb ├── OME-TIFF_Conversion.ipynb ├── anndata_conversion.ipynb ├── cell_neighbors_analysis.ipynb ├── example_fiber_segmentation.ipynb ├── example_neighborhood_analysis_script.ipynb ├── example_visualization.ipynb ├── ez_segmenter.ipynb ├── generic_cell_clustering.ipynb └── mask_generation.ipynb ├── tests ├── analysis │ ├── __init__.py │ ├── cell_neighborhood_stats_test.py │ ├── dimensionality_reduction_test.py │ ├── neighborhood_analysis_test.py │ ├── spatial_analysis_utils_test.py │ └── visualize_test.py ├── phenotyping │ ├── __init__.py │ ├── cell_cluster_utils_test.py │ ├── cell_meta_clustering_test.py │ ├── cell_som_clustering_test.py │ ├── cluster_helpers_test.py │ ├── pixel_cluster_utils_test.py │ ├── pixel_meta_clustering_test.py │ ├── pixel_som_clustering_test.py │ ├── pixie_preprocessing_test.py │ ├── post_cluster_utils_test.py │ └── weighted_channel_comp_test.py ├── segmentation │ ├── __init__.py │ ├── ez_seg │ │ ├── composites_test.py │ │ ├── ez_object_segmentation_test.py │ │ ├── ez_seg_display_test.py │ │ ├── ez_seg_utils_test.py │ │ └── merge_masks_test.py │ ├── fiber_segmentation_test.py │ ├── marker_quantification_test.py │ ├── regionprops_extraction_test.py │ ├── segmentation_utils_test.py │ └── signal_extraction_test.py ├── spLDA │ ├── __init__.py │ └── processing_test.py ├── synthetic_spatial_datagen.py ├── test_utils.py └── utils │ ├── __init__.py │ ├── data_utils_test.py │ ├── deepcell_service_utils_test.py │ ├── example_dataset_test.py │ ├── masking_utils_test.py │ ├── metacluster_remap_gui │ ├── colormap_helper_test.py │ ├── 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