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src/ark/__init__.py
src/ark/settings.py
src/ark/analysis/__init__.py
src/ark/analysis/cell_neighborhood_stats.py
src/ark/analysis/dimensionality_reduction.py
src/ark/analysis/neighborhood_analysis.py
src/ark/analysis/spatial_analysis_utils.py
src/ark/analysis/spatial_enrichment.py
src/ark/analysis/visualize.py
src/ark/phenotyping/__init__.py
src/ark/phenotyping/cell_cluster_utils.py
src/ark/phenotyping/cell_meta_clustering.py
src/ark/phenotyping/cell_som_clustering.py
src/ark/phenotyping/cluster_helpers.py
src/ark/phenotyping/pixel_cluster_utils.py
src/ark/phenotyping/pixel_meta_clustering.py
src/ark/phenotyping/pixel_som_clustering.py
src/ark/phenotyping/pixie_preprocessing.py
src/ark/phenotyping/post_cluster_utils.py
src/ark/phenotyping/weighted_channel_comp.py
src/ark/segmentation/__init__.py
src/ark/segmentation/fiber_segmentation.py
src/ark/segmentation/marker_quantification.py
src/ark/segmentation/regionprops_extraction.py
src/ark/segmentation/segmentation_utils.py
src/ark/segmentation/signal_extraction.py
src/ark/segmentation/ez_seg/__init__.py
src/ark/segmentation/ez_seg/composites.py
src/ark/segmentation/ez_seg/ez_object_segmentation.py
src/ark/segmentation/ez_seg/ez_seg_display.py
src/ark/segmentation/ez_seg/ez_seg_utils.py
src/ark/segmentation/ez_seg/merge_masks.py
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src/ark/utils/spatial_lda_utils.py
src/ark/utils/metacluster_remap_gui/__init__.py
src/ark/utils/metacluster_remap_gui/colormap_helper.py
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templates/1_Segment_Image_Data.ipynb
templates/2_Pixie_Cluster_Pixels.ipynb
templates/3_Pixie_Cluster_Cells.ipynb
templates/4_Post_Clustering.ipynb
templates/Calculate_Mixing_Scores.ipynb
templates/Image_Stitching.ipynb
templates/LDA_Preprocessing.ipynb
templates/LDA_Training_and_Inference.ipynb
templates/OME-TIFF_Conversion.ipynb
templates/cell_neighbors_analysis.ipynb
templates/example_fiber_segmentation.ipynb
templates/example_neighborhood_analysis_script.ipynb
templates/example_visualization.ipynb
templates/ez_segmenter.ipynb
templates/generic_cell_clustering.ipynb
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tests/analysis/__init__.py
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tests/analysis/neighborhood_analysis_test.py
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tests/phenotyping/__init__.py
tests/phenotyping/cell_cluster_utils_test.py
tests/phenotyping/cell_meta_clustering_test.py
tests/phenotyping/cell_som_clustering_test.py
tests/phenotyping/cluster_helpers_test.py
tests/phenotyping/pixel_cluster_utils_test.py
tests/phenotyping/pixel_meta_clustering_test.py
tests/phenotyping/pixel_som_clustering_test.py
tests/phenotyping/pixie_preprocessing_test.py
tests/phenotyping/post_cluster_utils_test.py
tests/phenotyping/weighted_channel_comp_test.py
tests/segmentation/__init__.py
tests/segmentation/fiber_segmentation_test.py
tests/segmentation/marker_quantification_test.py
tests/segmentation/regionprops_extraction_test.py
tests/segmentation/segmentation_utils_test.py
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tests/segmentation/ez_seg/composites_test.py
tests/segmentation/ez_seg/ez_object_segmentation_test.py
tests/segmentation/ez_seg/ez_seg_display_test.py
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tests/utils/metacluster_remap_gui/metaclustergui_test.py
tests/utils/metacluster_remap_gui/throttle_test.py