.dockerignore
.gitignore
.readthedocs.yml
Dockerfile
LICENSE
README.md
conftest.py
pyproject.toml
setup.py
start_docker.sh
start_jupyter.sh
tox.ini
update_notebooks.sh
./src/ark/utils/_bootstrapping.c
.github/dependabot.yml
.github/workflows/build.yml
.github/workflows/ci.yml
.github/workflows/docker.yml
.github/workflows/pypi_publish.yml
.github/workflows/release-drafter.yml
.github/workflows/test.yml
docs/Makefile
docs/conf.py
docs/index.rst
docs/make.bat
docs/rtd-requirements.txt
docs/_images/ark_processing.png
docs/_images/docker_preferences.png
docs/_images/mantis_feature_file.png
docs/_images/mantis_feature_view.png
docs/_images/mantis_loading.png
docs/_rtd/contributing.md
docs/_rtd/data_types.md
docs/_rtd/development.md
docs/_rtd/faq.md
docs/_rtd/landing.md
docs/_rtd/pipeline.md
docs/_rtd/windows_setup.md
docs/_static/.gitkeep
docs/_templates/.gitkeep
src/ark/__init__.py
src/ark/settings.py
src/ark/analysis/__init__.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/spLDA/__init__.py
src/ark/spLDA/processing.py
src/ark/utils/__init__.py
src/ark/utils/_bootstrapping.pyx
src/ark/utils/data_utils.py
src/ark/utils/deepcell_service_utils.py
src/ark/utils/example_dataset.py
src/ark/utils/plot_utils.py
src/ark/utils/spatial_lda_utils.py
src/ark/utils/metacluster_remap_gui/__init__.py
src/ark/utils/metacluster_remap_gui/colormap_helper.py
src/ark/utils/metacluster_remap_gui/file_reader.py
src/ark/utils/metacluster_remap_gui/metaclusterdata.py
src/ark/utils/metacluster_remap_gui/metaclustergui.py
src/ark/utils/metacluster_remap_gui/throttle.py
src/ark/utils/metacluster_remap_gui/zscore_norm.py
src/ark_analysis.egg-info/PKG-INFO
src/ark_analysis.egg-info/SOURCES.txt
src/ark_analysis.egg-info/dependency_links.txt
src/ark_analysis.egg-info/requires.txt
src/ark_analysis.egg-info/top_level.txt
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/example_fiber_segmentation.ipynb
templates/example_neighborhood_analysis_script.ipynb
templates/example_visualization.ipynb
templates/generic_cell_clustering.ipynb
tests/synthetic_spatial_datagen.py
tests/test_utils.py
tests/analysis/__init__.py
tests/analysis/dimensionality_reduction_test.py
tests/analysis/neighborhood_analysis_test.py
tests/analysis/spatial_analysis_utils_test.py
tests/analysis/spatial_enrichment_test.py
tests/analysis/visualize_test.py
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
tests/segmentation/signal_extraction_test.py
tests/spLDA/__init__.py
tests/spLDA/processing_test.py
tests/utils/__init__.py
tests/utils/data_utils_test.py
tests/utils/deepcell_service_utils_test.py
tests/utils/example_dataset_test.py
tests/utils/notebook_update_test.py
tests/utils/notebooks_test.py
tests/utils/notebooks_test_utils.py
tests/utils/plot_utils_test.py
tests/utils/spatial_lda_utils_test.py
tests/utils/synthetic_spatial_datagen_test.py
tests/utils/metacluster_remap_gui/colormap_helper_test.py
tests/utils/metacluster_remap_gui/conftest.py
tests/utils/metacluster_remap_gui/file_reader_test.py
tests/utils/metacluster_remap_gui/metaclusterdata_test.py
tests/utils/metacluster_remap_gui/metaclustergui_test.py
tests/utils/metacluster_remap_gui/throttle_test.py