.gitignore
.pre-commit-config.yaml
LICENSE
README.md
environment.yml
pyproject.toml
renovate.json
.github/workflows/ci.yml
.github/workflows/release.yml
docs/aim_gui.gif
docs/figure_2_1.png
sample_dataset/pairs.csv
sample_dataset/ST/index.csv
sample_dataset/ST/sample_st.h5ad
sample_dataset/scRNA/index.csv
sample_dataset/scRNA/sample_sc.h5ad
src/spatial_aim.egg-info/PKG-INFO
src/spatial_aim.egg-info/SOURCES.txt
src/spatial_aim.egg-info/dependency_links.txt
src/spatial_aim.egg-info/entry_points.txt
src/spatial_aim.egg-info/requires.txt
src/spatial_aim.egg-info/scm_file_list.json
src/spatial_aim.egg-info/scm_version.json
src/spatial_aim.egg-info/top_level.txt
src/spatialaim/__init__.py
src/spatialaim/__main__.py
src/spatialaim/adata_schema.py
src/spatialaim/aggregation.py
src/spatialaim/cli.py
src/spatialaim/clustering.py
src/spatialaim/config.py
src/spatialaim/io.py
src/spatialaim/sweep.py
src/spatialaim/tree.py
src/spatialaim/utils.py
src/spatialaim/analysis/__init__.py
src/spatialaim/analysis/coherence.py
src/spatialaim/analysis/loading.py
src/spatialaim/analysis/reconstruction.py
src/spatialaim/analysis/run.py
src/spatialaim/analysis/shape_consistency.py
src/spatialaim/analysis/spatial_organization.py
src/spatialaim/analysis/compare_ks/__init__.py
src/spatialaim/analysis/compare_ks/collect.py
src/spatialaim/analysis/compare_ks/criteria.py
src/spatialaim/analysis/compare_ks/run.py
src/spatialaim/analysis/compare_ks/scoring.py
src/spatialaim/analysis/compare_ks/selection.py
src/spatialaim/data/__init__.py
src/spatialaim/data/curate_datasets/README.md
src/spatialaim/data/curate_datasets/__init__.py
src/spatialaim/data/curate_datasets/_common.py
src/spatialaim/data/curate_datasets/_segmentation.py
src/spatialaim/data/curate_datasets/curate_01_mouse_ssp.py
src/spatialaim/data/curate_datasets/curate_02_colorectal_cancer.py
src/spatialaim/data/curate_datasets/curate_03_mouse_liver.py
src/spatialaim/data/curate_datasets/curate_04_mouse_kidney.py
src/spatialaim/data/curate_datasets/curate_05_mouse_embryo.py
src/spatialaim/data/curate_datasets/curate_06_mouse_retina.py
src/spatialaim/data/curate_datasets/curate_07_mouse_mpfc.py
src/spatialaim/data/curate_datasets/curate_08_mouse_visual_cortex.py
src/spatialaim/data/curate_datasets/curate_09_human_breast_cancer.py
src/spatialaim/data/curate_datasets/curate_10_human_mtg.py
src/spatialaim/data/curate_datasets/dump_retina_counts.R
src/spatialaim/data/curate_datasets/environment_retina_qs.yml
src/spatialaim/data/validate/__init__.py
src/spatialaim/data/validate/common.py
src/spatialaim/data/validate/runner.py
src/spatialaim/data/validate/validate_pair.py
src/spatialaim/data/validate/validate_sc.py
src/spatialaim/data/validate/validate_segmentation.py
src/spatialaim/data/validate/validate_st.py
src/spatialaim/gui/__init__.py
src/spatialaim/gui/__main__.py
src/spatialaim/gui/app.py
src/spatialaim/gui/compute.py
src/spatialaim/gui/data_access.py
src/spatialaim/gui/loaders.py
src/spatialaim/gui/scaffold.py
src/spatialaim/gui/sidebar.py
src/spatialaim/gui/state_names.py
src/spatialaim/gui/texts.py
src/spatialaim/gui/validation.py
src/spatialaim/gui/render/__init__.py
src/spatialaim/gui/render/cell_type.py
src/spatialaim/gui/render/common.py
src/spatialaim/gui/render/headline.py
src/spatialaim/gui/render/ksweep.py
src/spatialaim/gui/render/markers.py
src/spatialaim/gui/render/report.py
src/spatialaim/gui/render/scatter.py
src/spatialaim/gui/render/shape.py
src/spatialaim/gui/views/__init__.py
src/spatialaim/gui/views/cards.py
src/spatialaim/gui/views/cell_type_modal.py
src/spatialaim/gui/views/choose_k.py
src/spatialaim/gui/views/compare_tab.py
src/spatialaim/gui/views/controls.py
src/spatialaim/gui/views/mapper_tab.py
src/spatialaim/gui/views/reference_tab.py
src/spatialaim/gui/views/report.py
src/spatialaim/gui/widgets/__init__.py
src/spatialaim/gui/widgets/headline_plot.py
src/spatialaim/gui/widgets/linked_plot.py
src/spatialaim/gui/widgets/plotly_fit.py
src/spatialaim/gui/widgets/slider.py
src/spatialaim/mapping/__init__.py
src/spatialaim/mapping/base.py
src/spatialaim/mapping/confidence.py
src/spatialaim/mapping/nearest_centroid.py
src/spatialaim/mapping/reference.py
src/spatialaim/mapping/wann.py
src/spatialaim/metrics/__init__.py
src/spatialaim/metrics/cossim.py
src/spatialaim/metrics/modularity.py
src/spatialaim/metrics/shape_consistency.py
src/spatialaim/metrics/topology.py
src/spatialaim/reference_aligners/__init__.py
src/spatialaim/reference_aligners/environment_dot.yml
src/spatialaim/reference_aligners/environment_tacco.yml
src/spatialaim/reference_aligners/environment_tangram.yml
src/spatialaim/reference_aligners/registry.py
src/spatialaim/reference_aligners/run_dot.R
src/spatialaim/reference_aligners/run_dot.py
src/spatialaim/reference_aligners/run_tacco.py
src/spatialaim/reference_aligners/run_tangram.py
tests/test_cli.py
tests/test_gui_imports.py
tests/test_registry.py
tests/test_sweep_sample.py