.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/aim/__init__.py
src/aim/__main__.py
src/aim/adata_schema.py
src/aim/aggregation.py
src/aim/aim_config.py
src/aim/cli.py
src/aim/clustering.py
src/aim/io.py
src/aim/sweep.py
src/aim/tree.py
src/aim/analysis/__init__.py
src/aim/analysis/analysis.py
src/aim/analysis/biology.py
src/aim/analysis/confidence.py
src/aim/analysis/ksweep.py
src/aim/analysis/loading.py
src/aim/analysis/onehot.py
src/aim/analysis/reconstruction.py
src/aim/analysis/topology.py
src/aim/analysis/utils.py
src/aim/data/__init__.py
src/aim/data/prepare/__init__.py
src/aim/data/prepare/build_imaging_pairs.py
src/aim/data/prepare/build_xenium_breast_pair.py
src/aim/data/prepare/convertTsvToCsv.py
src/aim/data/prepare/convert_csv_to_h5ad.py
src/aim/data/prepare/createOnlyHVGDataset.py
src/aim/data/prepare/createSmallerDataset.py
src/aim/data/prepare/normalize_gene_names.py
src/aim/data/prepare/perturb_sc_noise.py
src/aim/data/prepare/register_st_patches.py
src/aim/data/prepare/split_st_into_islands.py
src/aim/data/prepare/split_st_into_patches.py
src/aim/data/prepare/subset_st_hvg.py
src/aim/data/validate/__init__.py
src/aim/data/validate/common.py
src/aim/data/validate/runner.py
src/aim/data/validate/validate_pair.py
src/aim/data/validate/validate_sc.py
src/aim/data/validate/validate_st.py
src/aim/gui/__init__.py
src/aim/gui/__main__.py
src/aim/gui/app.py
src/aim/gui/compute.py
src/aim/gui/data_access.py
src/aim/gui/render.py
src/aim/gui/scaffold.py
src/aim/gui/widgets.py
src/aim/mapping/__init__.py
src/aim/mapping/base.py
src/aim/mapping/confidence.py
src/aim/mapping/nearest_centroid.py
src/aim/mapping/reference.py
src/aim/mapping/wann.py
src/aim/metrics/__init__.py
src/aim/metrics/biology.py
src/aim/metrics/cossim.py
src/aim/metrics/kselection.py
src/aim/metrics/onehot.py
src/aim/metrics/reconstruction.py
src/aim/metrics/topology.py
src/aim/reference_aligners/__init__.py
src/aim/reference_aligners/environment_dot.yml
src/aim/reference_aligners/environment_tacco.yml
src/aim/reference_aligners/environment_tangram.yml
src/aim/reference_aligners/registry.py
src/aim/reference_aligners/run_dot.R
src/aim/reference_aligners/run_dot.py
src/aim/reference_aligners/run_tacco.py
src/aim/reference_aligners/run_tangram.py
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
tests/test_cli.py
tests/test_gui_imports.py
tests/test_registry.py
tests/test_sweep_sample.py