├── Baselines ├── ReadMe ├── STAGE │ ├── LICENSE │ ├── README.md │ ├── README.rst │ ├── STAGE │ │ ├── __init__.py │ │ ├── dataset.py │ │ ├── loss.py │ │ ├── model.py │ │ └── utils.py │ ├── STAGE_overview.png │ ├── requirement.txt │ ├── setup.py │ └── tutorials │ │ ├── T1_DLPFC_recovery.ipynb │ │ ├── T2_mouse_brain.ipynb │ │ ├── T3_PDAC.ipynb │ │ ├── T4_breast_cancer.ipynb │ │ └── T5_3d_model.ipynb ├── TESLA │ ├── LICENSE │ ├── README.md │ ├── TESLA.egg-info │ │ ├── PKG-INFO │ │ ├── SOURCES.txt │ │ ├── dependency_links.txt │ │ ├── requires.txt │ │ └── top_level.txt │ ├── TESLA │ │ ├── ConnectedComponents.py │ │ ├── TESLA.py │ │ ├── TLS_detection.py │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── ConnectedComponents.cpython-311.pyc │ │ │ ├── TESLA.cpython-311.pyc │ │ │ ├── TESLA.cpython-37.pyc │ │ │ ├── TLS_detection.cpython-311.pyc │ │ │ ├── __init__.cpython-311.pyc │ │ │ ├── __init__.cpython-37.pyc │ │ │ ├── annotation.cpython-311.pyc │ │ │ ├── annotation.cpython-37.pyc │ │ │ ├── calculate_dis.cpython-311.pyc │ │ │ ├── calculate_dis.cpython-37.pyc │ │ │ ├── contour_util.cpython-311.pyc │ │ │ ├── contour_util.cpython-37.pyc │ │ │ ├── imputation.cpython-311.pyc │ │ │ ├── imputation.cpython-37.pyc │ │ │ ├── models.cpython-311.pyc │ │ │ ├── models.cpython-37.pyc │ │ │ ├── tumor_edge_core.cpython-311.pyc │ │ │ ├── util.cpython-311.pyc │ │ │ └── util.cpython-37.pyc │ │ ├── annotation.py │ │ ├── calculate_dis.py │ │ ├── contour_util.py │ │ ├── imputation.py │ │ ├── models.py │ │ ├── tumor_edge_core.py │ │ └── util.py │ ├── TESLAforST.egg-info │ │ ├── PKG-INFO │ │ ├── SOURCES.txt │ │ ├── dependency_links.txt │ │ ├── requires.txt │ │ └── top_level.txt │ ├── build │ │ └── lib │ │ │ └── TESLA │ │ │ ├── ConnectedComponents.py │ │ │ ├── TESLA.py │ │ │ ├── TLS_detection.py │ │ │ ├── __init__.py │ │ │ ├── annotation.py │ │ │ ├── calculate_dis.py │ │ │ ├── contour_util.py │ │ │ ├── imputation.py │ │ │ ├── models.py │ │ │ ├── tumor_edge_core.py │ │ │ └── util.py │ ├── dist │ │ ├── TESLA-1.0.0-py3.7.egg │ │ ├── TESLAforST-1.2.0-py3-none-any.whl │ │ ├── TESLAforST-1.2.0.tar.gz │ │ ├── TESLAforST-1.2.1-py3-none-any.whl │ │ ├── TESLAforST-1.2.1.tar.gz │ │ ├── TESLAforST-1.2.2-py3-none-any.whl │ │ ├── TESLAforST-1.2.2.tar.gz │ │ └── TESLAforST-1.2.4-py3.7.egg │ └── setup.py ├── XFuse │ ├── LICENSE │ ├── README.org │ ├── poetry.lock │ ├── pyproject.toml │ ├── scripts │ │ ├── sync_version.py │ │ └── visualize_tissue_masks.py │ ├── setup.cfg │ ├── tests │ │ ├── __init__.py │ │ ├── analyze │ │ │ ├── test_differential_expression.py │ │ │ ├── test_gene_maps.py │ │ │ ├── test_metagenes.py │ │ │ └── test_prediction.py │ │ ├── conftest.py │ │ ├── data │ │ │ ├── files │ │ │ │ ├── image │ │ │ │ │ └── image.jpg │ │ │ │ ├── st │ │ │ │ │ ├── counts.tsv │ │ │ │ │ ├── image.jpg │ │ │ │ │ ├── mask.png │ │ │ │ │ └── spots.tsv │ │ │ │ ├── toydata.h5 │ │ │ │ └── visium │ │ │ │ │ ├── data.h5 │ │ │ │ │ ├── image.jpg │ │ │ │ │ ├── mask.png │ │ │ │ │ ├── scale_factors.json │ │ │ │ │ └── tissue_positions.csv │ │ │ ├── test_analysis_exit_status.1.toml │ │ │ ├── test_restore_session.1.toml │ │ │ ├── test_restore_session.2.toml │ │ │ ├── test_stats_writers.1.toml │ │ │ └── test_train_exit_status.1.toml │ │ ├── model │ │ │ └── experiment │ │ │ │ └── test_st.py │ │ ├── test_functional.py │ │ └── test_integration.py │ └── xfuse │ │ ├── __init__.py │ │ ├── __main__.py │ │ ├── __version__.py │ │ ├── _config.py │ │ ├── analyze │ │ ├── __init__.py │ │ ├── analyze.py │ │ ├── differential_expression.py │ │ ├── gene_maps.py │ │ ├── metagenes.py │ │ └── prediction.py │ │ ├── convert │ │ ├── __init__.py │ │ ├── image.py │ │ ├── st.py │ │ ├── utility.py │ │ └── visium.py │ │ ├── data │ │ ├── __init__.py │ │ ├── dataset.py │ │ ├── slide │ │ │ ├── __init__.py │ │ │ ├── data │ │ │ │ ├── __init__.py │ │ │ │ ├── annotated_image.py │ │ │ │ ├── slide_data.py │ │ │ │ └── st_slide.py │ │ │ ├── iterator │ │ │ │ ├── __init__.py │ │ │ │ ├── data_iterator.py │ │ │ │ ├── full_slide_iterator.py │ │ │ │ ├── random_iterator.py │ │ │ │ └── slide_iterator.py │ │ │ └── slide.py │ │ └── utility │ │ │ ├── __init__.py │ │ │ └── misc.py │ │ ├── logging │ │ ├── __init__.py │ │ ├── formatter.py │ │ └── logging.py │ │ ├── messengers │ │ ├── __init__.py │ │ ├── analysis_runner.py │ │ ├── checkpointer.py │ │ └── stats │ │ │ ├── __init__.py │ │ │ ├── conditions.py │ │ │ ├── elbo.py │ │ │ ├── image.py │ │ │ ├── latent.py │ │ │ ├── metagene_activation.py │ │ │ ├── rmse.py │ │ │ ├── scale.py │ │ │ ├── stats_handler.py │ │ │ └── writer │ │ │ ├── __init__.py │ │ │ ├── file.py │ │ │ ├── stats_writer.py │ │ │ └── tensorboard.py │ │ ├── model │ │ ├── __init__.py │ │ ├── experiment │ │ │ ├── __init__.py │ │ │ ├── experiment.py │ │ │ ├── image.py │ │ │ └── st │ │ │ │ ├── __init__.py │ │ │ │ ├── metagene_eval.py │ │ │ │ ├── metagene_expansion_strategy.py │ │ │ │ └── st.py │ │ ├── utility │ │ │ ├── __init__.py │ │ │ └── model_comparison.py │ │ └── xfuse.py │ │ ├── optim.py │ │ ├── run.py │ │ ├── session │ │ ├── __init__.py │ │ ├── io.py │ │ ├── items │ │ │ ├── __init__.py │ │ │ ├── colormap.py │ │ │ ├── covariates.py │ │ │ ├── dataloader.py │ │ │ ├── default_device.py │ │ │ ├── eval.py │ │ │ ├── genes.py │ │ │ ├── learning_rate.py │ │ │ ├── log_file.py │ │ │ ├── log_level.py │ │ │ ├── messengers.py │ │ │ ├── model.py │ │ │ ├── mpl_backend.py │ │ │ ├── optimizer.py │ │ │ ├── stats_writers.py │ │ │ ├── training_data.py │ │ │ └── work_dir.py │ │ ├── session.py │ │ └── session_item.py │ │ ├── train.py │ │ └── utility │ │ ├── __init__.py │ │ ├── core.py │ │ ├── file.py │ │ ├── mask.py │ │ ├── pyro.py │ │ ├── state │ │ ├── __init__.py │ │ ├── getters.py │ │ └── state.py │ │ ├── tensor.py │ │ └── visualization.py └── iStar │ ├── extract_features.py │ ├── get_mask.py │ ├── image.py │ ├── impute.py │ ├── impute_by_basic.py │ ├── run.sh │ ├── select_genes.py │ ├── train.py │ └── utils.py ├── LICENSE ├── Overview.png ├── README.md ├── RGB_feature_map.py ├── Supplementary Materials Final.pdf ├── 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