├── .gitignore ├── .readthedocs.yaml ├── LICENSE ├── MANIFEST.in ├── README.md ├── article ├── A1_synthetic_data │ ├── array_size_benchmark.ipynb │ ├── bm_functions.py │ ├── chrysalis_example.ipynb │ ├── contamination_benchmark.ipynb │ ├── data_generator │ │ ├── generate_synthetic_datasets.py │ │ ├── generate_truncated_samples.py │ │ ├── tissue_generator.py │ │ └── tools.py │ ├── main_synthetic_benchmark.ipynb │ └── method_scripts │ │ ├── array_size_benchmark │ │ ├── chrysalis.py │ │ ├── graphst.py │ │ ├── mefisto.py │ │ ├── nsf.py │ │ └── stagate.py │ │ ├── contamination_benchmark │ │ ├── chrysalis.py │ │ ├── graphst.py │ │ ├── mefisto.py │ │ ├── nsf.py │ │ └── stagate.py │ │ └── main_synthetic_benchmark │ │ ├── chrysalis.py │ │ ├── graphst.py │ │ ├── mefisto.py │ │ ├── nsf.py │ │ └── stagate.py ├── A2_human_lymph_node │ ├── SVG_detection_methods │ │ ├── 1_bsp_spatialde_sepal.ipynb │ │ ├── 2_spark.R │ │ └── 3_method_comparison.ipynb │ ├── benchmarking │ │ ├── graphst.py │ │ ├── mefisto.py │ │ ├── nsf.py │ │ ├── spatialpca.R │ │ └── stagate.py │ ├── chrysalis_analysis_and_validation.ipynb │ └── morans_i.ipynb ├── A3_human_breast_cancer │ ├── benchmarking.ipynb │ ├── benchmarking │ │ ├── graphst.py │ │ ├── mefisto.py │ │ ├── nsf.py │ │ ├── spatialpca.R │ │ └── stagate.py │ ├── chrysalis_analysis_and_validation.ipynb │ └── morphology_integration │ │ ├── 1_extract_image_tiles.ipynb │ │ ├── 2_autoencoder_training.py │ │ └── 3_integrate_morphology.ipynb ├── A4_mouse_brain │ ├── ff │ │ ├── mouse_brain_ff.ipynb │ │ └── mouse_brain_integration.ipynb │ └── ffpe │ │ ├── benchmark │ │ ├── graphst.py │ │ ├── mefisto.py │ │ ├── nsf.py │ │ └── stagate.py │ │ ├── map_annotations.py │ │ ├── mouse_brain_ffpe.ipynb │ │ └── mouse_brain_ffpe_benchmark.ipynb ├── A5_visium_hd │ └── visium_hd_analysis.ipynb ├── A6_slide_seqv2 │ └── slide_seqv2_analysis.ipynb ├── A7_stereo_seq │ └── stereo_seq_analysis.ipynb └── readme.md ├── chrysalis ├── __init__.py ├── core.py ├── functions.py ├── plots.py ├── test │ └── test.py └── utils.py ├── docs ├── Makefile ├── _static │ ├── css │ │ └── custom.css │ ├── images │ │ ├── after.png │ │ └── before.png │ └── js │ │ └── custom.js ├── api.md ├── conf.py ├── docs_logo.svg ├── docs_logo_prev.svg ├── favicon.svg ├── favicon_prev.svg ├── index.md ├── make.bat ├── overview │ ├── getting-started.md │ └── installation.md ├── requirements.txt └── tutorials │ ├── advanced_integration_tutorial.ipynb │ ├── lymph_node_tutorial.ipynb │ └── mouse_brain_integration_tutorial.ipynb ├── gallery └── readme.md ├── misc ├── banner.png ├── demo.png ├── demo.svg ├── deprecated_functions.py ├── human_lymph_node.jpg ├── logo.svg ├── panel_1.png └── panel_2.png ├── plots ├── V1_Human_Lymph_Node.png ├── V1_Human_Lymph_Node.svg ├── V1_Mouse_Brain_Sagittal_Anterior.png ├── V1_Mouse_Brain_Sagittal_Anterior.svg ├── V1_Mouse_Brain_Sagittal_Posterior.png ├── V1_Mouse_Brain_Sagittal_Posterior.svg ├── V1_Mouse_Kidney.png ├── V1_Mouse_Kidney.svg └── gallery │ ├── Parent_Visium_Human_BreastCancer.png │ ├── Parent_Visium_Human_BreastCancer.svg │ ├── Parent_Visium_Human_Cerebellum.png │ ├── Parent_Visium_Human_Cerebellum.svg │ ├── Parent_Visium_Human_ColorectalCancer.png │ ├── Parent_Visium_Human_ColorectalCancer.svg │ ├── Parent_Visium_Human_Glioblastoma.png │ ├── Parent_Visium_Human_Glioblastoma.svg │ ├── Parent_Visium_Human_OvarianCancer.png │ ├── Parent_Visium_Human_OvarianCancer.svg │ ├── V1_Adult_Mouse_Brain.png │ ├── V1_Adult_Mouse_Brain.svg │ ├── V1_Adult_Mouse_Brain_Coronal_Section_1.png │ ├── V1_Adult_Mouse_Brain_Coronal_Section_1.svg │ ├── V1_Adult_Mouse_Brain_Coronal_Section_2.png │ ├── V1_Adult_Mouse_Brain_Coronal_Section_2.svg │ ├── V1_Breast_Cancer_Block_A_Section_1.png │ ├── V1_Breast_Cancer_Block_A_Section_1.svg │ ├── V1_Breast_Cancer_Block_A_Section_2.png │ ├── V1_Breast_Cancer_Block_A_Section_2.svg │ ├── V1_Human_Heart.png │ ├── V1_Human_Heart.svg │ ├── V1_Human_Lymph_Node.png │ ├── V1_Human_Lymph_Node.svg │ ├── 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