├── CCST.py ├── CCST_ST_utils.py ├── CCST_merfish_utils.py ├── Embedding_data ├── MERFISH │ ├── lambdaI0.8_epoch5000_Embed_X.npy │ └── types.txt └── V1_Breast_Cancer_Block_A_Section_1 │ └── lambdaI0.3_epoch5000_Embed_X.npy ├── README.md ├── data_generation_ST.py ├── data_generation_merfish.py ├── dataset ├── a └── merfish.zip ├── figure └── figure1.png ├── generated_data ├── MERFISH │ ├── Adjacent │ ├── all_distance_array.npy │ ├── all_distance_matrix.npy │ ├── all_genes.txt │ ├── cell_batch_info.npy │ ├── features.npy │ └── gene_names.txt └── V1_Breast_Cancer_Block_A_Section_1 │ ├── Adjacent │ ├── cell_types.npy │ ├── coordinates.npy │ ├── features.npy │ ├── spacial.png │ └── types_dic.txt ├── model ├── MERFISH │ └── DGI_lambdaI_0.8_epoch5000.pth.tar └── V1_Breast_Cancer_Block_A_Section_1 │ └── DGI_lambdaI_0.3_epoch5000.pth.tar └── run_CCST.py /CCST.py: -------------------------------------------------------------------------------- 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