zeyugao/SMMILe_SpatialAnnotation

Pixel Annotations of TCGA-RCC and TCGA-LU: are saved as PNG files, the region marked by white/red/green is the cancer region, and marked by blue is the abandoned region, which also can be regarded as background.

The PNG file name is the case_id of each WSI. Match the original TCGA name with dataset_csv files in our GitHub repo.

Each annotation mask's size equals level 3 of the corresponding WSI.

Patch Annotations of TCGA-STAD: are saved as CSV files, each raw indicates a patch with corresponding coordinates, sizes, (x_y_size, x and y stand for the upper left coordinate of each patch) and annotated labels.

Both coordinates and sizes are obtained at the maximum magnification of the corresponding SVS file.

The CSV file name is the case_id of each WSI. Match the original TCGA name with dataset_csv files in our GitHub repo.

The fine-grained subtype labels of WSIs can be obtained by counting whether patches of certain subtypes appear in each WSI.