zeyugao/SMMILe_PrivateDatasets

IH-RCC and IH-ESD datasets (Embeddings only)

Two in-house datasets (IH-RCC and IH-ESD) were collected with approval from the Ethics Committee of the First Affiliated Hospital of Xi’an Jiaotong University (KYLLSL2021-420 and KYLLSL2022-333). These data are not publicly available but are available from the corresponding author (cli@xjtu.edu.cn) upon reasonable request. All requests for in-house collected or curated data will be evaluated individually to ensure compliance with intellectual property and patient privacy obligations and can be shared upon reasonable request and subject to ethical approval.

Each ZIP file contains two folders: one for embeddings and the other for superpixel segmentations.

File Structure:

renal4_res50.zip

• resnet50/: ResNet-50 embeddings of image patches (1024-dimensional, stored as .npy files)
• sp_xxx/: Corresponding superpixel segmentation results (stored as .npy files)

renal4_conch.zip

• conch/: Conch embeddings of image patches (512-dimensional, stored as .npy files)
• sp_xxx/: Corresponding superpixel segmentation results (stored as .npy files)

gastricESD_res50.zip

• Follows the same structure as renal4_res50.zip

gastricESD_conch.zip

• Follows the same structure as renal4_conch.zip

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Embeddings (.npy files):

Keys in Embedding files:

• 'feature': Embeddings of image patches.
• 'inst_label': Annotated label of a patch, where -1 represents a non-annotated patch.
• 'index': Coordinates and size of a patch, formatted as x_y_size, where x and y represent the upper-left coordinates.

Superpixel Segmentations (.npy files):

Keys in Superpixel files:

• 'm_slic': Superpixel index of patches.
• 'm_adj': Superpixel adjacency matrix.

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WSI Labels:

• Renal-4 (IH-RCC):
  ccrcc, prcc, chrcc, and rocy represent clear cell RCC, papillary RCC, chromophobe RCC, and renal oncocytoma, respectively.

• Gastric_ESD (IH-ESD):
  The first and second digits of the label vector represent tumor, inflammation, respectively. For example, [0, 1] indicates the case has inflammation regions but no tumor regions.