SMMILe: WSI Embedding and Superpixel Data

This repository contains embedding and superpixel segmentation data for six publicly available whole-slide image (WSI) datasets. The embeddings were generated using two different encoders: ResNet-50 and Conch. Each dataset is available as a ZIP file containing both the embeddings and the corresponding superpixel segmentation results.

Datasets and Files

Each ZIP file contains the embeddings and superpixel segmentations for one dataset, processed using either ResNet-50 or Conch. The files are stored using Git LFS due to their large size.

File Overview:

Dataset	Encoder	File Name	Size
Breast	Conch	`camel_conch.zip`	5.76 GB
Breast	ResNet-50	`camel_res50.zip`	17.5 GB
Gastric	Conch	`gastric_conch.zip`	489 MB
Gastric	ResNet-50	`gastric_res50.zip`	1.13 GB
Lung	Conch	`lung_conch.zip`	1.4 GB
Lung	ResNet-50	`lung_res50.zip`	3.12 GB
Ovarian	Conch	`ovarian_conch.zip`	2.5 GB
Ovarian	ResNet-50	`ovarian_res50.zip`	6.42 GB
Prostate	Conch	`prostate_conch.zip`	35.6 MB
Prostate	ResNet-50	`prostate_res50.zip`	69.1 MB
Renal-3	Conch	`renal3_conch.zip`	1.47 GB
Renal-3	ResNet-50	`renal3_res50.zip`	3.2 GB

Structure of Each ZIP File:

Each ZIP file contains two folders:

Model Embeddings: Embeddings for patches extracted from WSIs, stored as .npy files.
Superpixel Segmentations: Corresponding superpixel segmentation results for each WSI, stored as .npy files.

Example File Structure:

camel_res50.zip
  ├── resnet50/            # ResNet-50 embeddings (1024-dimensional)
  └── sp_xxx/              # Superpixel segmentations

gastric_conch.zip
  ├── conch/               # Conch embeddings (512-dimensional)
  └── sp_xxx/              # Superpixel segmentations

Embeddings (.npy Files):

Keys in the Embedding Files:

'feature': Embedding vectors of image patches.
'inst_label': Annotated label of each patch. A value of -1 indicates a non-annotated patch.
'index': Coordinates and size of the patch in the format x_y_size, where x and y represent the top-left coordinates.

Superpixel Segmentations (.npy Files):

Keys in the Superpixel Files:

'm_slic': Superpixel index for each patch.
'm_adj': Adjacency matrix representing the relationships between superpixels.