metadata
license: cc-by-4.0
SMMILe: WSI Embedding Superpixel Data, and Checkpoints
This repository contains embedding superpixel segmentation and checkpoint 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
Checkpoints of SMMILe for different datasets and encoders are all saved in ckpt_submit.zip.
The rest of the ZIP files contain the embeddings and superpixel segmentations for one dataset, which are 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
.npyfiles. - Superpixel Segmentations: Corresponding superpixel segmentation results for each WSI, stored as
.npyfiles.
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-1indicates a non-annotated patch.'index': Coordinates and size of the patch in the formatx_y_size, wherexandyrepresent 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.