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license: cc-by-4.0 |
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# SMMILe: WSI Embedding Superpixel Data, and Checkpoints |
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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. |
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## Datasets and Files |
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Checkpoints of SMMILe for different datasets and encoders are all saved in `ckpt_submit.zip`. |
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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. |
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### File Overview: |
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| Dataset | Encoder | File Name | Size | |
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|------------------|---------------|--------------------------|----------| |
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| Breast | Conch | `camel_conch.zip` | 5.76 GB | |
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| Breast | ResNet-50 | `camel_res50.zip` | 17.5 GB | |
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| Gastric | Conch | `gastric_conch.zip` | 489 MB | |
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| Gastric | ResNet-50 | `gastric_res50.zip` | 1.13 GB | |
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| Lung | Conch | `lung_conch.zip` | 1.4 GB | |
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| Lung | ResNet-50 | `lung_res50.zip` | 3.12 GB | |
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| Ovarian | Conch | `ovarian_conch.zip` | 2.5 GB | |
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| Ovarian | ResNet-50 | `ovarian_res50.zip` | 6.42 GB | |
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| Prostate | Conch | `prostate_conch.zip` | 35.6 MB | |
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| Prostate | ResNet-50 | `prostate_res50.zip` | 69.1 MB | |
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| Renal-3 | Conch | `renal3_conch.zip` | 1.47 GB | |
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| Renal-3 | ResNet-50 | `renal3_res50.zip` | 3.2 GB | |
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## Structure of Each ZIP File: |
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Each ZIP file contains two folders: |
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- **Model Embeddings**: Embeddings for patches extracted from WSIs, stored as `.npy` files. |
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- **Superpixel Segmentations**: Corresponding superpixel segmentation results for each WSI, stored as `.npy` files. |
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### Example File Structure: |
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```plaintext |
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camel_res50.zip |
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├── resnet50/ # ResNet-50 embeddings (1024-dimensional) |
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└── sp_xxx/ # Superpixel segmentations |
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gastric_conch.zip |
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├── conch/ # Conch embeddings (512-dimensional) |
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└── sp_xxx/ # Superpixel segmentations |
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``` |
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## Embeddings (.npy Files): |
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**Keys in the Embedding Files:** |
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- `'feature'`: Embedding vectors of image patches. |
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- `'inst_label'`: Annotated label of each patch. A value of `-1` indicates a non-annotated patch. |
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- `'index'`: Coordinates and size of the patch in the format `x_y_size`, where `x` and `y` represent the top-left coordinates. |
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## Superpixel Segmentations (.npy Files): |
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**Keys in the Superpixel Files:** |
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- `'m_slic'`: Superpixel index for each patch. |
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- `'m_adj'`: Adjacency matrix representing the relationships between superpixels. |
