| --- |
| license: cc-by-nc-nd-4.0 |
| |
| |
| viewer: false |
| tags: |
| - pathology |
| - histopathology |
| - virtual-staining |
| - multiplex-immunofluorescence |
| task_categories: |
| - image-to-image |
| --- |
| |
| # QUEST tutorial data |
|
|
| The three staged cohorts the [QUEST](https://github.com/YAndrewL/QUEST) tutorials read. Weights |
| live in [`yandrewl/QUEST`](https://huggingface.co/yandrewl/QUEST); this repository is only the |
| data. |
|
|
| | cohort | tutorial | size | what it is | |
| |---|---|---|---| |
| | `stanford-pc/` | 1, 5 | 1.6 GB | 326 paired H&E / real-MIF patches over 29 regions, 42–52 markers each, plus the published per-patch cell composition | |
| | `bog-86337/` | 4 | 36 MB | one esophagus core: H&E mosaic, per-cell marker tables for its 16-region cohort on both the real and the predicted segmentation, and the frozen cell-state / neighbourhood vocabulary | |
| | `crc-metu/` | 6 | 73 MB | 62 colorectal slides from 57 patients, 37 events: per-patch virtual-MIF features, survival labels, and the fitted 5-fold out-of-fold MIL output | |
|
|
| ```python |
| from huggingface_hub import snapshot_download |
| |
| snapshot_download("yandrewl/QUEST-tutorial-data", repo_type="dataset", local_dir="data", |
| allow_patterns=["crc-metu/*", "bog-86337/*", "stanford-pc/*"]) |
| ``` |
|
|
| `QUEST_DATA` points elsewhere if you keep the cohorts outside the repo. |
| [Tutorial 0](https://github.com/YAndrewL/QUEST/blob/main/tutorials/00_data.ipynb) prints the shape |
| and dtype of every file here. |
|
|
| PathoCell (tutorials 2 and 3) is not staged: it is public and 36 GB whole, so |
| `questkit.cohort.fetch_pathocell(["reg016_B"])` fetches only the regions a tutorial asks for from |
| [`Kainmueller-Lab/PathoCell`](https://huggingface.co/datasets/Kainmueller-Lab/PathoCell). |
|
|
| ## Licence |
|
|
| CC BY-NC-ND 4.0, the same licence as the code and weights. |
|
|
