| --- |
| license: cc-by-nc-nd-4.0 |
| tags: |
| - pathology |
| - histopathology |
| - virtual-staining |
| - multiplex-immunofluorescence |
| extra_gated_heading: Request access to QUEST-data |
| extra_gated_prompt: >- |
| This dataset is released under CC BY-NC-ND 4.0 and may only be used for non-commercial |
| research with proper attribution. Any commercial use, sale or other monetisation of the |
| data or of models trained on it is prohibited and requires prior approval. The primary |
| email of your Hugging Face account must match your institutional email: requests from |
| free providers (@gmail, @outlook, @hotmail, @qq, @163, @foxmail and the like) are denied. |
| By downloading the data you attest that all information given below is correct and |
| up-to-date, and you agree not to distribute, publish, redistribute or reproduce a copy of |
| this dataset in whole or in part. If another user in your organisation wishes to use it, |
| they must register as an individual user and agree to these terms. You may not attempt to |
| re-identify the patients from whom these data were derived. Commercial entities should |
| contact the corresponding author. |
| extra_gated_fields: |
| Full name (first and last): text |
| Current affiliation (no abbreviations): text |
| Type of affiliation: |
| type: select |
| options: |
| - Academia |
| - Industry |
| - Hospital / clinical |
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| - label: Other |
| value: other |
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| extra_gated_button_content: Request access |
| --- |
| |
| # QUEST-data |
|
|
| Paired H&E / multiplex immunofluorescence evaluation regions for |
| [QUEST](https://github.com/YAndrewL/QUEST). |
|
|
| ## Stain cohorts |
|
|
| Each file is one region. The panel is per-region: `K` varies between files and the |
| channel order follows that file's own `biomarkers`, so index by marker name, never |
| by position. |
|
|
| | key | | | |
| |---|---|---| |
| | `he` | `(n, 224, 224, 3)` uint8 | H&E patches of that region | |
| | `mif` | `(n, 224, 224, K)` float16 | measured multiplex, same patches | |
| | `biomarkers` | `(K,)` str | that region's own panel | |
|
|
| | cohort | regions | patches | K | size | |
| |---|---|---|---|---| |
| | `crc_stain` | 100 | 12,154 | 50-54 | 17 GB | |
| | `breast_stain` | 100 | 10,789 | 53-54 | 13 GB | |
| | `lung_stain` | 100 | 20,585 | 36-54 | 23 GB | |
| | `melanoma_stain` | 77 | 6,768 | 45-54 | 9.4 GB | |
|
|
| ## Mixed_10K |
| |
| 10,000 patches in 10 shards of 1,000, on one fixed 52-marker panel with the channel |
| axis second. `gt_mask` marks which channels were measured for each patch; |
| unmeasured channels are zero-filled and cannot be told from a true negative without |
| it. |
|
|
| | key | | | |
| |---|---|---| |
| | `he` | `(n, 224, 224, 3)` uint8 | | |
| | `mif` | `(n, 52, 224, 224)` float16 | | |
| | `biomarkers` | `(52,)` str | fixed panel | |
| | `gt_mask` | `(n, 52)` bool | measured channels | |
|
|
| ```python |
| from huggingface_hub import snapshot_download |
| snapshot_download("yandrewl/QUEST-data", repo_type="dataset", |
| allow_patterns="crc_stain/*", local_dir="data") |
| ``` |
|
|
