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QUEST-data
Paired H&E / multiplex immunofluorescence evaluation regions for 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 |
from huggingface_hub import snapshot_download
snapshot_download("yandrewl/QUEST-data", repo_type="dataset",
allow_patterns="crc_stain/*", local_dir="data")
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