README.md

metadata

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:
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    type: select
    options:
      - Academia
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      - Hospital / clinical
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      - label: Other
        value: other
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  Country: country
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  I agree not to distribute, publish or reproduce this dataset; another user in my organisation must register individually: checkbox
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extra_gated_button_content: Request access

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")