pretty_name: HESRT — Human-reviewed spatial-omics resource
language:
- en
license: other
license_name: source-specific
license_link: https://huggingface.co/datasets/Biogod/HESRT/blob/main/docs/REUSE.md
size_categories:
- 1K<n<10K
tags:
- spatial-transcriptomics
- spatial-omics
- histology
- multimodal
- anndata
- biology
- biomedical
- provenance
configs:
- config_name: reviewed_catalog
default: true
data_files:
- split: reviewed
path: releases/2026-09-17/catalog.parquet
- config_name: studies
data_files:
- split: studies
path: releases/2026-09-17/studies.parquet
- config_name: visual_preview
data_files:
- split: examples
path: releases/2026-09-17/visual_preview.parquet
HESRT
Human-reviewed, accession-level spatial-omics artifacts with tissue images, expression matrices and source provenance.
| Samples (GSMs) | Studies (GSEs) | Expression observations | Compressed packages |
|---|---|---|---|
| 4,682 | 530 | 54,902,915 | 421.75 GB |
Each sample is a self-contained, checksummed tar.zst package. Browse the catalog, select the accessions you need, then download those samples. The full collection contains approximately 656.57 GB of uncompressed member data; do not clone the repository to try one sample.
The counts describe sample artifacts and source-defined observations (spots, cells or bins), not independent donors. Every included package has a recorded human visual-review PASS. Source interpretation and outstanding verification annotations remain available in the catalog and known issues.
See the data
These eight examples span human cortex, mouse brain, spinal cord, pancreas, liver, Visium HD, FFPE, CytAssist and Xenium labels. They are selected illustrations, not a representative sample or a new quality assessment. Each thumbnail comes from a released package, with source hashes and display details in preview provenance. The visual_preview Dataset Viewer configuration pairs tissue thumbnails with the package's existing alignment-QC graphic.
Full preview gallery · Usage guide · Schema · Ontology mapping · Known issues · Reuse and citation
Access
HESRT is public. No sign-in, access request or form is needed: the catalog and every sample package can be downloaded directly, in a browser or with huggingface_hub. The maintainers receive no information about who downloads the data. The original source-specific data-use terms still apply.
Start with a 3.2 MB sample
Python 3.11+. Download the current example tools; they resolve the pinned data release 2026-09-17-v1.6 to a single commit, verify checksums, extract to disk and open the matrix in backed mode.
python -m pip install "huggingface_hub>=0.34,<2"
python -c "from huggingface_hub import snapshot_download; snapshot_download('Biogod/HESRT', repo_type='dataset', revision='main', allow_patterns=['examples/*'], local_dir='hesrt_tools', max_workers=4)"
python -m pip install -r hesrt_tools/examples/requirements.txt
python hesrt_tools/examples/quickstart.py --output hesrt_demo
This loads GSM8915497 / GSE294669, verifies every package member, and reports matrix dimensions, coordinate shape and image format. For filtering, complete-study downloads, local verification and evaluation-split examples, see the usage guide.
Browse and filter
from huggingface_hub import HfApi, hf_hub_download
import pandas as pd
revision = HfApi().dataset_info(
"Biogod/HESRT", revision="2026-09-17-v1.6"
).sha
catalog = pd.read_parquet(hf_hub_download(
"Biogod/HESRT", "releases/2026-09-17/catalog.parquet",
repo_type="dataset", revision=revision
))
human = catalog.loc[catalog.organism.eq("Homo sapiens")]
print(human[["gsm_id", "tissue", "technology", "n_obs", "archive_bytes"]].head())
The native Viewer has three configurations: reviewed_catalog (4,682 rows, 96 columns), studies (530 rows), and visual_preview (eight examples). These are lightweight indexes and previews, not streamed full-resolution matrices. reviewed is an inventory split, not a train/test assignment.
Composition
| Exact catalog label | Samples |
|---|---|
| Homo sapiens | 2,829 |
| Mus musculus | 1,651 |
| 10x Genomics Visium | 4,135 |
| Spatial Transcriptomics | 267 |
| 10x Genomics Visium for FFPE | 108 |
| 10x Genomics Visium HD | 61 |
| 10x Genomics Visium CytAssist | 41 |
| 10x Genomics Xenium In Situ | 8 |
Technology and tissue labels are source-derived. Labels can be heterogeneous, and null disease values mean unknown. The counts above use exact catalog labels; related technologies are not silently merged.
Ontology harmonization
The catalog now includes a conservative machine-readable ontology layer while preserving every original metadata field. Organisms map to NCBI Taxonomy; animal anatomy maps to UBERON; plant anatomy maps to Plant Ontology; disease maps to MONDO. No fuzzy match is accepted automatically.
Current coverage is 4,679/4,682 organism records, 3,021/4,682 tissue labels, and 1,893/2,398 non-null disease labels. A further 105 disease labels are explicitly classified as control/reference/non-disease states rather than being forced into MONDO. Compound tumor/specimen phrases that do not identify an ontology term with sufficient confidence stay unresolved.
Use *_ontology_status and *_ontology_match_type to distinguish exact mappings, source-validated aliases, controls, ambiguity and unresolved values. See the ontology mapping protocol and audit.
Package contents
GSM....tar.zst
spatial.h5ad Expression matrix and spatial coordinates
wsi.tif Selected tissue image; inspect actual format
metadata.json Source-associated sample metadata
metadata.normalized.json Normalized values, raw fields and statuses
provenance.json Source and processing provenance
review.json Recorded visual-review decision
alignment_qc.png Existing QC graphic, when available
alignment_strict_qc.png Additional QC graphic, when available
manifest.json Per-member sizes and SHA256 hashes
Expression/image binaries are unchanged by lossless packaging of the selected standardized artifacts. Release 2026-09-17-v1.5 replaced 12 packages and withdrew 6 after every released value was compared with the GEO deposit; the replaced packages store coordinates differently and have no QC graphic. Release 2026-09-17-v1.6 withdrew 9 more packages whose spots do not sit on the tissue in the image (see known issues). HESRT does not claim that every X matrix contains source-verified raw UMI counts. A release-wide numerical audit identified eight samples whose X matrices contain clear non-integer values: GSM7781044 (GSE243225) and GSM8243007–GSM8243013 (GSE266244). These source-defined matrices are retained as deposited/standardized rather than reverse-engineered into synthetic counts. Analyses that require integer raw counts should exclude or source-verify these eight samples. The remaining matrices are integer-typed or numerically integer-like in the audit, but that alone is not proof of raw-count provenance. Coordinate frame, units and expression representation should be interpreted using provenance. The name wsi.tif does not guarantee a TIFF file, a specific stain, or a full-resolution whole-slide scan.
Release files
The immutable release namespace is releases/2026-09-17/. Sample catalog and CSV fallback support selective download. Study index, schema, metadata coverage, ontology sidecar, ontology mapping summary, package manifest, SHA256SUMS, and release record provide machine-readable provenance. Prior repository paths remain intact.
For evaluation, keep studies and shared content together, resolve donor/cohort overlap and freeze the exact revision. The provided split script is an illustrative leakage-aware starting point, not an official benchmark protocol.
Related resources
HESRT is the human-reviewed H&E-paired collection produced by the earlier SpatialDataAgent pipeline. Its samples are also integrated into SpatialDataAgent-DB (more than 12,000 samples, most HESRT samples among them after deduplication; see its card for the current release), which uses a different per-sample layout and its own access policy. Do not concatenate the two collections without resolving overlap. The public SpatialDataAgent-DB catalog and the spatial-data-agent-db toolkit support search and download.
Reuse and citation
Underlying source materials retain their source-specific terms; no blanket redistribution license is asserted. Cite the source GEO accessions/publications and HESRT release 2026-09-17-v1.6, recording its resolved Hub commit. See reuse and citation and release notes. This resource is intended for research, not clinical decision making.