Request access to HESRT
Manual review. Use a verified institutional email added to your Hugging Face account, as a primary or additional email. No primary-email change is required.
Access requests are reviewed manually. Use an email address issued by your institution that has been added and verified in your Hugging Face account. It may be your primary email or an additional email; you do not need to change your primary email.
Hugging Face automatically shares your primary email with the maintainers. If that is already your institutional address, you may use it for this request. If your institutional address is an additional email, enter it in the additional institutional email field below; this is required in that case.
A personal primary email, such as Gmail, does not by itself disqualify your request. The institutional contact address used for review must be issued by your institution. Personal providers such as Gmail, Hotmail/Outlook.com, Yahoo, iCloud, QQ, 163/126 and Proton Mail cannot serve as that institutional contact address. Institution-controlled domains hosted through Google Workspace or Microsoft 365 are acceptable.
Provide your full name, official institution and department, and intended research use. Each user must apply through their own account and wait for manual approval. Original source-specific data-use terms and attribution requirements remain applicable.
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HESRT
Human-reviewed, accession-level spatial-omics artifacts with tissue images, expression matrices and source provenance.
| Samples (GSMs) | Studies (GSEs) | Expression observations | Compressed packages |
|---|---|---|---|
| 4,468 | 507 | 37,054,005 | 413.94 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 647.72 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 nine examples span human cortex, mouse brain, spinal cord, pancreas, Visium HD, FFPE, CytAssist, legacy spatial transcriptomics 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 requirements
HESRT files require manual access approval and a verified institutional email registered in your Hugging Face account. The institutional email may be your primary or an additional email. You do not need to change your primary email.
- Add and verify the email address issued by your university, research institute, hospital or company in your existing Hugging Face account. It may remain an additional email.
- Hugging Face automatically shares your primary email with the maintainers. If your primary email is already your institutional address, you may use it and leave the additional-email field blank. Otherwise, enter your verified institutional address in the additional institutional email field. A personal primary email such as Gmail may remain unchanged.
- Complete the form with your full name, official institution and department, research purpose and commercial involvement. Confirm that the institutional email used for the request has been added and verified in the same Hugging Face account.
- Wait for manual review before downloading files. Each person must apply using their own account.
The institutional contact address must be issued by your institution. Gmail/Googlemail, Hotmail/Outlook.com, Yahoo, iCloud, QQ, 163/126 and Proton Mail addresses cannot serve as the institutional contact, but a personal address may remain your Hugging Face primary email. Official institutional domains hosted through Google Workspace or Microsoft 365 are eligible; an unfamiliar or personal custom domain is not automatically institutional. Institutional domains are not limited to .edu.
Requests without a verified institutional address registered in the same Hugging Face account, or with unverifiable affiliations, will not be approved. This access policy does not replace the original source-specific data-use terms.
Once access is approved, sign in locally with hf auth login. The examples below use your saved Hugging Face credentials.
Start with a 3.2 MB sample
Python 3.11+, after access approval. Download the current example tools; they resolve the pinned data release 2026-09-17-v1.3 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"
hf auth login
python -c "from huggingface_hub import snapshot_download; snapshot_download('Biogod/HESRT', repo_type='dataset', revision='main', allow_patterns=['examples/*'], local_dir='hesrt_tools', token=True, 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(token=True).dataset_info(
"Biogod/HESRT", revision="2026-09-17-v1.3"
).sha
catalog = pd.read_parquet(hf_hub_download(
"Biogod/HESRT", "releases/2026-09-17/catalog.parquet",
repo_type="dataset", revision=revision, token=True
))
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 (4,468 rows, 96 columns), studies (507 rows), and visual_preview (nine 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 | 2,736 |
| Mus musculus | 1,533 |
| 10x Genomics Visium | 3,943 |
| Spatial Transcriptomics | 267 |
| 10x Genomics Visium for FFPE | 108 |
| 10x Genomics Visium HD | 57 |
| 10x Genomics Visium CytAssist | 22 |
| 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 4,468/4,468 organism records, 2,844/4,468 tissue labels, and 1,800/2,304 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. 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.
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-v1.3, recording its resolved Hub commit. See reuse and citation and release notes. This resource is intended for research, not clinical decision making.
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