Datasets:
Request access to SpatialDataAgent-DB
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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SpatialDataAgent-DB
Left to right: H&E and GFAP from the same Visium section (GSM9721856), Xenium DAPI (GSM9301054), and a CosMx composite (GSM9372712). The GFAP panel displays all 3,416 recorded spots using the existing log1p preview values.
SpatialDataAgent-DB brings standardized spatial expression measurements, coordinates, matched tissue images, quality annotations and source evidence together in a versioned collection.
Complete, verified sample release. All files in the selected export inventory passed content verification. Use the v1.0.0-20261025 release tag for reproducible downloads.
| Selected source snapshot | Size |
|---|---|
| Samples | 12,163 |
| Spatial observations | 635,240,170 |
| Samples with images | 8,211 |
| Published study folders | 1,265 |
| SDA-All / HESRT samples | 7,777 / 4,386 |
The source is sda-unified-20261010-v3, including its applied deduplication. Spatial observations include spots, bins, cells and beads; they are not independent patients. This collection integrates SDA-All and HESRT records and should not be concatenated with the full HESRT release without checking overlap.
Explore the collection
Sample counts by platform, image availability, source collection and retained split (n = 12,163; source snapshot: sda-unified-20261010-v3).
The SDA-All Spatial Atlas is the companion exploration interface. The downloadable catalog provides one row per sample, with study, platform, organism, tissue, expression state, coordinate units, available images, registration, review, QC, content group and split. Study counts, sample counts and observation counts answer different questions.
The companion portal organizes metadata into Biology, Assay, Evidence and Provenance. This export also supplies source-bound atlas-sample-metadata.jsonl and atlas-study-metadata.jsonl: disease/condition, reported age and sex, available donor identifiers, publication links, study titles/designs and existing audit evidence. Missing values remain explicit; vocabulary, age units and organism labels have not been harmonized into ontologies or a resolved species count.
The portal's Metadata view supports linked distributions, cross-tabs, completeness and numeric ranges with sample or observation weighting. Those are exploration tools; this Dataset Card reports the full inventory without selecting a favorable subset.
| Platform | Samples |
|---|---|
| Visium | 6512 |
| Xenium | 1785 |
| ST (legacy) | 1098 |
| CosMx | 1092 |
| MERFISH/MERSCOPE | 463 |
| Slide-seq | 380 |
| Other | 299 |
| Visium HD | 223 |
| Stereo-seq | 208 |
| Molecular Cartography | 47 |
| DBiT-seq | 32 |
| BMK S1000 | 24 |
Access requirements
The public metadata catalog can be browsed without data access approval. Companion portal access is managed separately from Hugging Face access.
SpatialDataAgent-DB 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.
Sample format
catalog/
samples.parquet
samples.csv
studies.csv
schema.json
summary.json
atlas-sample-metadata.jsonl
atlas-study-metadata.jsonl
samples/<study>/<sample>/
spatial.h5ad
sample.json
image.tif # when available
provenance/
file-manifest.jsonl # added after the upload manifest is frozen
spatial.h5ad stores expression and observation coordinates. Keep original feature IDs, expression state and coordinate units when combining samples. image.tif is the selected tiled pyramidal image; sample.json carries its spatial-to-pixel transform, modality, registration and provenance. Original H5AD/TIFF contents are preserved. Historical machine paths in exported JSON are converted to source-reference:// identifiers; these identify provenance and are not download URLs.
Some ancillary segmentation and molecule records identify original source assets rather than supplying the assets themselves. Their presence in metadata does not imply the files are included in this upload.
Download the catalog and a sample
After access is approved:
from huggingface_hub import hf_hub_download
path = hf_hub_download(
repo_id="Biogod/SpatialDataAgent-DB",
repo_type="dataset",
filename="catalog/samples.parquet",
token=True,
)
The catalog's sample_dir column is the repository-relative sample directory. Use sample_dir + "/spatial.h5ad" for expression, sample_dir + "/sample.json" for metadata, and sample_dir + "/image.tif" only when has_image is true. These are downloadable repository paths; historical source-reference:// provenance identifiers are not.
After the full upload completes, for example:
import pandas as pd
from huggingface_hub import hf_hub_download
catalog = pd.read_parquet(path)
row = catalog.loc[catalog["gsm"] == "GSM9721856"].iloc[0]
expression_path = hf_hub_download(
repo_id="Biogod/SpatialDataAgent-DB",
repo_type="dataset",
filename=f"{row['sample_dir']}/spatial.h5ad",
token=True,
)
AnnData/Scanpy can read expression_path after download. Pin a completed release tag via the revision parameter for reproducibility.
Machine learning and streaming
This initial upload publishes full samples and their catalog. Streaming-ready expression/image training shards and a convenience SDK are planned follow-up outputs and are not claimed to be available in this release. Streaming the catalog alone does not stream the expression matrices.
Keep H&E, DAPI, other fluorescence and no-image profiles distinct. Unmeasured genes differ from measured zero expression; preserve feature panel masks and species-specific identifiers. Use only expression explicitly verified as counts when raw counts are required.
Splits and quality
Existing source-bound counts-capability checks cover 7,777 SDA-All samples: 7,336 VERIFIED, 24 UNRESOLVED and 417 ABSENT. These checks are not recorded for the 4,386 HESRT records, whose legacy integer/non-integer expression annotations remain distinct. These are capability annotations, not model accuracy or an all-sample human-review rate.
The retained source split has 9,249 training, 1,316 validation and 1,598 test samples. It uses the recorded series grouping. It does not prove donor independence across studies; content groups, aliases and known donor information require additional leakage checks for a particular benchmark.
QC annotations, expression verification, image registration and human review describe different checks. Not every sample has human review or a confirmed H&E image. Heuristic stain labels and unresolved units remain explicit in the catalog.
Version and provenance
Source snapshot: sda-unified-20261010-v3. Source catalog SHA256: 909c4ec50e71c636eadc7bf01a9479fef1b4fd480ac348dfea6b785e566c7bed.
Every uploaded measurement is checked against the source content hash and verified against the remote object metadata before integration. A release tag is created only after the entire selected file inventory passes final verification. Later collection cycles require a new source snapshot and are not silently mixed into this one.
Data use and source terms
Records retain their original study accessions, attribution and source-specific terms. This aggregation does not replace the original sources' permissions with a single permissive license. Consult the relevant source study before redistribution or reuse requiring additional permission. Contact the repository maintainers through Hugging Face for collection issues.
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