Visium
Human mucosa
GSM8283904
bronze Interactive viewer H&E head and neck squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8283904_P5736_hires_image': DataArray[cyx] (3, 2000, 1931)
│ └── 'GSM8283904_P5736_lowres_image': DataArray[cyx] (3, 600, 579)
├── Shapes
│ └── 'GSM8283904_P5736': GeoDataFrame shape: (4992, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4992, 36634)
with coordinate systems:
▸ 'GSM8283904_P5736', with elements:
GSM8283904_P5736_hires_image (Images), GSM8283904_P5736_lowres_image (Images), GSM8283904_P5736 (Shapes)
▸ 'GSM8283904_P5736_downscaled_hires', with elements:
GSM8283904_P5736_hires_image (Images), GSM8283904_P5736 (Shapes)
▸ 'GSM8283904_P5736_downscaled_lowres', with elements:
GSM8283904_P5736_lowres_image (Images), GSM8283904_P5736 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("yh9TpLN4i07bnfHj0000")
ds.elements() # inspect without downloading
sdata = ds.to_sdata() # cached locally, reused
print(sdata) Python · lamindb
Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("yh9TpLN4i07bnfHj") # stem uid: Lamin resolves it to the latest version
sdata = artifact.load() # cache, then load into memory
group = artifact.open() # stream without downloading
path = artifact.cache() # sync into the local cache, returns the path Shell
# sddb client: download the .zarr into data/
sddb-cli download yh9TpLN4i07bnfHj0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/yh9TpLN4i07bnfHj
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid yh9TpLN4i07bnfHjLicense: NCBI GEO policy
Part of collection
Spatial transcriptomic analysis of tumor heterogeneity in HPV+ and HPV- Head and Neck Squamous Cell Carcinoma→ 26 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- mucosa
- Condition
- head and neck squamous cell carcinoma
- Modality
- RNA
- Observations (spots)
- 4,992
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 1,931 × 2,000 px
- mpp
- 3.681 µm/px
- Size
- 93.4 MB
- Sample ID
- GSM8283904
- License
- NCBI GEO policy
- Published
- Jun 24, 2026
Cite this dataset
doi.org/10.1038/s41588-026-02723-7 ↗ BibTeX
@article{Simkin_2026,
title = {Spatial analysis of head and neck cancer identifies two ecosystems with distinct modes of epithelial-to-mesenchymal transition},
volume = {58},
ISSN = {1546-1718},
url = {http://dx.doi.org/10.1038/s41588-026-02723-7},
DOI = {10.1038/s41588-026-02723-7},
number = {9},
journal = {Nature Genetics},
publisher = {Springer Science and Business Media LLC},
author = {Simkin, Dor and Barrett, Thomas F. and Zhang, Lingling and Moore, Michael J. and Greenwald, Alissa C. and Galili, Noam and Mints, Michael and Ramadan, Salma and Yu, Victoria and Mullins, Riley D. Z. and Zaretsky, Jesse and Bischoff, Porter and Adkins, Douglas and Thorstad, Wade L. and Karam, Sana D. and Paniello, Randall C. and Rich, Jason T. and Jackson, Ryan S. and Pipkorn, Patrik and Zolkind, Paul A. and Peng, Guangyong and Harbison, R. Alex and Chernock, Rebecca and Parikh, Anuraag S. and Puram, Sidharth V. and Tirosh, Itay},
year = {2026},
month = Aug,
pages = {2240–2253}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB