Visium

Human palatine tonsil

GSM8789933

bronze Interactive viewer H&E oropharynx squamous cell carcinoma Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'GSM8789933_ST2_hires_image': DataArray[cyx] (3, 1564, 2000)
│     └── 'GSM8789933_ST2_lowres_image': DataArray[cyx] (3, 469, 600)
├── Shapes
│     └── 'GSM8789933_ST2': GeoDataFrame shape: (4962, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (4962, 18085)
with coordinate systems:
    ▸ 'GSM8789933_ST2', with elements:
        GSM8789933_ST2_hires_image (Images), GSM8789933_ST2_lowres_image (Images), GSM8789933_ST2 (Shapes)
    ▸ 'GSM8789933_ST2_downscaled_hires', with elements:
        GSM8789933_ST2_hires_image (Images), GSM8789933_ST2 (Shapes)
    ▸ 'GSM8789933_ST2_downscaled_lowres', with elements:
        GSM8789933_ST2_lowres_image (Images), GSM8789933_ST2 (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("h9p40ugKEyGw4dNA0000")
ds.elements()          # inspect without downloading
sdata = ds.to_sdata()  # cached locally, reused
print(sdata)

Install (Python 3.12+) Docs →

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("h9p40ugKEyGw4dNA")   # 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

Install (Python 3.12+) Docs →

Shell

# sddb client: download the .zarr into data/
sddb-cli download h9p40ugKEyGw4dNA0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/h9p40ugKEyGw4dNA

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid h9p40ugKEyGw4dNA

Install (Python 3.12+) Docs →

License: NCBI GEO policy

View on Lamin ↗ Open in Vitessce ↗ Flag a data issue

Part of collection

Intratumoral spatiotemporal heterogeneity of HPV status in HPV-associated oropharyngeal squamous cell carcinoma with clinical record→

3 datasets · replicates

Metadata

Technology: Visium
Organism: human
Tissue: palatine tonsil
Condition: oropharynx squamous cell carcinoma
Modality: RNA
Observations (spots): 4,962
Tier: bronze
Chemistry: Visium v1
Magnification: other
Resolution: 2,000 × 1,564 px
mpp: 6.293 µm/px
Size: 86.2 MB
Sample ID: GSM8789933
License: NCBI GEO policy
Published: May 20, 2026

Cite this dataset

doi.org/10.1186/s12967-026-08082-5 ↗

BibTeX

@article{Ahn_2026,
  title = {Intratumoral spatiotemporal heterogeneity of HPV DNA status in HPV-associated oropharyngeal squamous cell carcinoma with clinical record},
  volume = {24},
  ISSN = {1479-5876},
  url = {http://dx.doi.org/10.1186/s12967-026-08082-5},
  DOI = {10.1186/s12967-026-08082-5},
  number = {1},
  journal = {Journal of Translational Medicine},
  publisher = {Springer Science and Business Media LLC},
  author = {Ahn, Bokyung and Park, Chae Won and Song, Joon Seon and Lee, Hee-Jin and Kim, Wonkyung and Lee, Yoon Se and Jung, Young Ho and Choi, Seung-Ho and Nam, Soon Yuhl and Kim, Sang Yoon and Oh, Ji-Hye and Kang, Young Gwang and Oh, Da Eun and Sung, Chang Ohk and Cho, Kyung-Ja},
  year = {2026},
  month = Apr
}

Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB