Visium

Mouse brain

GSM9613870

silver Interactive viewer H&E stroke disorder ✓ Verified publication

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'GSM9613870_PTS_LGG_full_image': DataTree[cyx] (3, 3000, 3000), (3, 1500, 1500), (3, 750, 750), (3, 375, 375), (3, 187, 187)
│     ├── 'GSM9613870_PTS_LGG_hires_image': DataArray[cyx] (3, 2000, 2000)
│     └── 'GSM9613870_PTS_LGG_lowres_image': DataArray[cyx] (3, 600, 600)
├── Shapes
│     └── 'GSM9613870_PTS_LGG': GeoDataFrame shape: (2206, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (2206, 19465)
with coordinate systems:
    ▸ 'GSM9613870_PTS_LGG', with elements:
        GSM9613870_PTS_LGG_full_image (Images), GSM9613870_PTS_LGG_hires_image (Images), GSM9613870_PTS_LGG_lowres_image (Images), GSM9613870_PTS_LGG (Shapes)
    ▸ 'GSM9613870_PTS_LGG_downscaled_hires', with elements:
        GSM9613870_PTS_LGG_hires_image (Images), GSM9613870_PTS_LGG (Shapes)
    ▸ 'GSM9613870_PTS_LGG_downscaled_lowres', with elements:
        GSM9613870_PTS_LGG_lowres_image (Images), GSM9613870_PTS_LGG (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("7UOzXvxCina3gqwR0000")
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("7UOzXvxCina3gqwR")   # 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 7UOzXvxCina3gqwR0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/7UOzXvxCina3gqwR

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 7UOzXvxCina3gqwR

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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Metadata

Technology: Visium
Organism: mouse
Tissue: brain
Condition: stroke disorder
Modality: RNA
Observations (spots): 2,206
Tier: silver
Chemistry: Visium CytAssist v2
Resolution: 3,000 × 3,000 px
mpp: 3.655 µm/px
Size: 54.3 MB
Sample ID: GSM9613870
License: NCBI GEO policy
Published: Jun 29, 2026

Cite this dataset

doi.org/10.1038/s43018-026-01238-8 ↗

BibTeX

@article{Ye_2026,
  title = {Stroke drives glioma progression through the emergence of tumor-associated astrocytes with reduced Ca2+ activity},
  ISSN = {2662-1347},
  url = {http://dx.doi.org/10.1038/s43018-026-01238-8},
  DOI = {10.1038/s43018-026-01238-8},
  journal = {Nature Cancer},
  publisher = {Springer Science and Business Media LLC},
  author = {Ye, Qi and Madamba, Christine and Woo, Junsung and Choy, Tiffany J. and Wheeler, Kate F. and Zhan, Jiangshan and Cristobal, Carlo D. and Spjut, Catalina and Shin, Donghui and Jo, Juyeon and Ailani, Roshan R. and Smith, Joshua and Latha, Khatri and Harmanci, Akdes Serin and Yalamanchili, Hari Krishna and Gallo, Marco and Yun, Kyuson and Reshetnyak, Yana K. and Kim, Eunhee and Kim, Yongsoo and Rao, Ganesh and Deneen, Benjamin and Lee, Hyun Kyoung},
  year = {2026},
  month = Sept
}

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