Visium

Mouse brain

GSM8674928

bronze Interactive viewer H&E glioblastoma Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'GSM8674928_TNP_mouse_hires_image': DataArray[cyx] (3, 1995, 2000)
│     └── 'GSM8674928_TNP_mouse_lowres_image': DataArray[cyx] (3, 599, 600)
├── Shapes
│     └── 'GSM8674928_TNP_mouse': GeoDataFrame shape: (2116, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (2116, 31253)
with coordinate systems:
    ▸ 'GSM8674928_TNP_mouse', with elements:
        GSM8674928_TNP_mouse_hires_image (Images), GSM8674928_TNP_mouse_lowres_image (Images), GSM8674928_TNP_mouse (Shapes)
    ▸ 'GSM8674928_TNP_mouse_downscaled_hires', with elements:
        GSM8674928_TNP_mouse_hires_image (Images), GSM8674928_TNP_mouse (Shapes)
    ▸ 'GSM8674928_TNP_mouse_downscaled_lowres', with elements:
        GSM8674928_TNP_mouse_lowres_image (Images), GSM8674928_TNP_mouse (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("6cXrwLGhSl1tZemd0000")
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("6cXrwLGhSl1tZemd")   # 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 6cXrwLGhSl1tZemd0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/6cXrwLGhSl1tZemd

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 6cXrwLGhSl1tZemd

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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

Part of collection

Spatially resolved chimeric analysis reveals extracellular CKB-mediated ATP uptake at the glioma-astrocyte invasive front→

4 datasets · other

Metadata

Technology: Visium
Organism: mouse
Tissue: brain
Condition: glioblastoma
Modality: RNA
Observations (spots): 2,116
Tier: bronze
Chemistry: Visium v1
Magnification: other
Resolution: 2,000 × 1,995 px
mpp: 3.317 µm/px
Size: 38.7 MB
Sample ID: GSM8674928
License: NCBI GEO policy
Published: Jun 30, 2025

Cite this dataset

doi.org/10.1126/sciadv.adv5673 ↗

BibTeX

@article{Yang_2025,
  title = {Glioblastoma exploits ATP from leading-edge astrocytes to fuel its infiltrative growth revealed by spatially resolved chimeric analysis},
  volume = {11},
  ISSN = {2375-2548},
  url = {http://dx.doi.org/10.1126/sciadv.adv5673},
  DOI = {10.1126/sciadv.adv5673},
  number = {39},
  journal = {Science Advances},
  publisher = {American Association for the Advancement of Science (AAAS)},
  author = {Yang, Gaoxia and Niu, Xiaodong and Gan, Jieying and Yu, Tianping and Li, Menghan and Xiao, Peng and Zhang, Rui and He, Ping and Yang, Yuan and Cui, Yi and Huang, Xiaoyi and Wang, Yuan and Mao, Qing and Zhou, Ran},
  year = {2025},
  month = Sept
}

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