10x Xenium
Human brain
GSM9054461
bronze Interactive viewer ependymoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 20482, 14293), (1, 10241, 7146), (1, 5120, 3573), (1, 2560, 1786), (1, 1280, 893)
├── Points
│ └── 'transcripts': DataFrame with shape: (10586358, 11) (3D points)
├── Shapes
│ └── 'cell_circles': GeoDataFrame shape: (40976, 2) (2D shapes)
└── Tables
└── 'table': AnnData (40976, 366)
with coordinate systems:
▸ 'global', with elements:
morphology_mip (Images), transcripts (Points), cell_circles (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("VDViGKExmEw6jlzW0000")
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("VDViGKExmEw6jlzW") # 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 VDViGKExmEw6jlzW0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/VDViGKExmEw6jlzW
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid VDViGKExmEw6jlzWLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- brain
- Condition
- ependymoma
- Modality
- RNA
- Observations (cells)
- 40,976
- Transcripts
- 10,586,358
- Tier
- bronze
- Size
- 728 MB
- Sample ID
- GSM9054461
- License
- NCBI GEO policy
- Published
- Dec 9, 2025
Cite this dataset
doi.org/10.1038/s41586-026-10214-2 ↗ BibTeX
@article{geo:GSM9054461,
doi = {10.1038/s41586-026-10214-2},
title = {GSM9054461},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB