10x Xenium
Human brain
GSM9054425
bronze Interactive viewer ependymoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 23872, 25617), (1, 11936, 12808), (1, 5968, 6404), (1, 2984, 3202), (1, 1492, 1601)
├── Points
│ └── 'transcripts': DataFrame with shape: (18580337, 10) (3D points)
├── Shapes
│ └── 'cell_circles': GeoDataFrame shape: (103335, 2) (2D shapes)
└── Tables
└── 'table': AnnData (103335, 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("AgFFC7wbTNs5LkZS0000")
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("AgFFC7wbTNs5LkZS") # 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 AgFFC7wbTNs5LkZS0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/AgFFC7wbTNs5LkZS
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid AgFFC7wbTNs5LkZSLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- brain
- Condition
- ependymoma
- Modality
- RNA
- Observations (cells)
- 103,335
- Transcripts
- 18,580,337
- Tier
- bronze
- Size
- 1.2 GB
- Sample ID
- GSM9054425
- License
- NCBI GEO policy
- Published
- Dec 9, 2025
Cite this dataset
doi.org/10.1038/s41586-026-10214-2 ↗ BibTeX
@article{geo:GSM9054425,
doi = {10.1038/s41586-026-10214-2},
title = {GSM9054425},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB