10x Xenium
Human brain
GSM8672828
bronze Interactive viewer atypical teratoid rhabdoid tumor Provisional
print(sdata)
SpatialData object
├── Labels
│ ├── 'cell_labels': DataTree[yx] (8083, 14583), (4041, 7291), (2020, 3645), (1010, 1822), (505, 911)
│ └── 'nucleus_labels': DataTree[yx] (8036, 14537), (4018, 7268), (2009, 3634), (1004, 1817), (502, 908)
├── Points
│ └── 'transcripts': DataFrame with shape: (1408583, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (13178, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (13178, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (13178, 2) (2D shapes)
└── Tables
└── 'table': AnnData (13178, 475)
with coordinate systems:
▸ 'global', with elements:
cell_labels (Labels), nucleus_labels (Labels), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("Q3HCqe4rvspRDbV4") # 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 Load from the CLI
# one-shot: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/Q3HCqe4rvspRDbV4
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid Q3HCqe4rvspRDbV4 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["Q3HCqe4rvspRDbV40000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- brain
- Condition
- atypical teratoid rhabdoid tumor
- Modality
- RNA
- Observations
- 13,178
- Transcripts
- 1,408,583
- Tier
- bronze
- Size
- 71 MB
- Sample ID
- GSM8672828
- License
- unknown
- Published
- Jul 24, 2025
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB