10x Xenium
Human brain
GSM9886366
silver Interactive viewer glioblastoma No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 27296, 19951), (1, 13648, 9975), (1, 6824, 4987), (1, 3412, 2493), (1, 1706, 1246)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (27253, 19887), (13626, 9943), (6813, 4971), (3406, 2485), (1703, 1242)
│ └── 'nucleus_labels': DataTree[yx] (27253, 19887), (13626, 9943), (6813, 4971), (3406, 2485), (1703, 1242)
├── Points
│ └── 'transcripts': DataFrame with shape: (10670227, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (27417, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (27417, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (27417, 2) (2D shapes)
└── Tables
└── 'table': AnnData (27417, 5101)
with coordinate systems:
▸ 'global', with elements:
morphology_mip (Images), 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("xIrBgyTq0Ry0mQp5") # 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/xIrBgyTq0Ry0mQp5
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid xIrBgyTq0Ry0mQp5 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["xIrBgyTq0Ry0mQp50000"])[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
- glioblastoma
- Modality
- RNA
- Observations
- 27,417
- Transcripts
- 10,670,227
- Tier
- silver
- Size
- 742 MB
- Sample ID
- GSM9886366
- License
- unknown
- Published
- Oct 1, 2026
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB