10x Xenium
Mouse brain
GSM9304331
silver Interactive viewer No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 20480, 14298), (1, 10240, 7149), (1, 5120, 3574), (1, 2560, 1787), (1, 1280, 893)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (20309, 14145), (10154, 7072), (5077, 3536), (2538, 1768), (1269, 884)
│ └── 'nucleus_labels': DataTree[yx] (20301, 14136), (10150, 7068), (5075, 3534), (2537, 1767), (1268, 883)
├── Points
│ └── 'transcripts': DataFrame with shape: (20132532, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (104906, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (104906, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (108067, 2) (2D shapes)
└── Tables
└── 'table': AnnData (104906, 347)
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("y31Pc89vb3sPrMj3") # 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/y31Pc89vb3sPrMj3
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid y31Pc89vb3sPrMj3 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["y31Pc89vb3sPrMj30000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- brain
- Modality
- RNA
- Observations
- 104,906
- Transcripts
- 20,132,532
- Tier
- silver
- Size
- 1.2 GB
- Sample ID
- GSM9304331
- License
- unknown
- Published
- Aug 12, 2026
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB