10x Xenium
Mouse brain
GSM9304336
silver Interactive viewer No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 20486, 31272), (1, 10243, 15636), (1, 5121, 7818), (1, 2560, 3909), (1, 1280, 1954)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (20485, 29884), (10242, 14942), (5121, 7471), (2560, 3735), (1280, 1867)
│ └── 'nucleus_labels': DataTree[yx] (20457, 29876), (10228, 14938), (5114, 7469), (2557, 3734), (1278, 1867)
├── Points
│ └── 'transcripts': DataFrame with shape: (30922491, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (115479, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (115479, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (115534, 2) (2D shapes)
└── Tables
└── 'table': AnnData (115479, 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("YNU3ERme6ajZbm9K") # 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/YNU3ERme6ajZbm9K
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid YNU3ERme6ajZbm9K Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["YNU3ERme6ajZbm9K0000"])[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
- 115,479
- Transcripts
- 30,922,491
- Tier
- silver
- Size
- 1.9 GB
- Sample ID
- GSM9304336
- 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