10x Xenium
Rat kidney
GSM9866600
bronze Interactive viewer acute kidney failure Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 23941, 54010), (1, 11970, 27005), (1, 5985, 13502), (1, 2992, 6751), (1, 1496, 3375)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (22522, 51263), (11261, 25631), (5630, 12815), (2815, 6407), (1407, 3203)
│ └── 'nucleus_labels': DataTree[yx] (22477, 51216), (11238, 25608), (5619, 12804), (2809, 6402), (1404, 3201)
├── Points
│ └── 'transcripts': DataFrame with shape: (34018526, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (377793, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (377793, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (377793, 2) (2D shapes)
└── Tables
└── 'table': AnnData (377793, 50)
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("CnjYcEsHCUdjJ497") # 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/CnjYcEsHCUdjJ497
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid CnjYcEsHCUdjJ497 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["CnjYcEsHCUdjJ4970000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- rat
- Tissue
- kidney
- Condition
- acute kidney failure
- Modality
- RNA
- Observations
- 377,793
- Transcripts
- 34,018,526
- Tier
- bronze
- Size
- 3.0 GB
- Sample ID
- GSM9866600
- License
- unknown
- Published
- Jul 10, 2026
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB