10x Xenium
Rat kidney
GSM9866599
bronze Interactive viewer acute kidney failure Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 27333, 45504), (1, 13666, 22752), (1, 6833, 11376), (1, 3416, 5688), (1, 1708, 2844)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (26541, 44563), (13270, 22281), (6635, 11140), (3317, 5570), (1658, 2785)
│ └── 'nucleus_labels': DataTree[yx] (26495, 44517), (13247, 22258), (6623, 11129), (3311, 5564), (1655, 2782)
├── Points
│ └── 'transcripts': DataFrame with shape: (44631002, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (324796, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (324796, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (324796, 2) (2D shapes)
└── Tables
└── 'table': AnnData (324796, 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("CYBqvwquJHEGvRrZ") # 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/CYBqvwquJHEGvRrZ
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid CYBqvwquJHEGvRrZ Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["CYBqvwquJHEGvRrZ0000"])[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
- 324,796
- Transcripts
- 44,631,002
- Tier
- bronze
- Size
- 3.1 GB
- Sample ID
- GSM9866599
- 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