10x Xenium
Human kidney
GSM9210731
bronze Interactive viewer anti-neutrophil cytoplasmic antibody-associated vasculitis Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 20504, 28471), (1, 10252, 14235), (1, 5126, 7117), (1, 2563, 3558), (1, 1281, 1779)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (20303, 28308), (10151, 14154), (5075, 7077), (2537, 3538), (1268, 1769)
│ └── 'nucleus_labels': DataTree[yx] (20276, 27635), (10138, 13817), (5069, 6908), (2534, 3454), (1267, 1727)
├── Points
│ └── 'transcripts': DataFrame with shape: (6358263, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (54143, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (54143, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (54035, 2) (2D shapes)
└── Tables
└── 'table': AnnData (54143, 480)
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("mhUVgmN7Np9ERjpD") # 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/mhUVgmN7Np9ERjpD
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid mhUVgmN7Np9ERjpD Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["mhUVgmN7Np9ERjpD0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- kidney
- Condition
- anti-neutrophil cytoplasmic antibody-associated vasculitis
- Modality
- RNA
- Observations
- 54,143
- Transcripts
- 6,358,263
- Tier
- bronze
- Size
- 796 MB
- Sample ID
- GSM9210731
- License
- unknown
- Published
- May 5, 2026
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB