10x Xenium
Human kidney
GSM9210729
bronze Interactive viewer anti-neutrophil cytoplasmic antibody-associated vasculitis Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 13725, 22811), (1, 6862, 11405), (1, 3431, 5702), (1, 1715, 2851), (1, 857, 1425)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (13684, 22729), (6842, 11364), (3421, 5682), (1710, 2841), (855, 1420)
│ └── 'nucleus_labels': DataTree[yx] (13505, 21602), (6752, 10801), (3376, 5400), (1688, 2700), (844, 1350)
├── Points
│ └── 'transcripts': DataFrame with shape: (3767432, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (26648, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (26648, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (26504, 2) (2D shapes)
└── Tables
└── 'table': AnnData (26648, 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("mv6fU7wRDHoMkjEc") # 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/mv6fU7wRDHoMkjEc
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid mv6fU7wRDHoMkjEc Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["mv6fU7wRDHoMkjEc0000"])[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
- 26,648
- Transcripts
- 3,767,432
- Tier
- bronze
- Size
- 445 MB
- Sample ID
- GSM9210729
- 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