10x Xenium
Human kidney
GSM9210733
bronze Interactive viewer anti-neutrophil cytoplasmic antibody-associated vasculitis Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 20545, 28496), (1, 10272, 14248), (1, 5136, 7124), (1, 2568, 3562), (1, 1284, 1781)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (20365, 28170), (10182, 14085), (5091, 7042), (2545, 3521), (1272, 1760)
│ └── 'nucleus_labels': DataTree[yx] (17969, 28120), (8984, 14060), (4492, 7030), (2246, 3515), (1123, 1757)
├── Points
│ └── 'transcripts': DataFrame with shape: (6854540, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (50676, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (50676, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (50466, 2) (2D shapes)
└── Tables
└── 'table': AnnData (50676, 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) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("L5mkoJJzSphZlN9B0000")
ds.elements() # inspect without downloading
sdata = ds.to_sdata() # cached locally, reused
print(sdata) Python · lamindb
Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("L5mkoJJzSphZlN9B") # stem uid: Lamin resolves it to the 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 Shell
# sddb client: download the .zarr into data/
sddb-cli download L5mkoJJzSphZlN9B0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/L5mkoJJzSphZlN9B
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid L5mkoJJzSphZlN9BLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- kidney
- Condition
- anti-neutrophil cytoplasmic antibody-associated vasculitis
- Modality
- RNA
- Observations (cells)
- 50,676
- Transcripts
- 6,854,540
- Tier
- bronze
- Size
- 911 MB
- Sample ID
- GSM9210733
- License
- NCBI GEO policy
- Published
- May 5, 2026
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB