10x Xenium
Human kidney
GSM9210728
bronze Interactive viewer anti-neutrophil cytoplasmic antibody-associated vasculitis Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 20507, 14304), (1, 10253, 7152), (1, 5126, 3576), (1, 2563, 1788), (1, 1281, 894)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (20072, 13638), (10036, 6819), (5018, 3409), (2509, 1704), (1254, 852)
│ └── 'nucleus_labels': DataTree[yx] (18913, 12500), (9456, 6250), (4728, 3125), (2364, 1562), (1182, 781)
├── Points
│ └── 'transcripts': DataFrame with shape: (5804143, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (41251, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (41251, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (41192, 2) (2D shapes)
└── Tables
└── 'table': AnnData (41251, 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("dKcT7MwGFgz6GRVT0000")
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("dKcT7MwGFgz6GRVT") # 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 dKcT7MwGFgz6GRVT0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/dKcT7MwGFgz6GRVT
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid dKcT7MwGFgz6GRVTLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- kidney
- Condition
- anti-neutrophil cytoplasmic antibody-associated vasculitis
- Modality
- RNA
- Observations (cells)
- 41,251
- Transcripts
- 5,804,143
- Tier
- bronze
- Size
- 563 MB
- Sample ID
- GSM9210728
- 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