10x Xenium
Human kidney
GSM9844161
silver Interactive viewer acute tubulointerstitial nephritis No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 6949, 34119), (1, 3474, 17059), (1, 1737, 8529), (1, 868, 4264), (1, 434, 2132)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (6756, 33675), (3378, 16837), (1689, 8418), (844, 4209), (422, 2104)
│ └── 'nucleus_labels': DataTree[yx] (5915, 33671), (2957, 16835), (1478, 8417), (739, 4208), (369, 2104)
├── Points
│ └── 'transcripts': DataFrame with shape: (1687665, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (21387, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (21387, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (21419, 2) (2D shapes)
└── Tables
└── 'table': AnnData (21387, 5101)
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("LBfQ9z6MgVp7oZFc0000")
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("LBfQ9z6MgVp7oZFc") # 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 LBfQ9z6MgVp7oZFc0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/LBfQ9z6MgVp7oZFc
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid LBfQ9z6MgVp7oZFcLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- kidney
- Condition
- acute tubulointerstitial nephritis
- Modality
- RNA
- Observations (cells)
- 21,387
- Transcripts
- 1,687,665
- Tier
- silver
- Size
- 228 MB
- Sample ID
- GSM9844161
- License
- NCBI GEO policy
- Published
- Aug 18, 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