10x Xenium
Rat kidney
GSM9866598
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 34116, 51183), (1, 17058, 25591), (1, 8529, 12795), (1, 4264, 6397), (1, 2132, 3198)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (30752, 50731), (15376, 25365), (7688, 12682), (3844, 6341), (1922, 3170)
│ └── 'nucleus_labels': DataTree[yx] (30707, 50685), (15353, 25342), (7676, 12671), (3838, 6335), (1919, 3167)
├── Points
│ └── 'transcripts': DataFrame with shape: (48806115, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (347622, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (347622, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (347622, 2) (2D shapes)
└── Tables
└── 'table': AnnData (347622, 50)
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("icN0CKaKLDkdF9C70000")
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("icN0CKaKLDkdF9C7") # 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 icN0CKaKLDkdF9C70000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/icN0CKaKLDkdF9C7
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid icN0CKaKLDkdF9C7License: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- rat
- Tissue
- kidney
- Modality
- RNA
- Observations (cells)
- 347,622
- Transcripts
- 48,806,115
- Tier
- bronze
- Size
- 4.1 GB
- Sample ID
- GSM9866598
- License
- NCBI GEO policy
- Published
- Jul 10, 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