10x Xenium
Rat kidney
GSM9866599
bronze Interactive viewer acute kidney failure Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 27333, 45504), (1, 13666, 22752), (1, 6833, 11376), (1, 3416, 5688), (1, 1708, 2844)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (26541, 44563), (13270, 22281), (6635, 11140), (3317, 5570), (1658, 2785)
│ └── 'nucleus_labels': DataTree[yx] (26495, 44517), (13247, 22258), (6623, 11129), (3311, 5564), (1655, 2782)
├── Points
│ └── 'transcripts': DataFrame with shape: (44631002, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (324796, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (324796, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (324796, 2) (2D shapes)
└── Tables
└── 'table': AnnData (324796, 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("CYBqvwquJHEGvRrZ0000")
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("CYBqvwquJHEGvRrZ") # 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 CYBqvwquJHEGvRrZ0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/CYBqvwquJHEGvRrZ
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid CYBqvwquJHEGvRrZLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- rat
- Tissue
- kidney
- Condition
- acute kidney failure
- Modality
- RNA
- Observations (cells)
- 324,796
- Transcripts
- 44,631,002
- Tier
- bronze
- Size
- 3.4 GB
- Sample ID
- GSM9866599
- 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