10x Xenium
Human urinary bladder
GSM9625561
silver Interactive viewer urinary bladder carcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 13735, 19970), (1, 6867, 9985), (1, 3433, 4992), (1, 1716, 2496), (1, 858, 1248)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (13319, 18889), (6659, 9444), (3329, 4722), (1664, 2361), (832, 1180)
│ └── 'nucleus_labels': DataTree[yx] (12734, 18837), (6367, 9418), (3183, 4709), (1591, 2354), (795, 1177)
├── Points
│ └── 'transcripts': DataFrame with shape: (39300520, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (42825, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (42825, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (42787, 2) (2D shapes)
└── Tables
└── 'table': AnnData (42825, 5001)
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) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("kWTEYp5bdmFtd48y") # 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 Load from the CLI
# one-shot: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/kWTEYp5bdmFtd48y
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid kWTEYp5bdmFtd48y Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["kWTEYp5bdmFtd48y0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- urinary bladder
- Condition
- urinary bladder carcinoma
- Modality
- RNA
- Observations
- 42,825
- Transcripts
- 39,300,520
- Tier
- silver
- Size
- 1.1 GB
- Sample ID
- GSM9625561
- License
- unknown
- Published
- May 5, 2026
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB