10x Xenium
Human urinary bladder
GSM9625562
silver Interactive viewer urinary bladder carcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 13742, 19960), (1, 6871, 9980), (1, 3435, 4990), (1, 1717, 2495), (1, 858, 1247)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (11324, 19417), (5662, 9708), (2831, 4854), (1415, 2427), (707, 1213)
│ └── 'nucleus_labels': DataTree[yx] (11294, 19380), (5647, 9690), (2823, 4845), (1411, 2422), (705, 1211)
├── Points
│ └── 'transcripts': DataFrame with shape: (10585569, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (16587, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (16587, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (16142, 2) (2D shapes)
└── Tables
└── 'table': AnnData (16587, 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("c21lLxjvmd9t7Oth") # 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/c21lLxjvmd9t7Oth
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid c21lLxjvmd9t7Oth Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["c21lLxjvmd9t7Oth0000"])[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
- 16,587
- Transcripts
- 10,585,569
- Tier
- silver
- Size
- 437 MB
- Sample ID
- GSM9625562
- 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