10x Xenium
Human urinary bladder
GSM9625559
silver Interactive viewer urinary bladder carcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 13727, 22786), (1, 6863, 11393), (1, 3431, 5696), (1, 1715, 2848), (1, 857, 1424)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (13472, 20009), (6736, 10004), (3368, 5002), (1684, 2501), (842, 1250)
│ └── 'nucleus_labels': DataTree[yx] (13458, 19985), (6729, 9992), (3364, 4996), (1682, 2498), (841, 1249)
├── Points
│ └── 'transcripts': DataFrame with shape: (36624855, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (29816, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (29816, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (29880, 2) (2D shapes)
└── Tables
└── 'table': AnnData (29816, 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) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("VFADvU9JcZwYGckg0000")
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("VFADvU9JcZwYGckg") # 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 VFADvU9JcZwYGckg0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/VFADvU9JcZwYGckg
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid VFADvU9JcZwYGckgLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- urinary bladder
- Condition
- urinary bladder carcinoma
- Modality
- RNA
- Observations (cells)
- 29,816
- Transcripts
- 36,624,855
- Tier
- silver
- Size
- 1.1 GB
- Sample ID
- GSM9625559
- License
- NCBI GEO policy
- Published
- May 5, 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