10x Xenium
Human pleura
GSM9654052
bronze Interactive viewer pleural mesothelioma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 13748, 28480), (1, 6874, 14240), (1, 3437, 7120), (1, 1718, 3560), (1, 859, 1780)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (13459, 28097), (6729, 14048), (3364, 7024), (1682, 3512), (841, 1756)
│ └── 'nucleus_labels': DataTree[yx] (12884, 28051), (6442, 14025), (3221, 7012), (1610, 3506), (805, 1753)
├── Points
│ └── 'transcripts': DataFrame with shape: (22014264, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (65607, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (65607, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (67449, 2) (2D shapes)
└── Tables
└── 'table': AnnData (65607, 477)
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("65wrc2XFWIwdqRQi") # 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/65wrc2XFWIwdqRQi
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 65wrc2XFWIwdqRQi Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["65wrc2XFWIwdqRQi0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- pleura
- Condition
- pleural mesothelioma
- Modality
- RNA
- Observations
- 65,607
- Transcripts
- 22,014,264
- Tier
- bronze
- Size
- 1.1 GB
- Sample ID
- GSM9654052
- License
- unknown
- Published
- Apr 8, 2026
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB