10x Xenium
Human pleura
GSM9654051
bronze Interactive viewer pleural mesothelioma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 20508, 19995), (1, 10254, 9997), (1, 5127, 4998), (1, 2563, 2499), (1, 1281, 1249)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (20098, 19888), (10049, 9944), (5024, 4972), (2512, 2486), (1256, 1243)
│ └── 'nucleus_labels': DataTree[yx] (19290, 18501), (9645, 9250), (4822, 4625), (2411, 2312), (1205, 1156)
├── Points
│ └── 'transcripts': DataFrame with shape: (6323663, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (48293, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (48293, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (48134, 2) (2D shapes)
└── Tables
└── 'table': AnnData (48293, 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("oVDijmTNJwp6IeaJ") # 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/oVDijmTNJwp6IeaJ
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid oVDijmTNJwp6IeaJ Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["oVDijmTNJwp6IeaJ0000"])[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
- 48,293
- Transcripts
- 6,323,663
- Tier
- bronze
- Size
- 681 MB
- Sample ID
- GSM9654051
- 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