10x Xenium
Human pleura
GSM9654048
bronze Interactive viewer pleural mesothelioma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 47656, 39862), (1, 23828, 19931), (1, 11914, 9965), (1, 5957, 4982), (1, 2978, 2491)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (47181, 39755), (23590, 19877), (11795, 9938), (5897, 4969), (2948, 2484)
│ └── 'nucleus_labels': DataTree[yx] (46405, 39378), (23202, 19689), (11601, 9844), (5800, 4922), (2900, 2461)
├── Points
│ └── 'transcripts': DataFrame with shape: (109512121, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (298395, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (298395, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (309771, 2) (2D shapes)
└── Tables
└── 'table': AnnData (298395, 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("8jShmJ4enfEA7kVs") # 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/8jShmJ4enfEA7kVs
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 8jShmJ4enfEA7kVs Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["8jShmJ4enfEA7kVs0000"])[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
- 298,395
- Transcripts
- 109,512,121
- Tier
- bronze
- Size
- 5.3 GB
- Sample ID
- GSM9654048
- 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