10x Xenium
Human lung
GSM8313612
bronze Interactive viewer asthma Provisional
print(sdata)
SpatialData object
├── Labels
│ ├── 'cell_labels': DataTree[yx] (101078, 46863), (50539, 23431), (25269, 11715), (12634, 5857), (6317, 2928)
│ └── 'nucleus_labels': DataTree[yx] (100938, 46724), (50469, 23362), (25234, 11681), (12617, 5840), (6308, 2920)
├── Points
│ └── 'transcripts': DataFrame with shape: (3466729, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (62732, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (62732, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (62732, 1) (2D shapes)
└── Tables
└── 'table': AnnData (62732, 339)
with coordinate systems:
▸ 'global', with elements:
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("vqYHMsTq8LgVyDDk") # 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/vqYHMsTq8LgVyDDk
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid vqYHMsTq8LgVyDDk Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["vqYHMsTq8LgVyDDk0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- lung
- Condition
- asthma
- Modality
- RNA
- Observations
- 62,732
- Transcripts
- 3,466,729
- Tier
- bronze
- Size
- 205 MB
- Sample ID
- GSM8313612
- License
- unknown
- Published
- Apr 8, 2025
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB