10x Xenium
Human brain
GSM8840048
bronze Interactive viewer medulloblastoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 20475, 53897), (1, 10237, 26948), (1, 5118, 13474), (1, 2559, 6737), (1, 1279, 3368)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (20475, 53897), (10237, 26948), (5118, 13474), (2559, 6737), (1279, 3368)
│ └── 'nucleus_labels': DataTree[yx] (20475, 53897), (10237, 26948), (5118, 13474), (2559, 6737), (1279, 3368)
├── Points
│ └── 'transcripts': DataFrame with shape: (42381361, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (211673, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (211673, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (211673, 1) (2D shapes)
└── Tables
└── 'table': AnnData (211673, 345)
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("b6iONndzByBC2hC4") # 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/b6iONndzByBC2hC4
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid b6iONndzByBC2hC4 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["b6iONndzByBC2hC40000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- brain
- Condition
- medulloblastoma
- Modality
- RNA
- Observations
- 211,673
- Transcripts
- 42,381,361
- Tier
- bronze
- Size
- 2.9 GB
- Sample ID
- GSM8840048
- License
- unknown
- Published
- Mar 17, 2025
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB