10x Xenium
Mouse tongue
GSM9096732
bronze Interactive viewer head and neck squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 23901, 22811), (1, 11950, 11405), (1, 5975, 5702), (1, 2987, 2851), (1, 1493, 1425)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (23769, 22659), (11884, 11329), (5942, 5664), (2971, 2832), (1485, 1416)
│ └── 'nucleus_labels': DataTree[yx] (22138, 22423), (11069, 11211), (5534, 5605), (2767, 2802), (1383, 1401)
├── Points
│ └── 'transcripts': DataFrame with shape: (58888510, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (50212, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (50212, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (48360, 2) (2D shapes)
└── Tables
└── 'table': AnnData (50212, 5046)
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("TTL4KkP6uDvIplI7") # 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/TTL4KkP6uDvIplI7
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid TTL4KkP6uDvIplI7 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["TTL4KkP6uDvIplI70000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- tongue
- Condition
- head and neck squamous cell carcinoma
- Modality
- RNA
- Observations
- 50,212
- Transcripts
- 58,888,510
- Tier
- bronze
- Size
- 1.6 GB
- Sample ID
- GSM9096732
- License
- unknown
- Published
- Jul 9, 2025
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB