10x Xenium
Mouse tongue
GSM9096733
bronze Interactive viewer head and neck squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 20510, 17147), (1, 10255, 8573), (1, 5127, 4286), (1, 2563, 2143), (1, 1281, 1071)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (20357, 16987), (10178, 8493), (5089, 4246), (2544, 2123), (1272, 1061)
│ └── 'nucleus_labels': DataTree[yx] (20312, 16092), (10156, 8046), (5078, 4023), (2539, 2011), (1269, 1005)
├── Points
│ └── 'transcripts': DataFrame with shape: (50084294, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (75178, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (75178, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (74533, 2) (2D shapes)
└── Tables
└── 'table': AnnData (75178, 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("wOTjyv3bu2fUd60a") # 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/wOTjyv3bu2fUd60a
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid wOTjyv3bu2fUd60a Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["wOTjyv3bu2fUd60a0000"])[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
- 75,178
- Transcripts
- 50,084,294
- Tier
- bronze
- Size
- 1.5 GB
- Sample ID
- GSM9096733
- 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