10x Xenium
Mouse tongue
GSM9096729
bronze Interactive viewer head and neck squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 64601, 48290), (1, 32300, 24145), (1, 16150, 12072), (1, 8075, 6036), (1, 4037, 3018)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (64546, 48284), (32273, 24142), (16136, 12071), (8068, 6035), (4034, 3017)
│ └── 'nucleus_labels': DataTree[yx] (64097, 47402), (32048, 23701), (16024, 11850), (8012, 5925), (4006, 2962)
├── Points
│ └── 'transcripts': DataFrame with shape: (209118503, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (142943, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (142943, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (138285, 2) (2D shapes)
└── Tables
└── 'table': AnnData (142943, 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("ZF6BWbJYGaoOv1gg") # 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/ZF6BWbJYGaoOv1gg
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid ZF6BWbJYGaoOv1gg Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["ZF6BWbJYGaoOv1gg0000"])[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
- 142,943
- Transcripts
- 209,118,503
- Tier
- bronze
- Size
- 5.1 GB
- Sample ID
- GSM9096729
- 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