10x Xenium
Mouse tongue
GSM9096726
bronze Interactive viewer head and neck squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 30691, 17139), (1, 15345, 8569), (1, 7672, 4284), (1, 3836, 2142), (1, 1918, 1071)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (30520, 17139), (15260, 8569), (7630, 4284), (3815, 2142), (1907, 1071)
│ └── 'nucleus_labels': DataTree[yx] (30286, 16906), (15143, 8453), (7571, 4226), (3785, 2113), (1892, 1056)
├── Points
│ └── 'transcripts': DataFrame with shape: (111423996, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (86655, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (86655, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (85029, 2) (2D shapes)
└── Tables
└── 'table': AnnData (86655, 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("ZtLdTHPs3X9U8Px0") # 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/ZtLdTHPs3X9U8Px0
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid ZtLdTHPs3X9U8Px0 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["ZtLdTHPs3X9U8Px00000"])[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
- 86,655
- Transcripts
- 111,423,996
- Tier
- bronze
- Size
- 2.7 GB
- Sample ID
- GSM9096726
- 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