10x Xenium
Human larynx
GSM9589058
bronze Interactive viewer head and neck squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 13742, 42594), (1, 6871, 21297), (1, 3435, 10648), (1, 1717, 5324), (1, 858, 2662)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (9584, 42594), (4792, 21297), (2396, 10648), (1198, 5324), (599, 2662)
│ └── 'nucleus_labels': DataTree[yx] (9444, 42542), (4722, 21271), (2361, 10635), (1180, 5317), (590, 2658)
├── Points
│ └── 'transcripts': DataFrame with shape: (2644930, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (7727, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (7727, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (7727, 1) (2D shapes)
└── Tables
└── 'table': AnnData (7727, 377)
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("lgNdqeQkBgj1TARp") # 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/lgNdqeQkBgj1TARp
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid lgNdqeQkBgj1TARp Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["lgNdqeQkBgj1TARp0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- larynx
- Condition
- head and neck squamous cell carcinoma
- Modality
- RNA
- Observations
- 7,727
- Transcripts
- 2,644,930
- Tier
- bronze
- Size
- 430 MB
- Sample ID
- GSM9589058
- License
- unknown
- Published
- May 11, 2026
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB