10x Xenium
Human oropharynx
GSM9589066
bronze Interactive viewer head and neck squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 17053, 42619), (1, 8526, 21309), (1, 4263, 10654), (1, 2131, 5327), (1, 1065, 2663)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (13397, 41555), (6698, 20777), (3349, 10388), (1674, 5194), (837, 2597)
│ └── 'nucleus_labels': DataTree[yx] (13257, 41415), (6628, 20707), (3314, 10353), (1657, 5176), (828, 2588)
├── Points
│ └── 'transcripts': DataFrame with shape: (2742830, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (8552, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (8552, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (8552, 1) (2D shapes)
└── Tables
└── 'table': AnnData (8552, 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("ZVYLDOqknFndCRpf") # 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/ZVYLDOqknFndCRpf
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid ZVYLDOqknFndCRpf Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["ZVYLDOqknFndCRpf0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- oropharynx
- Condition
- head and neck squamous cell carcinoma
- Modality
- RNA
- Observations
- 8,552
- Transcripts
- 2,742,830
- Tier
- bronze
- Size
- 430 MB
- Sample ID
- GSM9589066
- 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