10x Xenium
Human larynx
GSM9589061
bronze Interactive viewer head and neck squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 34033, 8718), (1, 17016, 4359), (1, 8508, 2179), (1, 4254, 1089), (1, 2127, 544)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (33224, 8594), (16612, 4297), (8306, 2148), (4153, 1074), (2076, 537)
│ └── 'nucleus_labels': DataTree[yx] (33083, 8461), (16541, 4230), (8270, 2115), (4135, 1057), (2067, 528)
├── Points
│ └── 'transcripts': DataFrame with shape: (998103, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (5389, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (5389, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (5389, 1) (2D shapes)
└── Tables
└── 'table': AnnData (5389, 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("hd1n6AZ0sr17er8C") # 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/hd1n6AZ0sr17er8C
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid hd1n6AZ0sr17er8C Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["hd1n6AZ0sr17er8C0000"])[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
- 5,389
- Transcripts
- 998,103
- Tier
- bronze
- Size
- 267 MB
- Sample ID
- GSM9589061
- 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