10x Xenium
Human larynx
GSM9054481
bronze Interactive viewer laryngeal squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 17111, 14304), (1, 8555, 7152), (1, 4277, 3576), (1, 2138, 1788), (1, 1069, 894)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (17003, 14180), (8501, 7090), (4250, 3545), (2125, 1772), (1062, 886)
│ └── 'nucleus_labels': DataTree[yx] (15612, 11216), (7806, 5608), (3903, 2804), (1951, 1402), (975, 701)
├── Points
│ └── 'transcripts': DataFrame with shape: (5043283, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (23496, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (23496, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (23299, 2) (2D shapes)
└── Tables
└── 'table': AnnData (23496, 476)
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("ObORyTPEMJiSVjwN") # 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/ObORyTPEMJiSVjwN
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid ObORyTPEMJiSVjwN Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["ObORyTPEMJiSVjwN0000"])[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
- laryngeal squamous cell carcinoma
- Modality
- RNA
- Observations
- 23,496
- Transcripts
- 5,043,283
- Tier
- bronze
- Size
- 424 MB
- Sample ID
- GSM9054481
- License
- unknown
- Published
- Aug 6, 2025
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB