10x Xenium
Human oropharynx
GSM9054473
bronze Interactive viewer oropharynx squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 34086, 34153), (1, 17043, 17076), (1, 8521, 8538), (1, 4260, 4269), (1, 2130, 2134)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (33751, 33772), (16875, 16886), (8437, 8443), (4218, 4221), (2109, 2110)
│ └── 'nucleus_labels': DataTree[yx] (32462, 33634), (16231, 16817), (8115, 8408), (4057, 4204), (2028, 2102)
├── Points
│ └── 'transcripts': DataFrame with shape: (88942788, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (268328, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (268328, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (285080, 2) (2D shapes)
└── Tables
└── 'table': AnnData (268328, 477)
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("W7DDj4yqc2QPd6QR") # 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/W7DDj4yqc2QPd6QR
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid W7DDj4yqc2QPd6QR Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["W7DDj4yqc2QPd6QR0000"])[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
- oropharynx squamous cell carcinoma
- Modality
- RNA
- Observations
- 268,328
- Transcripts
- 88,942,788
- Tier
- bronze
- Size
- 4.2 GB
- Sample ID
- GSM9054473
- 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