10x Xenium
Human oropharynx
GSM9054486
bronze Interactive viewer oropharynx squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 34085, 19995), (1, 17042, 9997), (1, 8521, 4998), (1, 4260, 2499), (1, 2130, 1249)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (33984, 19914), (16992, 9957), (8496, 4978), (4248, 2489), (2124, 1244)
│ └── 'nucleus_labels': DataTree[yx] (33543, 18171), (16771, 9085), (8385, 4542), (4192, 2271), (2096, 1135)
├── Points
│ └── 'transcripts': DataFrame with shape: (16267852, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (39583, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (39583, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (38809, 2) (2D shapes)
└── Tables
└── 'table': AnnData (39583, 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("3OzoBrlnv3h13403") # 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/3OzoBrlnv3h13403
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 3OzoBrlnv3h13403 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["3OzoBrlnv3h134030000"])[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
- 39,583
- Transcripts
- 16,267,852
- Tier
- bronze
- Size
- 1.3 GB
- Sample ID
- GSM9054486
- 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