10x Xenium
Human lymph node
GSM9682593
silver Interactive viewer triple-negative breast carcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 23841, 37045), (1, 11920, 18522), (1, 5960, 9261), (1, 2980, 4630), (1, 1490, 2315)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (23525, 36905), (11762, 18452), (5881, 9226), (2940, 4613), (1470, 2306)
│ └── 'nucleus_labels': DataTree[yx] (20785, 36744), (10392, 18372), (5196, 9186), (2598, 4593), (1299, 2296)
├── Points
│ └── 'transcripts': DataFrame with shape: (207932396, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (291682, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (291682, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (298010, 2) (2D shapes)
└── Tables
└── 'table': AnnData (291682, 5001)
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("iQ1O8FAHDykvMVY4") # 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/iQ1O8FAHDykvMVY4
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid iQ1O8FAHDykvMVY4 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["iQ1O8FAHDykvMVY40000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- lymph node
- Condition
- triple-negative breast carcinoma
- Modality
- RNA
- Observations
- 291,682
- Transcripts
- 207,932,396
- Tier
- silver
- Size
- 5.3 GB
- Sample ID
- GSM9682593
- License
- unknown
- Published
- Jun 27, 2026
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB