10x Xenium
Human lymph node
GSM9682594
silver Interactive viewer triple-negative breast carcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 17230, 34196), (1, 8615, 17098), (1, 4307, 8549), (1, 2153, 4274), (1, 1076, 2137)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (17230, 34190), (8615, 17095), (4307, 8547), (2153, 4273), (1076, 2136)
│ └── 'nucleus_labels': DataTree[yx] (17217, 34156), (8608, 17078), (4304, 8539), (2152, 4269), (1076, 2134)
├── Points
│ └── 'transcripts': DataFrame with shape: (139974216, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (258566, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (258566, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (267246, 2) (2D shapes)
└── Tables
└── 'table': AnnData (258566, 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("GHgEhgzPZwG3FvHG") # 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/GHgEhgzPZwG3FvHG
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid GHgEhgzPZwG3FvHG Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["GHgEhgzPZwG3FvHG0000"])[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
- 258,566
- Transcripts
- 139,974,216
- Tier
- silver
- Size
- 3.8 GB
- Sample ID
- GSM9682594
- 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