10x Xenium
Human lymph node
GSM9682591
silver Interactive viewer triple-negative breast carcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 20519, 34199), (1, 10259, 17099), (1, 5129, 8549), (1, 2564, 4274), (1, 1282, 2137)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (20355, 33320), (10177, 16660), (5088, 8330), (2544, 4165), (1272, 2082)
│ └── 'nucleus_labels': DataTree[yx] (20203, 32655), (10101, 16327), (5050, 8163), (2525, 4081), (1262, 2040)
├── Points
│ └── 'transcripts': DataFrame with shape: (154436200, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (260137, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (260137, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (268073, 2) (2D shapes)
└── Tables
└── 'table': AnnData (260137, 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("l3w1ZGQqXWlIR0sz") # 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/l3w1ZGQqXWlIR0sz
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid l3w1ZGQqXWlIR0sz Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["l3w1ZGQqXWlIR0sz0000"])[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
- 260,137
- Transcripts
- 154,436,200
- Tier
- silver
- Size
- 4.0 GB
- Sample ID
- GSM9682591
- 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