10x Xenium
Human lymph node
GSM9682590
silver Interactive viewer triple-negative breast carcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 17157, 17197), (1, 8578, 8598), (1, 4289, 4299), (1, 2144, 2149), (1, 1072, 1074)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (17154, 16688), (8577, 8344), (4288, 4172), (2144, 2086), (1072, 1043)
│ └── 'nucleus_labels': DataTree[yx] (16853, 16665), (8426, 8332), (4213, 4166), (2106, 2083), (1053, 1041)
├── Points
│ └── 'transcripts': DataFrame with shape: (52478873, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (144744, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (144744, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (149354, 2) (2D shapes)
└── Tables
└── 'table': AnnData (144744, 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("eVgqkHJbtq5CBieB") # 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/eVgqkHJbtq5CBieB
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid eVgqkHJbtq5CBieB Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["eVgqkHJbtq5CBieB0000"])[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
- 144,744
- Transcripts
- 52,478,873
- Tier
- silver
- Size
- 1.6 GB
- Sample ID
- GSM9682590
- 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