10x Xenium
Mouse liver
GSM9256796
bronze Interactive viewer hepatocellular carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 20516, 45462), (1, 10258, 22731), (1, 5129, 11365), (1, 2564, 5682), (1, 1282, 2841)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (20467, 44865), (10233, 22432), (5116, 11216), (2558, 5608), (1279, 2804)
│ └── 'nucleus_labels': DataTree[yx] (20441, 44860), (10220, 22430), (5110, 11215), (2555, 5607), (1277, 2803)
├── Points
│ └── 'transcripts': DataFrame with shape: (174791350, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (121919, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (121919, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (126606, 2) (2D shapes)
└── Tables
└── 'table': AnnData (121919, 440)
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("7LKwj12Em7Bcrvdi") # 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/7LKwj12Em7Bcrvdi
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 7LKwj12Em7Bcrvdi Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["7LKwj12Em7Bcrvdi0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- liver
- Condition
- hepatocellular carcinoma
- Modality
- RNA
- Observations
- 121,919
- Transcripts
- 174,791,350
- Tier
- bronze
- Size
- 4.5 GB
- Sample ID
- GSM9256796
- License
- unknown
- Published
- Nov 10, 2025
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB