10x Xenium
Mouse liver
GSM9256795
bronze Interactive viewer hepatocellular carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 20499, 45468), (1, 10249, 22734), (1, 5124, 11367), (1, 2562, 5683), (1, 1281, 2841)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (20491, 44534), (10245, 22267), (5122, 11133), (2561, 5566), (1280, 2783)
│ └── 'nucleus_labels': DataTree[yx] (20463, 44508), (10231, 22254), (5115, 11127), (2557, 5563), (1278, 2781)
├── Points
│ └── 'transcripts': DataFrame with shape: (139285708, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (162483, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (162483, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (169493, 2) (2D shapes)
└── Tables
└── 'table': AnnData (162483, 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("ybYk1BaXNYEpMpst") # 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/ybYk1BaXNYEpMpst
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid ybYk1BaXNYEpMpst Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["ybYk1BaXNYEpMpst0000"])[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
- 162,483
- Transcripts
- 139,285,708
- Tier
- bronze
- Size
- 4.0 GB
- Sample ID
- GSM9256795
- 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