10x Xenium
Human kidney
GSM9428109
silver Interactive viewer No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_focus': DataTree[cyx] (4, 61200, 45469), (4, 30600, 22734), (4, 15300, 11367), (4, 7650, 5683), (4, 3825, 2841)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (61200, 45469), (30600, 22734), (15300, 11367), (7650, 5683), (3825, 2841)
│ └── 'nucleus_labels': DataTree[yx] (61200, 45469), (30600, 22734), (15300, 11367), (7650, 5683), (3825, 2841)
├── Points
│ └── 'transcripts': DataFrame with shape: (370538943, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (288214, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (288214, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (291847, 2) (2D shapes)
└── Tables
└── 'table': AnnData (288214, 5092)
with coordinate systems:
▸ 'global', with elements:
morphology_focus (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("PxwiWsETZbkmvrXp") # 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/PxwiWsETZbkmvrXp
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid PxwiWsETZbkmvrXp Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["PxwiWsETZbkmvrXp0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- kidney
- Modality
- RNA
- Observations
- 288,214
- Transcripts
- 370,538,943
- Tier
- silver
- Chemistry
- Xenium Prime
- Size
- 13 GB
- Sample ID
- GSM9428109
- License
- NCBI GEO policy
- Published
- Jan 6, 2026
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB