10x Xenium
Human kidney
GSM9428107
silver Interactive viewer No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_focus': DataTree[cyx] (4, 64655, 48348), (4, 32327, 24174), (4, 16163, 12087), (4, 8081, 6043), (4, 4040, 3021)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (64655, 48348), (32327, 24174), (16163, 12087), (8081, 6043), (4040, 3021)
│ └── 'nucleus_labels': DataTree[yx] (64655, 48348), (32327, 24174), (16163, 12087), (8081, 6043), (4040, 3021)
├── Points
│ └── 'transcripts': DataFrame with shape: (227146294, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (338916, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (338916, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (343154, 2) (2D shapes)
└── Tables
└── 'table': AnnData (338916, 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) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("elq84hBG3qJTOsxl0000")
ds.elements() # inspect without downloading
sdata = ds.to_sdata() # cached locally, reused
print(sdata) Python · lamindb
Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("elq84hBG3qJTOsxl") # stem uid: Lamin resolves it to the 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 Shell
# sddb client: download the .zarr into data/
sddb-cli download elq84hBG3qJTOsxl0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/elq84hBG3qJTOsxl
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid elq84hBG3qJTOsxlLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- kidney
- Modality
- RNA
- Observations (cells)
- 338,916
- Transcripts
- 227,146,294
- Tier
- silver
- Chemistry
- Xenium Prime
- Size
- 14.2 GB
- Sample ID
- GSM9428107
- 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