10x Xenium
Human amygdala
GSM9927390
silver Interactive viewer No linked publication
print(sdata)
SpatialData object
├── Labels
│ ├── 'cell_labels': DataTree[yx] (105333, 54283), (52666, 27141), (26333, 13570), (13166, 6785), (6583, 3392)
│ └── 'nucleus_labels': DataTree[yx] (105299, 54249), (52649, 27124), (26324, 13562), (13162, 6781), (6581, 3390)
├── Points
│ └── 'transcripts': DataFrame with shape: (54200373, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (287576, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (287576, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (287576, 2) (2D shapes)
└── Tables
└── 'table': AnnData (287576, 366)
with coordinate systems:
▸ 'global', with elements:
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("CFp2pZmXUwa7EIxE0000")
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("CFp2pZmXUwa7EIxE") # 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 CFp2pZmXUwa7EIxE0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/CFp2pZmXUwa7EIxE
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid CFp2pZmXUwa7EIxELicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- amygdala
- Modality
- RNA
- Observations (cells)
- 287,576
- Transcripts
- 54,200,373
- Tier
- silver
- Size
- 2.1 GB
- Sample ID
- GSM9927390
- License
- NCBI GEO policy
- Published
- Aug 24, 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