10x Xenium
Human amygdala
GSM9927391
silver Interactive viewer No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 91756, 54294), (1, 45878, 27147), (1, 22939, 13573), (1, 11469, 6786), (1, 5734, 3393)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (90499, 54293), (45249, 27146), (22624, 13573), (11312, 6786), (5656, 3393)
│ └── 'nucleus_labels': DataTree[yx] (90451, 54255), (45225, 27127), (22612, 13563), (11306, 6781), (5653, 3390)
├── Points
│ └── 'transcripts': DataFrame with shape: (61592168, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (252807, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (252807, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (252807, 2) (2D shapes)
└── Tables
└── 'table': AnnData (252807, 366)
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) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("McuUjxBYwiPIO1EZ0000")
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("McuUjxBYwiPIO1EZ") # 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 McuUjxBYwiPIO1EZ0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/McuUjxBYwiPIO1EZ
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid McuUjxBYwiPIO1EZLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- amygdala
- Modality
- RNA
- Observations (cells)
- 252,807
- Transcripts
- 61,592,168
- Tier
- silver
- Size
- 9.3 GB
- Sample ID
- GSM9927391
- 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