10x Xenium
Human amygdala
GSM9927392
silver Interactive viewer No linked publication
print(sdata)
SpatialData object
├── Labels
│ ├── 'cell_labels': DataTree[yx] (102053, 54308), (51026, 27154), (25513, 13577), (12756, 6788), (6378, 3394)
│ └── 'nucleus_labels': DataTree[yx] (101998, 54269), (50999, 27134), (25499, 13567), (12749, 6783), (6374, 3391)
├── Points
│ └── 'transcripts': DataFrame with shape: (136794786, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (287565, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (287565, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (287565, 1) (2D shapes)
└── Tables
└── 'table': AnnData (287565, 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("LD2hVc1JBDGGpP3o0000")
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("LD2hVc1JBDGGpP3o") # 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 LD2hVc1JBDGGpP3o0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/LD2hVc1JBDGGpP3o
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid LD2hVc1JBDGGpP3oLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- amygdala
- Modality
- RNA
- Observations (cells)
- 287,565
- Transcripts
- 136,794,786
- Tier
- silver
- Size
- 4.7 GB
- Sample ID
- GSM9927392
- 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