10x Xenium
Human spleen
GSM9638045
silver Interactive viewer No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 27269, 28461), (1, 13634, 14230), (1, 6817, 7115), (1, 3408, 3557), (1, 1704, 1778)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (26982, 26663), (13491, 13331), (6745, 6665), (3372, 3332), (1686, 1666)
│ └── 'nucleus_labels': DataTree[yx] (26936, 26616), (13468, 13308), (6734, 6654), (3367, 3327), (1683, 1663)
├── Points
│ └── 'transcripts': DataFrame with shape: (27341509, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (331582, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (331582, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (342940, 2) (2D shapes)
└── Tables
└── 'table': AnnData (331582, 5093)
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("jeMx6MToKJpK6SkQ0000")
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("jeMx6MToKJpK6SkQ") # 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 jeMx6MToKJpK6SkQ0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/jeMx6MToKJpK6SkQ
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid jeMx6MToKJpK6SkQLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- spleen
- Modality
- RNA
- Observations (cells)
- 331,582
- Transcripts
- 27,341,509
- Tier
- silver
- Size
- 2.0 GB
- Sample ID
- GSM9638045
- License
- NCBI GEO policy
- Published
- Apr 30, 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