10x Xenium
Human brain
GSM9461747
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 24015, 25745), (1, 12007, 12872), (1, 6003, 6436), (1, 3001, 3218), (1, 1500, 1609)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (24010, 25692), (12005, 12846), (6002, 6423), (3001, 3211), (1500, 1605)
│ └── 'nucleus_labels': DataTree[yx] (23980, 25653), (11990, 12826), (5995, 6413), (2997, 3206), (1498, 1603)
├── Points
│ └── 'transcripts': DataFrame with shape: (1397636, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (66278, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (66278, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (66481, 2) (2D shapes)
└── Tables
└── 'table': AnnData (66278, 5001)
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("jP32z6Rnj6vetmPm0000")
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("jP32z6Rnj6vetmPm") # 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 jP32z6Rnj6vetmPm0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/jP32z6Rnj6vetmPm
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid jP32z6Rnj6vetmPmLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- brain
- Modality
- RNA
- Observations (cells)
- 66,278
- Transcripts
- 1,397,636
- Tier
- bronze
- Size
- 1.0 GB
- Sample ID
- GSM9461747
- License
- NCBI GEO policy
- Published
- Mar 9, 2026
Cite this dataset
doi.org/10.1038/s41467-026-71803-3 ↗ BibTeX
@article{geo:GSM9461747,
doi = {10.1038/s41467-026-71803-3},
title = {GSM9461747},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB