10x Xenium
Mouse brain
GSM9496852
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 112050, 36890), (1, 56025, 18445), (1, 28012, 9222), (1, 14006, 4611), (1, 7003, 2305)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (109483, 32338), (54741, 16169), (27370, 8084), (13685, 4042), (6842, 2021)
│ └── 'nucleus_labels': DataTree[yx] (109377, 32198), (54688, 16099), (27344, 8049), (13672, 4024), (6836, 2012)
├── Points
│ └── 'transcripts': DataFrame with shape: (162861045, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (329560, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (329560, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (329560, 1) (2D shapes)
└── Tables
└── 'table': AnnData (329560, 297)
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("VbEKyo4vKF4svqyG0000")
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("VbEKyo4vKF4svqyG") # 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 VbEKyo4vKF4svqyG0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/VbEKyo4vKF4svqyG
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid VbEKyo4vKF4svqyGLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- brain
- Modality
- RNA
- Observations (cells)
- 329,560
- Transcripts
- 162,861,045
- Tier
- bronze
- Size
- 10.4 GB
- Sample ID
- GSM9496852
- License
- NCBI GEO policy
- Published
- Jul 6, 2026
Cite this dataset
doi.org/10.1016/j.isci.2026.116906 ↗ BibTeX
@article{geo:GSM9496852,
doi = {10.1016/j.isci.2026.116906},
title = {GSM9496852},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB