10x Xenium
Mouse brain
GSM9496850
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 112058, 36975), (1, 56029, 18487), (1, 28014, 9243), (1, 14007, 4621), (1, 7003, 2310)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (110812, 34955), (55406, 17477), (27703, 8738), (13851, 4369), (6925, 2184)
│ └── 'nucleus_labels': DataTree[yx] (110672, 34873), (55336, 17436), (27668, 8718), (13834, 4359), (6917, 2179)
├── Points
│ └── 'transcripts': DataFrame with shape: (150695701, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (329439, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (329439, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (329439, 1) (2D shapes)
└── Tables
└── 'table': AnnData (329439, 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("olky1LbSNWxa5tGy0000")
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("olky1LbSNWxa5tGy") # 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 olky1LbSNWxa5tGy0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/olky1LbSNWxa5tGy
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid olky1LbSNWxa5tGyLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- brain
- Modality
- RNA
- Observations (cells)
- 329,439
- Transcripts
- 150,695,701
- Tier
- bronze
- Size
- 10.2 GB
- Sample ID
- GSM9496850
- License
- NCBI GEO policy
- Published
- Jul 6, 2026
Cite this dataset
doi.org/10.1016/j.isci.2026.116906 ↗ BibTeX
@article{geo:GSM9496850,
doi = {10.1016/j.isci.2026.116906},
title = {GSM9496850},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB