10x Xenium
Mouse brain
GSM9852121
silver Interactive viewer No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 23922, 39829), (1, 11961, 19914), (1, 5980, 9957), (1, 2990, 4978), (1, 1495, 2489)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (23906, 37257), (11953, 18628), (5976, 9314), (2988, 4657), (1494, 2328)
│ └── 'nucleus_labels': DataTree[yx] (23867, 36721), (11933, 18360), (5966, 9180), (2983, 4590), (1491, 2295)
├── Points
│ └── 'transcripts': DataFrame with shape: (69287672, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (60866, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (60866, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (61389, 2) (2D shapes)
└── Tables
└── 'table': AnnData (60866, 347)
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("vmKiQhAaGZNa4y860000")
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("vmKiQhAaGZNa4y86") # 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 vmKiQhAaGZNa4y860000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/vmKiQhAaGZNa4y86
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid vmKiQhAaGZNa4y86License: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- brain
- Modality
- RNA
- Observations (cells)
- 60,866
- Transcripts
- 69,287,672
- Tier
- silver
- Size
- 2.5 GB
- Sample ID
- GSM9852121
- License
- NCBI GEO policy
- Published
- Jul 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