10x Xenium
Mouse embryo
GSM9304326
silver Interactive viewer No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 17092, 22790), (1, 8546, 11395), (1, 4273, 5697), (1, 2136, 2848), (1, 1068, 1424)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (16680, 22790), (8340, 11395), (4170, 5697), (2085, 2848), (1042, 1424)
│ └── 'nucleus_labels': DataTree[yx] (16062, 21714), (8031, 10857), (4015, 5428), (2007, 2714), (1003, 1357)
├── Points
│ └── 'transcripts': DataFrame with shape: (18597840, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (87360, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (87360, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (88439, 2) (2D shapes)
└── Tables
└── 'table': AnnData (87360, 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("07yjhkQMivAamVKb0000")
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("07yjhkQMivAamVKb") # 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 07yjhkQMivAamVKb0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/07yjhkQMivAamVKb
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 07yjhkQMivAamVKbLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- embryo
- Modality
- RNA
- Observations (cells)
- 87,360
- Transcripts
- 18,597,840
- Tier
- silver
- Size
- 1.2 GB
- Sample ID
- GSM9304326
- License
- NCBI GEO policy
- Published
- Aug 12, 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