10x Xenium
Mouse embryo
GSM9304329
silver Interactive viewer No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 13701, 19957), (1, 6850, 9978), (1, 3425, 4989), (1, 1712, 2494), (1, 856, 1247)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (13639, 19955), (6819, 9977), (3409, 4988), (1704, 2494), (852, 1247)
│ └── 'nucleus_labels': DataTree[yx] (13610, 19929), (6805, 9964), (3402, 4982), (1701, 2491), (850, 1245)
├── Points
│ └── 'transcripts': DataFrame with shape: (17265929, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (85639, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (85639, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (88556, 2) (2D shapes)
└── Tables
└── 'table': AnnData (85639, 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) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("kDggig9Jsto8Yng1") # 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 Load from the CLI
# one-shot: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/kDggig9Jsto8Yng1
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid kDggig9Jsto8Yng1 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["kDggig9Jsto8Yng10000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- embryo
- Modality
- RNA
- Observations
- 85,639
- Transcripts
- 17,265,929
- Tier
- silver
- Size
- 1.0 GB
- Sample ID
- GSM9304329
- License
- unknown
- Published
- Aug 12, 2026
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB