10x Xenium
Human skin of body
GSM9079629
silver Interactive viewer acne No linked publication
print(sdata)
SpatialData object
├── Labels
│ ├── 'cell_labels': DataTree[yx] (16359, 24251), (8179, 12125), (4089, 6062), (2044, 3031), (1022, 1515)
│ └── 'nucleus_labels': DataTree[yx] (15921, 22800), (7960, 11400), (3980, 5700), (1990, 2850), (995, 1425)
├── Points
│ └── 'transcripts': DataFrame with shape: (1404026, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (10450, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (10450, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (10411, 2) (2D shapes)
└── Tables
└── 'table': AnnData (10450, 100)
with coordinate systems:
▸ 'global', with elements:
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("igOi45RRTtaWWwKy") # 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/igOi45RRTtaWWwKy
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid igOi45RRTtaWWwKy Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["igOi45RRTtaWWwKy0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- skin of body
- Condition
- acne
- Modality
- RNA
- Observations
- 10,450
- Transcripts
- 1,404,026
- Tier
- silver
- Size
- 54 MB
- Sample ID
- GSM9079629
- License
- unknown
- Published
- Dec 3, 2025
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB