10x Xenium
Human skin of body
GSM9079633
silver Interactive viewer No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 17203, 14283), (1, 8601, 7141), (1, 4300, 3570), (1, 2150, 1785), (1, 1075, 892)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (14792, 12022), (7396, 6011), (3698, 3005), (1849, 1502), (924, 751)
│ └── 'nucleus_labels': DataTree[yx] (14788, 10345), (7394, 5172), (3697, 2586), (1848, 1293), (924, 646)
├── Points
│ └── 'transcripts': DataFrame with shape: (598326, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (5384, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (5384, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (5351, 2) (2D shapes)
└── Tables
└── 'table': AnnData (5384, 100)
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("OtQgNIuIv75Nhexu") # 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/OtQgNIuIv75Nhexu
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid OtQgNIuIv75Nhexu Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["OtQgNIuIv75Nhexu0000"])[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
- Modality
- RNA
- Observations
- 5,384
- Transcripts
- 598,326
- Tier
- silver
- Size
- 215 MB
- Sample ID
- GSM9079633
- 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