10x Xenium
Human skin of body
GSM9079621
silver Interactive viewer acne No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 20466, 17393), (1, 10233, 8696), (1, 5116, 4348), (1, 2558, 2174), (1, 1279, 1087)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (18748, 17013), (9374, 8506), (4687, 4253), (2343, 2126), (1171, 1063)
│ └── 'nucleus_labels': DataTree[yx] (17177, 16893), (8588, 8446), (4294, 4223), (2147, 2111), (1073, 1055)
├── Points
│ └── 'transcripts': DataFrame with shape: (3178787, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (19271, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (19271, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (19393, 2) (2D shapes)
└── Tables
└── 'table': AnnData (19271, 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("CCA4l3OD2iZfYzlq") # 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/CCA4l3OD2iZfYzlq
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid CCA4l3OD2iZfYzlq Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["CCA4l3OD2iZfYzlq0000"])[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
- 19,271
- Transcripts
- 3,178,787
- Tier
- silver
- Size
- 465 MB
- Sample ID
- GSM9079621
- 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