10x Xenium
Human skin of body
GSM9079630
silver Interactive viewer acne No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 27368, 20012), (1, 13684, 10006), (1, 6842, 5003), (1, 3421, 2501), (1, 1710, 1250)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (25744, 19849), (12872, 9924), (6436, 4962), (3218, 2481), (1609, 1240)
│ └── 'nucleus_labels': DataTree[yx] (24690, 19573), (12345, 9786), (6172, 4893), (3086, 2446), (1543, 1223)
├── Points
│ └── 'transcripts': DataFrame with shape: (4241998, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (32861, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (32861, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (33037, 2) (2D shapes)
└── Tables
└── 'table': AnnData (32861, 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("qjXlm5zQPft4Nflc") # 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/qjXlm5zQPft4Nflc
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid qjXlm5zQPft4Nflc Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["qjXlm5zQPft4Nflc0000"])[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
- 32,861
- Transcripts
- 4,241,998
- Tier
- silver
- Size
- 605 MB
- Sample ID
- GSM9079630
- 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