10x Xenium
Human rectum
GSM9345492
bronze Interactive viewer ulcerative colitis Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 17102, 25625), (1, 8551, 12812), (1, 4275, 6406), (1, 2137, 3203), (1, 1068, 1601)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (16287, 22627), (8143, 11313), (4071, 5656), (2035, 2828), (1017, 1414)
│ └── 'nucleus_labels': DataTree[yx] (16147, 22489), (8073, 11244), (4036, 5622), (2018, 2811), (1009, 1405)
├── Points
│ └── 'transcripts': DataFrame with shape: (3120007, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (55979, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (55979, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (55979, 1) (2D shapes)
└── Tables
└── 'table': AnnData (55979, 377)
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("Xjav8IifSAXQfgmT") # 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/Xjav8IifSAXQfgmT
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid Xjav8IifSAXQfgmT Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["Xjav8IifSAXQfgmT0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- rectum
- Condition
- ulcerative colitis
- Modality
- RNA
- Observations
- 55,979
- Transcripts
- 3,120,007
- Tier
- bronze
- Size
- 478 MB
- Sample ID
- GSM9345492
- License
- unknown
- Published
- Mar 13, 2026
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB