10x Xenium
Human rectum
GSM9345498
bronze Interactive viewer ulcerative colitis Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 20498, 25628), (1, 10249, 12814), (1, 5124, 6407), (1, 2562, 3203), (1, 1281, 1601)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (19372, 25382), (9686, 12691), (4843, 6345), (2421, 3172), (1210, 1586)
│ └── 'nucleus_labels': DataTree[yx] (15347, 22481), (7673, 11240), (3836, 5620), (1918, 2810), (959, 1405)
├── Points
│ └── 'transcripts': DataFrame with shape: (550335, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (28223, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (28223, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (27273, 2) (2D shapes)
└── Tables
└── 'table': AnnData (28223, 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("rmOGF8SXF3pty8Kr") # 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/rmOGF8SXF3pty8Kr
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid rmOGF8SXF3pty8Kr Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["rmOGF8SXF3pty8Kr0000"])[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
- 28,223
- Transcripts
- 550,335
- Tier
- bronze
- Size
- 337 MB
- Sample ID
- GSM9345498
- 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