10x Xenium
Human rectum
GSM9345504
bronze Interactive viewer ulcerative colitis Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 13709, 8639), (1, 6854, 4319), (1, 3427, 2159), (1, 1713, 1079), (1, 856, 539)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (13126, 7855), (6563, 3927), (3281, 1963), (1640, 981), (820, 490)
│ └── 'nucleus_labels': DataTree[yx] (12248, 6750), (6124, 3375), (3062, 1687), (1531, 843), (765, 421)
├── Points
│ └── 'transcripts': DataFrame with shape: (2437070, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (23741, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (23741, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (22733, 2) (2D shapes)
└── Tables
└── 'table': AnnData (23741, 322)
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("87azfBtDhIUxT6hk") # 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/87azfBtDhIUxT6hk
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 87azfBtDhIUxT6hk Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["87azfBtDhIUxT6hk0000"])[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
- 23,741
- Transcripts
- 2,437,070
- Tier
- bronze
- Size
- 202 MB
- Sample ID
- GSM9345504
- 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