10x Xenium
Human ileum
GSM9345486
bronze Interactive viewer ulcerative colitis Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 20494, 22796), (1, 10247, 11398), (1, 5123, 5699), (1, 2561, 2849), (1, 1280, 1424)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (18955, 21503), (9477, 10751), (4738, 5375), (2369, 2687), (1184, 1343)
│ └── 'nucleus_labels': DataTree[yx] (18815, 21403), (9407, 10701), (4703, 5350), (2351, 2675), (1175, 1337)
├── Points
│ └── 'transcripts': DataFrame with shape: (2630176, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (38405, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (38405, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (38405, 1) (2D shapes)
└── Tables
└── 'table': AnnData (38405, 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("o8DNZ5KYTVQpuT7U") # 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/o8DNZ5KYTVQpuT7U
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid o8DNZ5KYTVQpuT7U Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["o8DNZ5KYTVQpuT7U0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- ileum
- Condition
- ulcerative colitis
- Modality
- RNA
- Observations
- 38,405
- Transcripts
- 2,630,176
- Tier
- bronze
- Size
- 464 MB
- Sample ID
- GSM9345486
- 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