10x Xenium
Human ileum
GSM9345485
bronze Interactive viewer ulcerative colitis Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 20498, 19963), (1, 10249, 9981), (1, 5124, 4990), (1, 2562, 2495), (1, 1281, 1247)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (16872, 17969), (8436, 8984), (4218, 4492), (2109, 2246), (1054, 1123)
│ └── 'nucleus_labels': DataTree[yx] (16732, 17881), (8366, 8940), (4183, 4470), (2091, 2235), (1045, 1117)
├── Points
│ └── 'transcripts': DataFrame with shape: (440742, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (32830, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (32830, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (32830, 1) (2D shapes)
└── Tables
└── 'table': AnnData (32830, 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("pMkEC84cmJEN7Ox9") # 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/pMkEC84cmJEN7Ox9
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid pMkEC84cmJEN7Ox9 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["pMkEC84cmJEN7Ox90000"])[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
- 32,830
- Transcripts
- 440,742
- Tier
- bronze
- Size
- 315 MB
- Sample ID
- GSM9345485
- 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