10x Xenium
Human rectum
GSM9345507
bronze Interactive viewer ulcerative colitis Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 13714, 25629), (1, 6857, 12814), (1, 3428, 6407), (1, 1714, 3203), (1, 857, 1601)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (11198, 24793), (5599, 12396), (2799, 6198), (1399, 3099), (699, 1549)
│ └── 'nucleus_labels': DataTree[yx] (11092, 23550), (5546, 11775), (2773, 5887), (1386, 2943), (693, 1471)
├── Points
│ └── 'transcripts': DataFrame with shape: (884037, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (39937, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (39937, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (39849, 2) (2D shapes)
└── Tables
└── 'table': AnnData (39937, 5001)
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) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("9XET7VRMamQd7gCb0000")
ds.elements() # inspect without downloading
sdata = ds.to_sdata() # cached locally, reused
print(sdata) Python · lamindb
Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("9XET7VRMamQd7gCb") # stem uid: Lamin resolves it to the 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 Shell
# sddb client: download the .zarr into data/
sddb-cli download 9XET7VRMamQd7gCb0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/9XET7VRMamQd7gCb
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 9XET7VRMamQd7gCbLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- rectum
- Condition
- ulcerative colitis
- Modality
- RNA
- Observations (cells)
- 39,937
- Transcripts
- 884,037
- Tier
- bronze
- Size
- 358 MB
- Sample ID
- GSM9345507
- License
- NCBI GEO policy
- Published
- Mar 13, 2026
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB