10x Xenium
Human rectum
GSM9345500
bronze Interactive viewer ulcerative colitis Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 13705, 11472), (1, 6852, 5736), (1, 3426, 2868), (1, 1713, 1434), (1, 856, 717)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (13181, 10525), (6590, 5262), (3295, 2631), (1647, 1315), (823, 657)
│ └── 'nucleus_labels': DataTree[yx] (11579, 6701), (5789, 3350), (2894, 1675), (1447, 837), (723, 418)
├── Points
│ └── 'transcripts': DataFrame with shape: (3270239, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (24369, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (24369, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (23675, 2) (2D shapes)
└── Tables
└── 'table': AnnData (24369, 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) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("ndZ2CItBxEwAbwll0000")
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("ndZ2CItBxEwAbwll") # 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 ndZ2CItBxEwAbwll0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/ndZ2CItBxEwAbwll
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid ndZ2CItBxEwAbwllLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- rectum
- Condition
- ulcerative colitis
- Modality
- RNA
- Observations (cells)
- 24,369
- Transcripts
- 3,270,239
- Tier
- bronze
- Size
- 242 MB
- Sample ID
- GSM9345500
- 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