10x Xenium
Human ileum
GSM9345479
bronze Interactive viewer Crohn disease Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 17104, 5798), (1, 8552, 2899), (1, 4276, 1449), (1, 2138, 724), (1, 1069, 362)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (15458, 5495), (7729, 2747), (3864, 1373), (1932, 686), (966, 343)
│ └── 'nucleus_labels': DataTree[yx] (15318, 5406), (7659, 2703), (3829, 1351), (1914, 675), (957, 337)
├── Points
│ └── 'transcripts': DataFrame with shape: (751875, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (14746, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (14746, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (14746, 1) (2D shapes)
└── Tables
└── 'table': AnnData (14746, 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("ZfOC1taxg7WfT9Sm0000")
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("ZfOC1taxg7WfT9Sm") # 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 ZfOC1taxg7WfT9Sm0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/ZfOC1taxg7WfT9Sm
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid ZfOC1taxg7WfT9SmLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- ileum
- Condition
- Crohn disease
- Modality
- RNA
- Observations (cells)
- 14,746
- Transcripts
- 751,875
- Tier
- bronze
- Size
- 132 MB
- Sample ID
- GSM9345479
- 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