10x Xenium
Human ileum
GSM9345477
bronze Interactive viewer Crohn disease Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 13705, 25616), (1, 6852, 12808), (1, 3426, 6404), (1, 1713, 3202), (1, 856, 1601)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (13568, 25326), (6784, 12663), (3392, 6331), (1696, 3165), (848, 1582)
│ └── 'nucleus_labels': DataTree[yx] (13432, 25188), (6716, 12594), (3358, 6297), (1679, 3148), (839, 1574)
├── Points
│ └── 'transcripts': DataFrame with shape: (138165, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (18573, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (18573, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (18573, 1) (2D shapes)
└── Tables
└── 'table': AnnData (18573, 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("PTwH3zhC92sOCBuM0000")
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("PTwH3zhC92sOCBuM") # 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 PTwH3zhC92sOCBuM0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/PTwH3zhC92sOCBuM
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid PTwH3zhC92sOCBuMLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- ileum
- Condition
- Crohn disease
- Modality
- RNA
- Observations (cells)
- 18,573
- Transcripts
- 138,165
- Tier
- bronze
- Size
- 199 MB
- Sample ID
- GSM9345477
- 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