10x Xenium
Human rectum
GSM9736166
bronze Interactive viewer ulcerative colitis Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 37427, 22810), (1, 18713, 11405), (1, 9356, 5702), (1, 4678, 2851), (1, 2339, 1425)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (36236, 21093), (18118, 10546), (9059, 5273), (4529, 2636), (2264, 1318)
│ └── 'nucleus_labels': DataTree[yx] (36679, 21061), (18339, 10530), (9169, 5265), (4584, 2632), (2292, 1316)
├── Points
│ └── 'transcripts': DataFrame with shape: (37455895, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (75372, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (75372, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (76460, 2) (2D shapes)
└── Tables
└── 'table': AnnData (75372, 480)
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("5ivAFASht6GIebaE0000")
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("5ivAFASht6GIebaE") # 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 5ivAFASht6GIebaE0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/5ivAFASht6GIebaE
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 5ivAFASht6GIebaELicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- rectum
- Condition
- ulcerative colitis
- Modality
- RNA
- Observations (cells)
- 75,372
- Transcripts
- 37,455,895
- Tier
- bronze
- Size
- 1.3 GB
- Sample ID
- GSM9736166
- License
- NCBI GEO policy
- Published
- Sep 3, 2026
Cite this dataset
doi.org/10.1126/science.aeh7112 ↗ BibTeX
@article{geo:GSM9736166,
doi = {10.1126/science.aeh7112},
title = {GSM9736166},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB