10x Xenium
Human rectum
GSM9736176
bronze Interactive viewer Crohn disease Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 17116, 35084), (1, 8558, 17542), (1, 4279, 8771), (1, 2139, 4385), (1, 1069, 2192)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (13064, 31215), (6532, 15607), (3266, 7803), (1633, 3901), (816, 1950)
│ └── 'nucleus_labels': DataTree[yx] (13614, 31197), (6807, 15598), (3403, 7799), (1701, 3899), (850, 1949)
├── Points
│ └── 'transcripts': DataFrame with shape: (72933009, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (51458, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (51458, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (52414, 2) (2D shapes)
└── Tables
└── 'table': AnnData (51458, 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("1agAfD3tdmdRXMDg0000")
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("1agAfD3tdmdRXMDg") # 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 1agAfD3tdmdRXMDg0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/1agAfD3tdmdRXMDg
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 1agAfD3tdmdRXMDgLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- rectum
- Condition
- Crohn disease
- Modality
- RNA
- Observations (cells)
- 51,458
- Transcripts
- 24,311,003
- Tier
- bronze
- Size
- 1.0 GB
- Sample ID
- GSM9736176
- License
- NCBI GEO policy
- Published
- Sep 3, 2026
Cite this dataset
doi.org/10.1126/science.aeh7112 ↗ BibTeX
@article{geo:GSM9736176,
doi = {10.1126/science.aeh7112},
title = {GSM9736176},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB