10x Xenium
Human ileum
GSM9345478
bronze Interactive viewer Crohn disease Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 30681, 14313), (1, 15340, 7156), (1, 7670, 3578), (1, 3835, 1789), (1, 1917, 894)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (26946, 12550), (13473, 6275), (6736, 3137), (3368, 1568), (1684, 784)
│ └── 'nucleus_labels': DataTree[yx] (26806, 12410), (13403, 6205), (6701, 3102), (3350, 1551), (1675, 775)
├── Points
│ └── 'transcripts': DataFrame with shape: (816950, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (43530, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (43530, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (43530, 1) (2D shapes)
└── Tables
└── 'table': AnnData (43530, 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) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("0NFDmnrrylHuN46R") # 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 Load from the CLI
# one-shot: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/0NFDmnrrylHuN46R
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 0NFDmnrrylHuN46R Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["0NFDmnrrylHuN46R0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- ileum
- Condition
- Crohn disease
- Modality
- RNA
- Observations
- 43,530
- Transcripts
- 816,950
- Tier
- bronze
- Size
- 391 MB
- Sample ID
- GSM9345478
- License
- unknown
- Published
- Mar 13, 2026
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB