10x Xenium
Human pancreas
GSM9372006
bronze Interactive viewer pancreatic adenocarcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataArray[cyx] (1, 44227, 48344)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (41963, 45644), (20981, 22822), (10490, 11411), (5245, 5705), (2622, 2852)
│ └── 'nucleus_labels': DataTree[yx] (41936, 45629), (20968, 22814), (10484, 11407), (5242, 5703), (2621, 2851)
├── Points
│ └── 'transcripts': DataFrame with shape: (53863654, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (159670, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (159670, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (158683, 2) (2D shapes)
└── Tables
└── 'table': AnnData (159670, 5101)
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("Jm7bhoa22mgdGTLh") # 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/Jm7bhoa22mgdGTLh
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid Jm7bhoa22mgdGTLh Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["Jm7bhoa22mgdGTLh0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Neoadjuvant modified FOLFIRINOX plus nivolumab in borderline-resectable pancreatic ductal adenocarcinoma: a pilot phase 1 trial→ 6 datasets · publication
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- pancreas
- Condition
- pancreatic adenocarcinoma
- Modality
- RNA
- Observations
- 159,670
- Transcripts
- 53,863,654
- Tier
- bronze
- Size
- 2.7 GB
- Sample ID
- GSM9372006
- License
- NCBI GEO policy
- Published
- Dec 15, 2025
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