10x Xenium

Human pancreas

GSM9372003

bronze Interactive viewer pancreatic adenocarcinoma Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'morphology_mip': DataArray[cyx] (1, 30683, 48344)
├── Labels
│     ├── 'cell_labels': DataTree[yx] (30677, 47178), (15338, 23589), (7669, 11794), (3834, 5897), (1917, 2948)
│     └── 'nucleus_labels': DataTree[yx] (30658, 47138), (15329, 23569), (7664, 11784), (3832, 5892), (1916, 2946)
├── Points
│     └── 'transcripts': DataFrame with shape: (58994585, 13) (3D points)
├── Shapes
│     ├── 'cell_boundaries': GeoDataFrame shape: (133272, 1) (2D shapes)
│     ├── 'cell_circles': GeoDataFrame shape: (133272, 2) (2D shapes)
│     └── 'nucleus_boundaries': GeoDataFrame shape: (133126, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (133272, 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)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("n9ZxbmGR8CCbUhgN0000")
ds.elements()          # inspect without downloading
sdata = ds.to_sdata()  # cached locally, reused
print(sdata)

Install (Python 3.12+) Docs →

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("n9ZxbmGR8CCbUhgN")   # 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

Install (Python 3.12+) Docs →

Shell

# sddb client: download the .zarr into data/
sddb-cli download n9ZxbmGR8CCbUhgN0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/n9ZxbmGR8CCbUhgN

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid n9ZxbmGR8CCbUhgN

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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Part 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 (cells): 133,272
Transcripts: 58,994,585
Tier: bronze
Size: 2.7 GB
Sample ID: GSM9372003
License: NCBI GEO policy
Published: Dec 15, 2025

Cite this dataset

doi.org/10.1038/s41467-026-68976-2 ↗

BibTeX

@article{Wainberg_2026,
  title = {Neoadjuvant modified FOLFIRINOX plus nivolumab in borderline-resectable pancreatic ductal adenocarcinoma: a pilot phase 1 trial},
  volume = {17},
  ISSN = {2041-1723},
  url = {http://dx.doi.org/10.1038/s41467-026-68976-2},
  DOI = {10.1038/s41467-026-68976-2},
  number = {1},
  journal = {Nature Communications},
  publisher = {Springer Science and Business Media LLC},
  author = {Wainberg, Zev A. and Link, Jason M. and Premji, Alykhan and Zheng, Serena and Srienc, Michael and Hammons, McKensie and Kim, Shineui E. and Li, Luyi and Liu, Zeyu and Tsvetkova, Olga and Abt, Evan R. and Rosen, Lee and Kim, Stephen and King, Jonathan and Hines, O. Joe and Girgis, Mark and Sadeghi, Saeed and Olevsky, Olga and Wong, Deborah and Yonemoto, Lisa and Siney, Ann Marie and Kelly, Kim and Kivork, Christine and Tseng, Chi-Hong and Radu, Caius G. and Dawson, David W. and Donahue, Timothy R.},
  year = {2026},
  month = Jan
}

Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB