10x Xenium

Mouse small intestine

GSM9394258

bronze Interactive viewer Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'morphology_focus': DataTree[cyx] (4, 44283, 39783), (4, 22141, 19891), (4, 11070, 9945), (4, 5535, 4972), (4, 2767, 2486)
├── Labels
│     ├── 'cell_labels': DataTree[yx] (44283, 39783), (22141, 19891), (11070, 9945), (5535, 4972), (2767, 2486)
│     └── 'nucleus_labels': DataTree[yx] (44283, 39783), (22141, 19891), (11070, 9945), (5535, 4972), (2767, 2486)
├── Shapes
│     ├── 'cell_boundaries': GeoDataFrame shape: (384151, 1) (2D shapes)
│     ├── 'cell_circles': GeoDataFrame shape: (384151, 2) (2D shapes)
│     └── 'nucleus_boundaries': GeoDataFrame shape: (372517, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (384151, 5006)
with coordinate systems:
    ▸ 'global', with elements:
        morphology_focus (Images), cell_labels (Labels), nucleus_labels (Labels), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("GU1UzXJqJQVDq5rX0000")
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("GU1UzXJqJQVDq5rX")   # 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 GU1UzXJqJQVDq5rX0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/GU1UzXJqJQVDq5rX

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid GU1UzXJqJQVDq5rX

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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Part of collection

Eosinophils Orchestrate Intestinal Remodeling and Promote Innate Defense During Reproduction→

8 datasets · comparison

Metadata

Technology: 10x Xenium
Organism: mouse
Tissue: small intestine
Modality: RNA
Observations (cells): 384,151
Tier: bronze
Size: 9.0 GB
Sample ID: GSM9394258
License: NCBI GEO policy
Published: Apr 30, 2026

Cite this dataset

doi.org/10.1038/s41586-026-10531-6 ↗

BibTeX

@article{Huang_2026,
  title = {Eosinophils drive intestinal remodelling and innate defence in reproduction},
  volume = {654},
  ISSN = {1476-4687},
  url = {http://dx.doi.org/10.1038/s41586-026-10531-6},
  DOI = {10.1038/s41586-026-10531-6},
  number = {8117},
  journal = {Nature},
  publisher = {Springer Science and Business Media LLC},
  author = {Huang, Chenyan and Sun, Amanda and Reyes, Jojo and Ribeiro de Souza, Jessica and Cafiero, Thomas R. and Antunes Fernandes, Krist H. and Oliveira, Fabricio Marcus Silva and Qiao, Yujie and Gazzinelli-Guimaraes, Pedro and Pritykin, Yuri and Lim, Ai Ing},
  year = {2026},
  month = May,
  pages = {209–218}
}

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