10x Xenium

Human small intestine

GSM8968706

bronze Interactive viewer Crohn disease Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'morphology_focus': DataTree[cyx] (4, 30714, 34179), (4, 15357, 17089), (4, 7678, 8544), (4, 3839, 4272), (4, 1919, 2136)
├── Labels
│     ├── 'cell_labels': DataTree[yx] (30053, 34032), (15026, 17016), (7513, 8508), (3756, 4254), (1878, 2127)
│     └── 'nucleus_labels': DataTree[yx] (28973, 33544), (14486, 16772), (7243, 8386), (3621, 4193), (1810, 2096)
├── Points
│     └── 'transcripts': DataFrame with shape: (17104013, 13) (3D points)
├── Shapes
│     ├── 'cell_boundaries': GeoDataFrame shape: (92990, 1) (2D shapes)
│     ├── 'cell_circles': GeoDataFrame shape: (92990, 2) (2D shapes)
│     └── 'nucleus_boundaries': GeoDataFrame shape: (85773, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (92990, 471)
with coordinate systems:
    ▸ 'global', with elements:
        morphology_focus (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("pseCWlpzybxMWO4d0000")
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("pseCWlpzybxMWO4d")   # 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 pseCWlpzybxMWO4d0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/pseCWlpzybxMWO4d

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid pseCWlpzybxMWO4d

Install (Python 3.12+) Docs →

License: NCBI GEO policy

View on Lamin ↗ Open in Vitessce ↗ Flag a data issue

Metadata

Technology: 10x Xenium
Organism: human
Tissue: small intestine
Condition: Crohn disease
Modality: RNA
Observations (cells): 92,990
Transcripts: 17,104,013
Tier: bronze
Size: 4.6 GB
Sample ID: GSM8968706
License: NCBI GEO policy
Published: Sep 17, 2025

Cite this dataset

doi.org/10.1016/j.cell.2025.08.029 ↗

BibTeX

@article{Bauer_Rowe_2025,
  title = {Creeping fat-derived mechanosensitive fibroblasts drive intestinal fibrosis in Crohn’s disease strictures},
  volume = {188},
  ISSN = {0092-8674},
  url = {http://dx.doi.org/10.1016/j.cell.2025.08.029},
  DOI = {10.1016/j.cell.2025.08.029},
  number = {23},
  journal = {Cell},
  publisher = {Elsevier BV},
  author = {Bauer-Rowe, Khristian E. and Pham, Benjamin and Griffin, Michelle and Liang, Norah E. and Kim, Alexia and Lu, John M. and Januszyk, Michael and Guo, Jason L. and De Santis, Stefania and Xing, Yue and Prystupa, Aleksandr and Sidhu, Ikjot and Suh, Elijah J. and Foster, Deshka S. and Korah, Maria and Goyal, Alka and Wan, Derrick C. and Norton, Jeffrey A. and Delitto, Daniel and Pizarro, Theresa T. and Naik, Shruti L. and Hyun, Jeong S. and Longaker, Michael T.},
  year = {2025},
  month = Nov,
  pages = {6536–6553.e26}
}

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