Xenium
Human colonic mucosa
Single-cell spatial transcriptomics of formalin-fixed, paraffin-embedded biopsies reveals colitis-associated cell networks [Xenium]: Xenium_HC-UC_290_Rep1 (Non-IBD controls and patients with ulcerative colitis (UC))
silver Under review Interactive viewer ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 105288, 51124), (1, 52644, 25562), (1, 26322, 12781), (1, 13161, 6390), (1, 6580, 3195)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (105288, 51124), (52644, 25562), (26322, 12781), (13161, 6390), (6580, 3195)
│ └── 'nucleus_labels': DataTree[yx] (105288, 51124), (52644, 25562), (26322, 12781), (13161, 6390), (6580, 3195)
├── Points
│ └── 'transcripts': DataFrame with shape: (64467461, 10) (3D points)
├── Shapes
│ └── 'cell_circles': GeoDataFrame shape: (434666, 2) (2D shapes)
└── Tables
└── 'table': AnnData (434666, 290)
with coordinate systems:
▸ 'global', with elements:
morphology_mip (Images), cell_labels (Labels), nucleus_labels (Labels), transcripts (Points), cell_circles (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("694cj6OPS3ClKCmA0000")
ds.elements() # inspect without downloading
sdata = ds.to_sdata() # cached locally, reused
print(sdata) 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("694cj6OPS3ClKCmA") # 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 Shell
# sddb client: download the .zarr into data/
sddb-cli download 694cj6OPS3ClKCmA0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/694cj6OPS3ClKCmA
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 694cj6OPS3ClKCmALicense: NCBI GEO policy
Metadata
- Technology
- Xenium
- Vendor
- 10x Genomics
- Organism
- human
- Tissue
- colonic mucosa
- Modality
- RNA
- Observations (cells)
- 434,666
- Transcripts
- 64,467,461
- Target genes
- 290
- Tier
- silver
- Size
- 5.7 GB
- Sample ID
- GSM8636483
- License
- NCBI GEO policy
- Published
- May 21, 2026
- Review
- per-sample diagnosis not stated: the slide carries biopsies of non-IBD controls and patients with ulcerative colitis (UC) with no per-biopsy disease field; disease stays unknown
Cite this dataset
doi.org/10.1172/JCI202488 ↗ BibTeX
@article{geo:GSE282123,
doi = {10.1172/JCI202488},
title = {Single-cell spatial transcriptomics of formalin-fixed, paraffin-embedded biopsies reveals colitis-associated cell networks [Xenium]: Xenium_HC-UC-ICI_290_Rep1 (Non-IBD controls and patients with either ulcerative colitis (UC) or immune checkpoint inhibitor-induced colitis (ICI))},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB