Human colonic mucosa

Single-cell spatial transcriptomics of formalin-fixed, paraffin-embedded biopsies reveals colitis-associated cell networks [Xenium]: Xenium_HC-UC-ICI_5k (Non-IBD controls and patients with either ulcerative colitis (UC) or immune checkpoint inhibitor-induced colitis (ICI))

SpatialData object
├── Images
│     └── 'morphology_focus': DataTree[cyx] (4, 91924, 42640), (4, 45962, 21320), (4, 22981, 10660), (4, 11490, 5330), (4, 5745, 2665)
├── Labels
│     ├── 'cell_labels': DataTree[yx] (91924, 42640), (45962, 21320), (22981, 10660), (11490, 5330), (5745, 2665)
│     └── 'nucleus_labels': DataTree[yx] (91924, 42640), (45962, 21320), (22981, 10660), (11490, 5330), (5745, 2665)
├── Points
│     └── 'transcripts': DataFrame with shape: (89973357, 11) (3D points)
├── Shapes
│     └── 'cell_circles': GeoDataFrame shape: (372549, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (372549, 4737)
with coordinate systems:
    ▸ 'global', with elements:
        morphology_focus (Images), cell_labels (Labels), nucleus_labels (Labels), transcripts (Points), cell_circles (Shapes)

from sddb import Catalog

ds = Catalog().dataset("PjLVuHVGbvZYE5Ci0000")
ds.elements()          # inspect without downloading
sdata = ds.to_sdata()  # cached locally, reused
print(sdata)

import lamindb as ln

db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("PjLVuHVGbvZYE5Ci")   # 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

# sddb client: download the .zarr into data/
sddb-cli download PjLVuHVGbvZYE5Ci0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/PjLVuHVGbvZYE5Ci

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid PjLVuHVGbvZYE5Ci

Metadata

Technology

Xenium

Vendor

10x Genomics

Organism

human

Tissue

colonic mucosa

Modality

RNA

Observations (cells)

372,549

Transcripts

89,973,357

Target genes

4737

Tier

silver

Size

16.0 GB

Sample ID

GSM9282953

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 either ulcerative colitis (UC) or immune checkpoint inhibitor-induced colitis (ICI) with no per-biopsy disease field; disease stays unknown

@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}
}