Visium

Human perianal skin

IPF3-ST

silver Interactive viewer H&E anal fistula ✓ Verified publication

Visium

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'GSM8521497_IPF3-ST_hires_image': DataArray[cyx] (3, 2000, 1964)
│     └── 'GSM8521497_IPF3-ST_lowres_image': DataArray[cyx] (3, 600, 589)
├── Shapes
│     └── 'GSM8521497_IPF3-ST': GeoDataFrame shape: (1890, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (1890, 18085)
with coordinate systems:
    ▸ 'GSM8521497_IPF3-ST', with elements:
        GSM8521497_IPF3-ST_hires_image (Images), GSM8521497_IPF3-ST_lowres_image (Images), GSM8521497_IPF3-ST (Shapes)
    ▸ 'GSM8521497_IPF3-ST_downscaled_hires', with elements:
        GSM8521497_IPF3-ST_hires_image (Images), GSM8521497_IPF3-ST (Shapes)
    ▸ 'GSM8521497_IPF3-ST_downscaled_lowres', with elements:
        GSM8521497_IPF3-ST_lowres_image (Images), GSM8521497_IPF3-ST (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("VkwI9LbxpVQtf55K0001")
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("VkwI9LbxpVQtf55K")   # 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 VkwI9LbxpVQtf55K0001 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/VkwI9LbxpVQtf55K

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid VkwI9LbxpVQtf55K

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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

Part of collection

Single-Cell and Spatial Multi-omics Reveal Interferon Signaling in the Pathogenesis of Perianal Fistulizing Crohn’s Disease→

6 datasets · other

Metadata

Technology: Visium
Vendor: 10x Genomics
Organism: human
Tissue: perianal skin
Condition: anal fistula
Modality: RNA
Observations (spots): 1,890
Tier: silver
Chemistry: Visium v1
Resolution: 1,964 × 2,000 px
mpp: 5.114 µm/px
Size: 29.3 MB
Sample ID: GSM8521497
License: NCBI GEO policy
Published: Jun 17, 2025

Cite this dataset

doi.org/10.1172/jci193413 ↗

BibTeX

@article{geo:GSE277387,
  doi = {10.1172/jci193413},
  title = {IPF2-ST}
}

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