Visium

Human perianal skin

GSM8521500

silver Interactive viewer H&E Crohn disease No linked publication

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'GSM8521500_PCD3-ST_full_image': DataTree[cyx] (3, 3000, 3000), (3, 1500, 1500), (3, 750, 750), (3, 375, 375), (3, 187, 187)
│     ├── 'GSM8521500_PCD3-ST_hires_image': DataArray[cyx] (3, 1228, 2000)
│     └── 'GSM8521500_PCD3-ST_lowres_image': DataArray[cyx] (3, 369, 600)
├── Shapes
│     └── 'GSM8521500_PCD3-ST': GeoDataFrame shape: (1791, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (1791, 18085)
with coordinate systems:
    ▸ 'GSM8521500_PCD3-ST', with elements:
        GSM8521500_PCD3-ST_full_image (Images), GSM8521500_PCD3-ST_hires_image (Images), GSM8521500_PCD3-ST_lowres_image (Images), GSM8521500_PCD3-ST (Shapes)
    ▸ 'GSM8521500_PCD3-ST_downscaled_hires', with elements:
        GSM8521500_PCD3-ST_hires_image (Images), GSM8521500_PCD3-ST (Shapes)
    ▸ 'GSM8521500_PCD3-ST_downscaled_lowres', with elements:
        GSM8521500_PCD3-ST_lowres_image (Images), GSM8521500_PCD3-ST (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("tXuz4jRNE9Eprv1l0000")
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("tXuz4jRNE9Eprv1l")   # 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 tXuz4jRNE9Eprv1l0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/tXuz4jRNE9Eprv1l

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid tXuz4jRNE9Eprv1l

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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Part of collection

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

6 datasets · comparison

Metadata

Technology: Visium
Organism: human
Tissue: perianal skin
Condition: Crohn disease
Modality: RNA
Observations (spots): 1,791
Tier: silver
Chemistry: Visium v1
Resolution: 2,000 × 1,228 px
mpp: 5.896 µm/px
Size: 51.9 MB
Sample ID: GSM8521500
License: NCBI GEO policy
Published: Jun 17, 2025

Cite this dataset

No linked publication found — please cite the data source: NCBI GEO ↗.

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