Visium

Human perianal skin

GSM8521498

silver Interactive viewer H&E Crohn disease No linked publication

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'GSM8521498_PCD1-ST_full_image': DataTree[cyx] (3, 3000, 3000), (3, 1500, 1500), (3, 750, 750), (3, 375, 375), (3, 187, 187)
│     ├── 'GSM8521498_PCD1-ST_hires_image': DataArray[cyx] (3, 1858, 2000)
│     └── 'GSM8521498_PCD1-ST_lowres_image': DataArray[cyx] (3, 557, 600)
├── Shapes
│     └── 'GSM8521498_PCD1-ST': GeoDataFrame shape: (7290, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (7290, 18085)
with coordinate systems:
    ▸ 'GSM8521498_PCD1-ST', with elements:
        GSM8521498_PCD1-ST_full_image (Images), GSM8521498_PCD1-ST_hires_image (Images), GSM8521498_PCD1-ST_lowres_image (Images), GSM8521498_PCD1-ST (Shapes)
    ▸ 'GSM8521498_PCD1-ST_downscaled_hires', with elements:
        GSM8521498_PCD1-ST_hires_image (Images), GSM8521498_PCD1-ST (Shapes)
    ▸ 'GSM8521498_PCD1-ST_downscaled_lowres', with elements:
        GSM8521498_PCD1-ST_lowres_image (Images), GSM8521498_PCD1-ST (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("3y06ryU7GYXVtnk90000")
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("3y06ryU7GYXVtnk9")   # 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 3y06ryU7GYXVtnk90000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/3y06ryU7GYXVtnk9

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 3y06ryU7GYXVtnk9

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): 7,290
Tier: silver
Chemistry: Visium v1
Resolution: 2,000 × 1,858 px
mpp: 4.548 µm/px
Size: 126 MB
Sample ID: GSM8521498
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