Visium
Human perianal skin
PCD1-ST
silver Interactive viewer H&E Crohn disease ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ ├── '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_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) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("3y06ryU7GYXVtnk90001")
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("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 Shell
# sddb client: download the .zarr into data/
sddb-cli download 3y06ryU7GYXVtnk90001 --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 3y06ryU7GYXVtnk9License: NCBI GEO policy
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
- 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
- 102 MB
- Sample ID
- GSM8521498
- 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