Visium
Human liver
GSM9876375
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM9876375_NL_3_hires_image': DataArray[cyx] (3, 1967, 2000)
│ └── 'GSM9876375_NL_3_lowres_image': DataArray[cyx] (3, 590, 600)
├── Shapes
│ └── 'GSM9876375_NL_3': GeoDataFrame shape: (1521, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1521, 37481)
with coordinate systems:
▸ 'GSM9876375_NL_3', with elements:
GSM9876375_NL_3_hires_image (Images), GSM9876375_NL_3_lowres_image (Images), GSM9876375_NL_3 (Shapes)
▸ 'GSM9876375_NL_3_downscaled_hires', with elements:
GSM9876375_NL_3_hires_image (Images), GSM9876375_NL_3 (Shapes)
▸ 'GSM9876375_NL_3_downscaled_lowres', with elements:
GSM9876375_NL_3_lowres_image (Images), GSM9876375_NL_3 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("COp1g4vswSBXjMVC0000")
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("COp1g4vswSBXjMVC") # 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 COp1g4vswSBXjMVC0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/COp1g4vswSBXjMVC
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid COp1g4vswSBXjMVCLicense: NCBI GEO policy
Part of collection
Spatial transcriptomics supports a role for SOX-4 driven signaling throughout the disease course of biliary atresia→ 16 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- liver
- Modality
- RNA
- Observations (spots)
- 1,521
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 2,000 × 1,967 px
- mpp
- 3.299 µm/px
- Size
- 21.6 MB
- Sample ID
- GSM9876375
- License
- NCBI GEO policy
- Published
- Jul 20, 2026
Cite this dataset
doi.org/10.1097/HC9.0000000000000992 ↗ BibTeX
@article{geo:GSM9876375,
doi = {10.1097/HC9.0000000000000992},
title = {GSM9876375},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB