Visium
Human entorhinal cortex
GSM9235045
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM9235045_V13B23-366_D1_hires_image': DataArray[cyx] (3, 2000, 1787)
│ └── 'GSM9235045_V13B23-366_D1_lowres_image': DataArray[cyx] (3, 600, 536)
├── Shapes
│ └── 'GSM9235045_V13B23-366_D1': GeoDataFrame shape: (4992, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4992, 36601)
with coordinate systems:
▸ 'GSM9235045_V13B23-366_D1', with elements:
GSM9235045_V13B23-366_D1_hires_image (Images), GSM9235045_V13B23-366_D1_lowres_image (Images), GSM9235045_V13B23-366_D1 (Shapes)
▸ 'GSM9235045_V13B23-366_D1_downscaled_hires', with elements:
GSM9235045_V13B23-366_D1_hires_image (Images), GSM9235045_V13B23-366_D1 (Shapes)
▸ 'GSM9235045_V13B23-366_D1_downscaled_lowres', with elements:
GSM9235045_V13B23-366_D1_lowres_image (Images), GSM9235045_V13B23-366_D1 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("AlqTeYiSRNzzoiP50000")
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("AlqTeYiSRNzzoiP5") # 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 AlqTeYiSRNzzoiP50000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/AlqTeYiSRNzzoiP5
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid AlqTeYiSRNzzoiP5License: NCBI GEO policy
Part of collection
Spatial and single cell transcriptomics in the human Entorhinal Cortex across diverse risk of Alzheimer’s disease [Visium]→ 31 datasets · other
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- entorhinal cortex
- Modality
- RNA
- Observations (spots)
- 4,992
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 1,787 × 2,000 px
- mpp
- 4.359 µm/px
- Size
- 17.1 MB
- Sample ID
- GSM9235045
- License
- NCBI GEO policy
- Published
- Nov 14, 2025
Cite this dataset
doi.org/10.1101/2025.11.20.689483 ↗ BibTeX
@article{Huuki_Myers_2025,
title = {<i>APOE</i>
E4 Alzheimer’s Risk Converges on an Oligodendrocyte Subtype in the Human Entorhinal Cortex},
url = {http://dx.doi.org/10.1101/2025.11.20.689483},
DOI = {10.1101/2025.11.20.689483},
publisher = {openRxiv},
author = {Huuki-Myers, Louise A. and Divecha, Heena R. and Bach, Svitlana V. and Valentine, Madeline R. and Eagles, Nicholas J. and Mulvey, Bernard and Bharadwaj, Rahul A. and Zhang, Ruth and Evans, James R. and Grant-Peters, Melissa and Miller, Ryan A. and Kleinman, Joel E. and Han, Shizhong and Hyde, Thomas M. and Page, Stephanie C. and Weinberger, Daniel R. and Martinowich, Keri and Ryten, Mina and Maynard, Kristen R. and Collado-Torres, Leonardo},
year = {2025},
month = Nov
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB