Visium
Mouse brain
brain5
silver Interactive viewer H&E ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8604634_20986X3_images_hires_image': DataArray[cyx] (3, 2000, 1413)
│ └── 'GSM8604634_20986X3_images_lowres_image': DataArray[cyx] (3, 600, 424)
├── Shapes
│ └── 'GSM8604634_20986X3_images': GeoDataFrame shape: (2808, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2808, 19465)
with coordinate systems:
▸ 'GSM8604634_20986X3_images', with elements:
GSM8604634_20986X3_images_hires_image (Images), GSM8604634_20986X3_images_lowres_image (Images), GSM8604634_20986X3_images (Shapes)
▸ 'GSM8604634_20986X3_images_downscaled_hires', with elements:
GSM8604634_20986X3_images_hires_image (Images), GSM8604634_20986X3_images (Shapes)
▸ 'GSM8604634_20986X3_images_downscaled_lowres', with elements:
GSM8604634_20986X3_images_lowres_image (Images), GSM8604634_20986X3_images (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("cKuvsUoeHQ9OAjqA0001")
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("cKuvsUoeHQ9OAjqA") # 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 cKuvsUoeHQ9OAjqA0001 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/cKuvsUoeHQ9OAjqA
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid cKuvsUoeHQ9OAjqALicense: NCBI GEO policy
Part of collection
Spatial component of: CELSR3 deficiency leads to tic-related behaviors and dopaminergic alterations in the striatum→ 4 datasets · other
Metadata
- Technology
- Visium
- Vendor
- 10x Genomics
- Organism
- mouse
- Tissue
- brain
- Modality
- RNA
- Observations (spots)
- 2,808
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 1,413 × 2,000 px
- mpp
- 5.303 µm/px
- Size
- 75.3 MB
- Sample ID
- GSM8604634
- License
- NCBI GEO policy
- Published
- Jun 12, 2025
Cite this dataset
doi.org/10.1038/s41380-025-02970-w ↗ BibTeX
@article{geo:GSE280709,
doi = {10.1038/s41380-025-02970-w},
title = {brain6},
year = {2025}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB