Visium
Mouse brain
GSM8711465
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8711465_3-5_C1_4wk_NT_hires_image': DataArray[cyx] (3, 1856, 2000)
│ └── 'GSM8711465_3-5_C1_4wk_NT_lowres_image': DataArray[cyx] (3, 557, 600)
├── Shapes
│ └── 'GSM8711465_3-5_C1_4wk_NT': GeoDataFrame shape: (2779, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2779, 32285)
with coordinate systems:
▸ 'GSM8711465_3-5_C1_4wk_NT', with elements:
GSM8711465_3-5_C1_4wk_NT_hires_image (Images), GSM8711465_3-5_C1_4wk_NT_lowres_image (Images), GSM8711465_3-5_C1_4wk_NT (Shapes)
▸ 'GSM8711465_3-5_C1_4wk_NT_downscaled_hires', with elements:
GSM8711465_3-5_C1_4wk_NT_hires_image (Images), GSM8711465_3-5_C1_4wk_NT (Shapes)
▸ 'GSM8711465_3-5_C1_4wk_NT_downscaled_lowres', with elements:
GSM8711465_3-5_C1_4wk_NT_lowres_image (Images), GSM8711465_3-5_C1_4wk_NT (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("HGSiH9w0bvhLg3Ab0000")
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("HGSiH9w0bvhLg3Ab") # 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 HGSiH9w0bvhLg3Ab0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/HGSiH9w0bvhLg3Ab
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid HGSiH9w0bvhLg3AbLicense: NCBI GEO policy
Part of collection
Distinct Molecular Patterns in R6/2 HD Mouse Brain: Insights from Spatiotemporal Transcriptomics [Spatial Transcriptomics]→ 16 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- brain
- Modality
- RNA
- Observations (spots)
- 2,779
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 1,856 px
- mpp
- 3.621 µm/px
- Size
- 31.5 MB
- Sample ID
- GSM8711465
- License
- NCBI GEO policy
- Published
- Jun 24, 2025
Cite this dataset
doi.org/10.1016/j.neuron.2025.05.014 ↗ BibTeX
@article{Burns_2025,
title = {Distinct molecular patterns in R6/2 HD mouse brain: Insights from spatiotemporal transcriptomics},
volume = {113},
ISSN = {0896-6273},
url = {http://dx.doi.org/10.1016/j.neuron.2025.05.014},
DOI = {10.1016/j.neuron.2025.05.014},
number = {15},
journal = {Neuron},
publisher = {Elsevier BV},
author = {Burns, Mara S. and Miramontes, Ricardo and Wu, Jie and Gulia, Ravinder and Saddala, Madhu S. and Lau, Alice L. and Quach, Tiffany and Reidling, John C. and Swarup, Vivek and La Spada, Albert R. and Lim, Ryan G. and Thompson, Leslie M.},
year = {2025},
month = Aug,
pages = {2416–2437.e6}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB