Visium
Rat brain
GSM9168624
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM9168624_8543_hires_image': DataArray[cyx] (3, 3000, 3000)
│ └── 'GSM9168624_8543_lowres_image': DataArray[cyx] (3, 600, 600)
├── Shapes
│ └── 'GSM9168624_8543': GeoDataFrame shape: (7036, 2) (2D shapes)
└── Tables
└── 'table': AnnData (7036, 19465)
with coordinate systems:
▸ 'GSM9168624_8543', with elements:
GSM9168624_8543_hires_image (Images), GSM9168624_8543_lowres_image (Images), GSM9168624_8543 (Shapes)
▸ 'GSM9168624_8543_downscaled_hires', with elements:
GSM9168624_8543_hires_image (Images), GSM9168624_8543 (Shapes)
▸ 'GSM9168624_8543_downscaled_lowres', with elements:
GSM9168624_8543_lowres_image (Images), GSM9168624_8543 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("csRGgcWa9JtmoxqB0000")
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("csRGgcWa9JtmoxqB") # 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 csRGgcWa9JtmoxqB0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/csRGgcWa9JtmoxqB
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid csRGgcWa9JtmoxqBLicense: NCBI GEO policy
Part of collection
Intercellular signaling and synaptic deconstruction uncovered by single-cell and spatial transcriptomics in an AD tauopathy model→ 4 datasets · time course
Metadata
- Technology
- Visium
- Organism
- rat
- Tissue
- brain
- Modality
- RNA
- Observations (spots)
- 7,036
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 3,000 × 3,000 px
- mpp
- 4.295 µm/px
- Size
- 59.3 MB
- Sample ID
- GSM9168624
- License
- NCBI GEO policy
- Published
- Dec 4, 2025
Cite this dataset
doi.org/10.1038/s42003-025-08959-z ↗ BibTeX
@article{Ji_2025,
title = {Intercellular signaling and synaptic deconstruction uncovered by single-cell and spatial transcriptomics in an AD tauopathy model},
volume = {8},
ISSN = {2399-3642},
url = {http://dx.doi.org/10.1038/s42003-025-08959-z},
DOI = {10.1038/s42003-025-08959-z},
number = {1},
journal = {Communications Biology},
publisher = {Springer Science and Business Media LLC},
author = {Ji, Jeff X. and Giles, Brian L. and Bhattacharjee, Surjyadipta and Kautzmann, Marie-Audrey I. and P. Masson, Alasdair and Do Carmo, Sonia and Cuello, A. Claudio and Bazan, Nicolas G.},
year = {2025},
month = Nov
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB