Visium
Mouse brain
GSM8396165
bronze Interactive viewer H&E glioma Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8396165_1070_Retpos_hires_image': DataArray[cyx] (3, 2000, 1996)
│ └── 'GSM8396165_1070_Retpos_lowres_image': DataArray[cyx] (3, 600, 599)
├── Shapes
│ └── 'GSM8396165_1070_Retpos': GeoDataFrame shape: (2725, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2725, 21834)
with coordinate systems:
▸ 'GSM8396165_1070_Retpos', with elements:
GSM8396165_1070_Retpos_hires_image (Images), GSM8396165_1070_Retpos_lowres_image (Images), GSM8396165_1070_Retpos (Shapes)
▸ 'GSM8396165_1070_Retpos_downscaled_hires', with elements:
GSM8396165_1070_Retpos_hires_image (Images), GSM8396165_1070_Retpos (Shapes)
▸ 'GSM8396165_1070_Retpos_downscaled_lowres', with elements:
GSM8396165_1070_Retpos_lowres_image (Images), GSM8396165_1070_Retpos (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("u2SzDyNzrEMFuxhG0000")
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("u2SzDyNzrEMFuxhG") # 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 u2SzDyNzrEMFuxhG0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/u2SzDyNzrEMFuxhG
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid u2SzDyNzrEMFuxhGLicense: NCBI GEO policy
Part of collection
Pericytes orchestrate a tumor-restraining microenvironment in glioblastoma [Spatial Transcriptomics]→ 8 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- brain
- Condition
- glioma
- Modality
- RNA
- Observations (spots)
- 2,725
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 1,996 × 2,000 px
- mpp
- 3.585 µm/px
- Size
- 53.0 MB
- Sample ID
- GSM8396165
- License
- NCBI GEO policy
- Published
- Oct 3, 2025
Cite this dataset
doi.org/10.1038/s41467-025-66985-1 ↗ BibTeX
@article{Braun_2025,
title = {Pericytes orchestrate a tumor-restraining microenvironment in glioblastoma},
volume = {16},
ISSN = {2041-1723},
url = {http://dx.doi.org/10.1038/s41467-025-66985-1},
DOI = {10.1038/s41467-025-66985-1},
number = {1},
journal = {Nature Communications},
publisher = {Springer Science and Business Media LLC},
author = {Braun, Sebastian and Bolivar, Paulina and Oudenaarden, Clara and Sjölund, Jonas and Bocci, Matteo and Harbst, Katja and Talkhoncheh, Mehrnaz Safaee and Phung, Bengt and Cordero, Eugenia and Rosberg, Rebecca and Johansson, Elinn and Jönsson, Göran B. and Pietras, Alexander and Pietras, Kristian},
year = {2025},
month = Dec
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB