Visium
Mouse brain
GSM8035258
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8035258_A1_0-2dpi_hires_image': DataArray[cyx] (3, 1955, 2000)
│ └── 'GSM8035258_A1_0-2dpi_lowres_image': DataArray[cyx] (3, 587, 600)
├── Shapes
│ └── 'GSM8035258_A1_0-2dpi': GeoDataFrame shape: (2743, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2743, 32285)
with coordinate systems:
▸ 'GSM8035258_A1_0-2dpi', with elements:
GSM8035258_A1_0-2dpi_hires_image (Images), GSM8035258_A1_0-2dpi_lowres_image (Images), GSM8035258_A1_0-2dpi (Shapes)
▸ 'GSM8035258_A1_0-2dpi_downscaled_hires', with elements:
GSM8035258_A1_0-2dpi_hires_image (Images), GSM8035258_A1_0-2dpi (Shapes)
▸ 'GSM8035258_A1_0-2dpi_downscaled_lowres', with elements:
GSM8035258_A1_0-2dpi_lowres_image (Images), GSM8035258_A1_0-2dpi (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("9QsmFNbj84nlxpo80000")
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("9QsmFNbj84nlxpo8") # 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 9QsmFNbj84nlxpo80000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/9QsmFNbj84nlxpo8
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 9QsmFNbj84nlxpo8License: NCBI GEO policy
Part of collection
Dynamic fibroblast-immune interactions shape recovery after brain injury [Visium]→ 4 datasets · time course
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- brain
- Modality
- RNA
- Observations (spots)
- 2,743
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 1,955 px
- mpp
- 3.550 µm/px
- Size
- 37.7 MB
- Sample ID
- GSM8035258
- License
- NCBI GEO policy
- Published
- Jun 30, 2025
Cite this dataset
doi.org/10.1038/s41586-025-09449-2 ↗ BibTeX
@article{Ewing_Crystal_2025,
title = {Dynamic fibroblast–immune interactions shape recovery after brain injury},
volume = {646},
ISSN = {1476-4687},
url = {http://dx.doi.org/10.1038/s41586-025-09449-2},
DOI = {10.1038/s41586-025-09449-2},
number = {8086},
journal = {Nature},
publisher = {Springer Science and Business Media LLC},
author = {Ewing-Crystal, Nathan A. and Mroz, Nicholas M. and Larpthaveesarp, Amara and Lizama, Carlos O. and Pennington, Remy and Chiaranunt, Pailin and Dennis, Jason I. and Chang, Anthony A. and Merrill, Eric Dean and Caryotakis, Sofia E. and Kirthivasan, Nikhita and Teo, Leon and Tsukui, Tatsuya and Katewa, Aditya and McKinsey, Gabriel L. and Nelson, Sophia C. K. and Ciesielska, Agnieszka and Lummis, Nicole C. and Pintarić, Lucija and Dahlgren, Madelene W. and Atakilit, Amha and Paidassi, Helena and Jain, Saket and Liu, Xiaodan and Xu, Duan and Aghi, Manish K. and Bourne, James A. and Paz, Jeanne T. and Daneman, Richard and Gonzalez, Fernando F. and Sheppard, Dean and Molofsky, Anna V. and Arnold, Thomas D. and Molofsky, Ari B.},
year = {2025},
month = Sept,
pages = {934–944}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB