Collections / Dynamic fibroblast-immune interactions shape recovery after brain injury [Visium]

Dynamic fibroblast-immune interactions shape recovery after brain injury [Visium]

Fibroblasts and immune cells coordinate tissue regeneration and necessary scarring after injury. In the brain, fibroblasts are border-enriched cells whose dynamic molecular states and immune interactions after injury remain unclear. We used spatial transcriptomics (10X Visium) to spatiotemporally profile CNS wound healing responses, including stromal and immune responses, after photothrombotic (PT) injury.

Datasets4
Size~158 MB
AssayVisium
Samplemouse · brain
KindTime course
Flag a data issue
PMID:40903576 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse254161")
cohort.members        # the 4 datasets as a table

print(cohort.licenses())              # check the terms before you download

sdatas = cohort.to_dict()             # {uid: SpatialData}, cached locally
# or keep the .zarr files in a folder of your choice:
# sdatas = cohort.to_dict(dest="data/")
Install (Python 3.12+) Docs →
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")
coll = db.Collection.get(key="geo-gse254161")
coll.ordered_artifacts.to_dataframe()   # the 4 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]
Install (Python 3.12+) Docs →
Shell 
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse254161 --dest data/
Install (Python 3.12+) Docs →

Licenses: 4 NCBI GEO policy

Member datasets · 4
Open in Vitessce
Visium
Mouse brain
GSM8035260
mouse brain 39.2 MB 2,170 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Size39.2 MB
Spots2,170
Magnificationother · 3.671 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM8035258
mouse brain 37.7 MB 2,743 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Size37.7 MB
Spots2,743
Magnificationother · 3.550 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM8035261
mouse brain 44.8 MB 2,502 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Size44.8 MB
Spots2,502
Magnificationother · 4.636 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM8035259
mouse brain 36.5 MB 1,925 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Size36.5 MB
Spots1,925
Magnificationother · 3.548 µm/px
bronze H&E NCBI GEO policy Open in Vitessce

Cite this collection

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}
}