Collections / Spatial transcriptomics of the mouse brain across three age groups

Spatial transcriptomics of the mouse brain across three age groups

Datasets6
Size~1.3 GB
AssayVisium
Samplemouse · brain
KindComparison
Flag a data issue
10.1016/j.cell.2023.07.027 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("doi-10-1016-j-cell-2023-07-027")
cohort.members        # the 6 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="doi-10.1016/j.cell.2023.07.027")
coll.ordered_artifacts.to_dataframe()   # the 6 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 doi-10-1016-j-cell-2023-07-027 --dest data/
Install (Python 3.12+) Docs →

Licenses: 6 CC BY-NC-SA 4.0

About the study

Atlas of the aging mouse brain reveals white matter as vulnerable foci.

Read the abstract at the source →
Member datasets · 6
Open in Vitessce
Visium
Mouse brain
NCBI717
mouse brain 207 MB 2,804 spots silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size207 MB
Spots2,804
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
NCBI720
mouse brain 216 MB 2,573 spots silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size216 MB
Spots2,573
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
NCBI715
mouse brain 222 MB 2,857 spots silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size222 MB
Spots2,857
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
NCBI718
mouse brain 237 MB 2,973 spots silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size237 MB
Spots2,973
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
NCBI719
mouse brain 213 MB 2,735 spots silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size213 MB
Spots2,735
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
NCBI716
mouse brain 231 MB 2,801 spots silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size231 MB
Spots2,801
silver H&E Open in Vitessce

Cite this collection

doi.org/10.1016/j.cell.2023.07.027 ↗
BibTeX 
@article{Hahn_2023,
  title = {Atlas of the aging mouse brain reveals white matter as vulnerable foci},
  volume = {186},
  ISSN = {0092-8674},
  url = {http://dx.doi.org/10.1016/j.cell.2023.07.027},
  DOI = {10.1016/j.cell.2023.07.027},
  number = {19},
  journal = {Cell},
  publisher = {Elsevier BV},
  author = {Hahn, Oliver and Foltz, Aulden G. and Atkins, Micaiah and Kedir, Blen and Moran-Losada, Patricia and Guldner, Ian H. and Munson, Christy and Kern, Fabian and Pálovics, Róbert and Lu, Nannan and Zhang, Hui and Kaur, Achint and Hull, Jacob and Huguenard, John R. and Grönke, Sebastian and Lehallier, Benoit and Partridge, Linda and Keller, Andreas and Wyss-Coray, Tony},
  year = {2023},
  month = Sept,
  pages = {4117–4133.e22}
}