Spatial & temporal transcriptomic atlas of mouse intestinal regeneration in the jejunum (Visium HD, radiation time-course).
from sddb import Catalog
cohort = Catalog().collection("geo-gse303705-mouse-intestine-regeneration")
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/")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-gse303705-mouse-intestine-regeneration")
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()]# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse303705-mouse-intestine-regeneration --dest data/Licenses: 4 NCBI GEO policy
