The tumor microenvironment of glioblastoma (GBM) is characterized by a high proportion of glioma-associated macrophages/microglia (GAMs). We performed spatial analysis (Visium) to profile GAMs in human GBM.
from sddb import Catalog
cohort = Catalog().collection("geo-gse273432")
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-gse273432")
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-gse273432 --dest data/Licenses: 4 NCBI GEO policy
@article{Matsuzaki_2025,
title = {Abnormal Vessels Potentially Accelerate Glioblastoma Proliferation by Inducing the Protumor Activation of Macrophages},
volume = {116},
ISSN = {1349-7006},
url = {http://dx.doi.org/10.1111/cas.70014},
DOI = {10.1111/cas.70014},
number = {4},
journal = {Cancer Science},
publisher = {Wiley},
author = {Matsuzaki, Hiroaki and Kai, Keitaro and Komohara, Yoshihiro and Yano, Hiromu and Pan, Cheng and Fujiwara, Yukio and Yamada, Rin and Iwauchi, Ai and Fukasawa, Nei and Tanaka, Toshihide and Shimoda, Masayuki and Watanabe, Hiroshi and Maruyama, Toru and Takeo, Toru and Mikami, Yoshiki and Mukasa, Akitake},
year = {2025},
month = Feb,
pages = {897–909}
}