Collections / geo-gse294759

geo-gse294759

Datasets3
Size~147 MB
AssayStereo-seq
Samplemultiple · multiple
KindOther
Flag a data issue
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse294759")
cohort.members        # the 3 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-gse294759")
coll.ordered_artifacts.to_dataframe()   # the 3 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-gse294759 --dest data/
Install (Python 3.12+) Docs →

Licenses: 3 NCBI GEO policy

Member datasets · 3
Open in Vitessce
Stereo-seq
Mouse heart
GSM8919110
mouse heart 64.5 MB 39,019 obs bronze NCBI GEO policy
TechnologyStereo-seq
Organismmouse
Tissueheart
Size64.5 MB
Obs39,019
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
Stereo-seq
Human lung
GSM8919113
human lung 13.7 MB 4,451 obs bronze NCBI GEO policy
TechnologyStereo-seq
Organismhuman
Tissuelung
Size13.7 MB
Obs4,451
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
Stereo-seq
Mouse head
GSM8919109
mouse head 68.6 MB 19,223 obs bronze NCBI GEO policy
TechnologyStereo-seq
Organismmouse
Tissuehead
Size68.6 MB
Obs19,223
bronze NCBI GEO policy Open in Vitessce