Collections / geo-gse294097

geo-gse294097

Datasets4
Size~1.3 MB
TechnologyStereo-seq
Samplezebrafish · brain
KindOther
Flag a data issue
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse294097")
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-gse294097")
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-gse294097 --dest data/
Install (Python 3.12+) Docs →

Licenses: 4 NCBI GEO policy

Member datasets · 4
Open in Vitessce
Stereo-seq
Zebrafish brain
GSM8898657
zebrafish brain 333 KB 5,609 obs bronze NCBI GEO policy
TechnologyStereo-seq
Organismzebrafish
Tissuebrain
Size333 KB
Obs5,609
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
Stereo-seq
Zebrafish brain
GSM8898655
zebrafish brain 380 KB 6,764 obs bronze NCBI GEO policy
TechnologyStereo-seq
Organismzebrafish
Tissuebrain
Size380 KB
Obs6,764
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
Stereo-seq
Zebrafish brain
GSM8898656
zebrafish brain 374 KB 6,663 obs bronze NCBI GEO policy
TechnologyStereo-seq
Organismzebrafish
Tissuebrain
Size374 KB
Obs6,663
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
Stereo-seq
Zebrafish brain
GSM8898654
zebrafish brain 260 KB 3,971 obs bronze NCBI GEO policy
TechnologyStereo-seq
Organismzebrafish
Tissuebrain
Size260 KB
Obs3,971
bronze NCBI GEO policy Open in Vitessce