Collections / geo-gse345644

geo-gse345644

Datasets1

Size~1.3 GB

Assay10x Xenium

Samplehuman · urinary bladder

KindOther

Flag a data issue

Download the whole collection

Client Lamin CLI

Python · sddb client

from sddb import Catalog

cohort = Catalog().collection("geo-gse345644")
cohort.members        # the 1 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-gse345644")
coll.ordered_artifacts.to_dataframe()   # the 1 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-gse345644 --dest data/

Install (Python 3.12+) Docs →

Licenses: 1 NCBI GEO policy

Member datasets · 1

10x Xenium

Human urinary bladder

GSM10012265

human urinary bladder 1.3 GB 89,585 cells silver NCBI GEO policy

Technology10x Xenium

Organismhuman

Tissueurinary bladder

Size1.3 GB

Cells89,585

silver NCBI GEO policy