Mouse intestine
NCBI685
mouse intestine ulcerative colitis 339 MB 3,547 spots silver H&E
TechnologyVisium
Organismmouse
Tissueintestine
Conditionulcerative colitis
Spots3,547
silver H&E
Collections / 10X Visium Spatial transcriptomics of murine colon at d14 (mucosa healing) in B cell sufficient-deficient mice
10X Visium Spatial transcriptomics of murine colon at d14 (mucosa healing) in B cell sufficient-deficient mice
Datasets2
Size~687 MB
AssayVisium
Samplemouse · intestine
KindComparison
Download the whole collection
Python · sddb client
from sddb import Catalog
cohort = Catalog().collection("hest-10x-visium-spatial-transcriptomics-of-murine-colon-at-d14-mucosa-healing-in-b-cell-sufficient-deficient-mice")
cohort.members # the 2 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/") 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="hest-10x-visium-spatial-transcriptomics-of-murine-colon-at-d14-mucosa-healing-in-b-cell-sufficient-deficient-mice")
coll.ordered_artifacts.to_dataframe() # the 2 members, ordered
# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()] Shell
# sddb client: download every member .zarr into data/
sddb-cli download --collection hest-10x-visium-spatial-transcriptomics-of-murine-colon-at-d14-mucosa-healing-in-b-cell-sufficient-deficient-mice --dest data/Licenses: 2 CC BY-NC-SA 4.0
Member datasets · 2
