Collections / Human ileum, Visium

Human ileum, Visium

Datasets4
Size~17.8 GB
AssayVisium
Samplehuman · intestine
KindPublication
Flag a data issue
10.1038/s41587-021-01075-3 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("doi-10-1038-s41587-021-01075-3")
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="doi-10.1038/s41587-021-01075-3")
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 doi-10-1038-s41587-021-01075-3 --dest data/
Install (Python 3.12+) Docs →

Licenses: 4 CC BY-NC-SA 4.0

About the study

Super-resolved spatial transcriptomics by deep data fusion.

Read the abstract at the source →
Member datasets · 4
Open in Vitessce
Visium
Human intestine
MEND36
human intestine 4.2 GB 3,214 spots silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Size4.2 GB
Spots3,214
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MEND35
human intestine 4.6 GB 3,320 spots silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Size4.6 GB
Spots3,320
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MEND33
human intestine 4.5 GB 3,291 spots silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Size4.5 GB
Spots3,291
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MEND34
human intestine 4.4 GB 3,294 spots silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Size4.4 GB
Spots3,294
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce

Cite this collection

doi.org/10.1038/s41587-021-01075-3 ↗
BibTeX 
@article{Bergenstr_hle_2021,
  title = {Super-resolved spatial transcriptomics by deep data fusion},
  volume = {40},
  ISSN = {1546-1696},
  url = {http://dx.doi.org/10.1038/s41587-021-01075-3},
  DOI = {10.1038/s41587-021-01075-3},
  number = {4},
  journal = {Nature Biotechnology},
  publisher = {Springer Science and Business Media LLC},
  author = {Bergenstråhle, Ludvig and He, Bryan and Bergenstråhle, Joseph and Abalo, Xesús and Mirzazadeh, Reza and Thrane, Kim and Ji, Andrew L. and Andersson, Alma and Larsson, Ludvig and Stakenborg, Nathalie and Boeckxstaens, Guy and Khavari, Paul and Zou, James and Lundeberg, Joakim and Maaskola, Jonas},
  year = {2021},
  month = Nov,
  pages = {476–479}
}