Collections / Human ileum, Visium

Human ileum, Visium

Datasets4
Size~17 GB
AssayVisium
Samplehuman · intestine
KindPublication
10.1038/s41587-021-01075-3 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="doi-10.1038/s41587-021-01075-3")
coll.ordered_artifacts.df()                 # the 4 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]

# …or load each straight into memory as a SpatialData object:
sdatas = {a.key: sd.read_zarr(a.cache()) for a in coll.ordered_artifacts.all()}
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 3.9 GB 3,214 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Size3.9 GB
Obs3,214
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MEND35
human intestine 4.3 GB 3,320 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Size4.3 GB
Obs3,320
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MEND33
human intestine 4.2 GB 3,291 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Size4.2 GB
Obs3,291
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MEND34
human intestine 4.1 GB 3,294 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Size4.1 GB
Obs3,294
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}
}