Collections / spatialLIBD

spatialLIBD

Datasets12
Size~5.7 GB
AssayVisium
Samplehuman · brain
KindPublication
Flag a data issue
10.1038/s41593-020-00787-0 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("doi-10-1038-s41593-020-00787-0")
cohort.members        # the 12 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/s41593-020-00787-0")
coll.ordered_artifacts.to_dataframe()   # the 12 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-s41593-020-00787-0 --dest data/
Install (Python 3.12+) Docs →

Licenses: 12 CC BY-NC-SA 4.0

About the study

Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex.

Read the abstract at the source →
Member datasets · 12
Open in Vitessce
Visium
Human brain
MISC2
human brain 447 MB 3,592 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Size447 MB
Spots3,592
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
MISC5
human brain 474 MB 4,015 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Size474 MB
Spots4,015
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
MISC12
human brain 493 MB 4,226 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Size493 MB
Spots4,226
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
MISC8
human brain 439 MB 3,661 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Size439 MB
Spots3,661
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
MISC4
human brain 464 MB 3,639 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Size464 MB
Spots3,639
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
MISC10
human brain 534 MB 4,789 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Size534 MB
Spots4,789
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
MISC3
human brain 460 MB 3,673 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Size460 MB
Spots3,673
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
MISC7
human brain 435 MB 3,498 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Size435 MB
Spots3,498
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
MISC11
human brain 494 MB 4,384 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Size494 MB
Spots4,384
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
MISC9
human brain 536 MB 4,634 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Size536 MB
Spots4,634
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
MISC6
human brain 475 MB 4,110 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Size475 MB
Spots4,110
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
MISC1
human brain 441 MB 3,460 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Size441 MB
Spots3,460
silver H&E Open in Vitessce

Cite this collection

doi.org/10.1038/s41593-020-00787-0 ↗
BibTeX 
@article{Maynard_2021,
  title = {Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex},
  volume = {24},
  ISSN = {1546-1726},
  url = {http://dx.doi.org/10.1038/s41593-020-00787-0},
  DOI = {10.1038/s41593-020-00787-0},
  number = {3},
  journal = {Nature Neuroscience},
  publisher = {Springer Science and Business Media LLC},
  author = {Maynard, Kristen R. and Collado-Torres, Leonardo and Weber, Lukas M. and Uytingco, Cedric and Barry, Brianna K. and Williams, Stephen R. and Catallini, Joseph L. and Tran, Matthew N. and Besich, Zachary and Tippani, Madhavi and Chew, Jennifer and Yin, Yifeng and Kleinman, Joel E. and Hyde, Thomas M. and Rao, Nikhil and Hicks, Stephanie C. and Martinowich, Keri and Jaffe, Andrew E.},
  year = {2021},
  month = Feb,
  pages = {425–436}
}