Mouse brain
NCBI668
mouse brain 3.3 GB 2,913 spots silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Spots2,913
Magnification40x · 0.172 µm/px
silver H&E
Collections / Spatial Multimodal Analysis: MALDI-MSI and Spatial Transcriptomics within the same tissue section
Spatial Multimodal Analysis: MALDI-MSI and Spatial Transcriptomics within the same tissue section
Datasets19
Size~76.1 GB
AssayVisium
Samplemultiple · brain
KindComparison
Download the whole collection
Python · sddb client
from sddb import Catalog
cohort = Catalog().collection("doi-10-1038-s41587-023-01937-y")
cohort.members # the 19 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="doi-10.1038/s41587-023-01937-y")
coll.ordered_artifacts.to_dataframe() # the 19 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 doi-10-1038-s41587-023-01937-y --dest data/Licenses: 19 CC BY-NC-SA 4.0
About the study
Spatial multimodal analysis of transcriptomes and metabolomes in tissues.
We present a spatial omics approach that combines histology, mass spectrometry imaging and spatial transcriptomics to facilitate precise measurements of mRNA transcripts and low-molecular-weight metabolites across tissue regions. The workflow is compatible with commercially available Visium glass slides. We demonstrate the potential of our method using mouse and human brain samples in the context of dopamine and Parkinson's disease.
Member datasets · 19
Mouse brain
NCBI660
mouse brain 3.0 GB 3,504 spots silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Spots3,504
Magnification40x · 0.172 µm/px
silver H&E
Human brain
NCBI653
human brain Parkinson disease 4.4 GB 4,633 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
ConditionParkinson disease
Spots4,633
Magnification40x · 0.172 µm/px
silver H&E
Mouse brain
NCBI663
mouse brain 3.7 GB 2,964 spots silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Spots2,964
Magnification40x · 0.172 µm/px
silver H&E
Mouse brain
NCBI669
mouse brain 3.4 GB 3,163 spots silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Spots3,163
Magnification40x · 0.172 µm/px
silver H&E
Mouse brain
NCBI666
mouse brain 4.2 GB 3,120 spots silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Spots3,120
Magnification40x · 0.172 µm/px
silver H&E
Mouse brain
NCBI662
mouse brain 4.0 GB 3,357 spots silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Spots3,357
Magnification40x · 0.172 µm/px
silver H&E
Mouse brain
NCBI658
mouse brain 3.1 GB 3,116 spots silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Spots3,116
Magnification40x · 0.172 µm/px
silver H&E
Mouse brain
NCBI667
mouse brain 3.9 GB 2,675 spots silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Spots2,675
Magnification40x · 0.171 µm/px
silver H&E
Mouse brain
NCBI671
mouse brain 3.6 GB 2,856 spots silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Spots2,856
Magnification40x · 0.172 µm/px
silver H&E
Human brain
NCBI657
human brain Parkinson disease 4.9 GB 3,900 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
ConditionParkinson disease
Spots3,900
Magnification40x · 0.172 µm/px
silver H&E
Mouse brain
NCBI659
mouse brain 3.2 GB 3,617 spots silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Spots3,617
Magnification40x · 0.172 µm/px
silver H&E
Mouse brain
NCBI664
mouse brain 3.9 GB 3,017 spots silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Spots3,017
Magnification40x · 0.172 µm/px
silver H&E
Human brain
NCBI655
human brain Parkinson disease 5.3 GB 4,984 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
ConditionParkinson disease
Spots4,984
Magnification40x · 0.172 µm/px
silver H&E
Mouse brain
NCBI661
mouse brain 3.9 GB 3,601 spots silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Spots3,601
Magnification40x · 0.172 µm/px
silver H&E
Human brain
NCBI654
human brain Parkinson disease 5.1 GB 4,868 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
ConditionParkinson disease
Spots4,868
Magnification40x · 0.172 µm/px
silver H&E
Mouse brain
NCBI670
mouse brain 3.6 GB 3,002 spots silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Spots3,002
Magnification40x · 0.172 µm/px
silver H&E
Human brain
NCBI656
human brain Parkinson disease 5.5 GB 4,968 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
ConditionParkinson disease
Spots4,968
Magnification40x · 0.172 µm/px
silver H&E
Mouse brain
NCBI665
mouse brain 4.2 GB 2,918 spots silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Spots2,918
Magnification40x · 0.173 µm/px
silver H&E
Cite this collection
doi.org/10.1038/s41587-023-01937-y ↗ BibTeX
@article{Vicari_2023,
title = {Spatial multimodal analysis of transcriptomes and metabolomes in tissues},
volume = {42},
ISSN = {1546-1696},
url = {http://dx.doi.org/10.1038/s41587-023-01937-y},
DOI = {10.1038/s41587-023-01937-y},
number = {7},
journal = {Nature Biotechnology},
publisher = {Springer Science and Business Media LLC},
author = {Vicari, Marco and Mirzazadeh, Reza and Nilsson, Anna and Shariatgorji, Reza and Bjärterot, Patrik and Larsson, Ludvig and Lee, Hower and Nilsson, Mats and Foyer, Julia and Ekvall, Markus and Czarnewski, Paulo and Zhang, Xiaoqun and Svenningsson, Per and Käll, Lukas and Andrén, Per E. and Lundeberg, Joakim},
year = {2023},
month = Sept,
pages = {1046–1050}
}