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~71 GB
AssayVisium
Samplemultiple · brain
KindComparison
10.1038/s41587-023-01937-y ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="doi-10.1038/s41587-023-01937-y")
coll.ordered_artifacts.df()                 # the 19 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

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
Open in Vitessce
Visium
Mouse brain
NCBI668
mouse brain 3.0 GB 2,913 obs silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size3.0 GB
Obs2,913
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
NCBI660
mouse brain 2.8 GB 3,504 obs silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size2.8 GB
Obs3,504
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
NCBI653
human brain Parkinson disease 4.1 GB 4,633 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
ConditionParkinson disease
Size4.1 GB
Obs4,633
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
NCBI663
mouse brain 3.5 GB 2,964 obs silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size3.5 GB
Obs2,964
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
NCBI669
mouse brain 3.2 GB 3,163 obs silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size3.2 GB
Obs3,163
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
NCBI666
mouse brain 3.9 GB 3,120 obs silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size3.9 GB
Obs3,120
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
NCBI662
mouse brain 3.7 GB 3,357 obs silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size3.7 GB
Obs3,357
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
NCBI658
mouse brain 2.9 GB 3,116 obs silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size2.9 GB
Obs3,116
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
NCBI667
mouse brain 3.6 GB 2,675 obs silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size3.6 GB
Obs2,675
Magnification40x · 0.171 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
NCBI671
mouse brain 3.4 GB 2,856 obs silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size3.4 GB
Obs2,856
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
NCBI657
human brain Parkinson disease 4.5 GB 3,900 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
ConditionParkinson disease
Size4.5 GB
Obs3,900
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
NCBI659
mouse brain 3.0 GB 3,617 obs silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size3.0 GB
Obs3,617
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
NCBI664
mouse brain 3.6 GB 3,017 obs silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size3.6 GB
Obs3,017
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
NCBI655
human brain Parkinson disease 4.9 GB 4,984 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
ConditionParkinson disease
Size4.9 GB
Obs4,984
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
NCBI661
mouse brain 3.7 GB 3,601 obs silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size3.7 GB
Obs3,601
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
NCBI654
human brain Parkinson disease 4.7 GB 4,868 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
ConditionParkinson disease
Size4.7 GB
Obs4,868
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
NCBI670
mouse brain 3.4 GB 3,002 obs silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size3.4 GB
Obs3,002
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
NCBI656
human brain Parkinson disease 5.1 GB 4,968 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
ConditionParkinson disease
Size5.1 GB
Obs4,968
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
NCBI665
mouse brain 3.9 GB 2,918 obs silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size3.9 GB
Obs2,918
Magnification40x · 0.173 µm/px
silver H&E Open in Vitessce

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}
}