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

We present a spatial omics approach that merges and expands the capabilities of independently performedin situassays on a single tissue section. Our spatial multimodal analysis combines histology, mass spectrometry imaging, and spatial transcriptomics to facilitate precise measurements of mRNA transcripts and low-molecular weight metabolites across tissue regions. We demonstrate the potential of our method using murine and human brain samples in the context of dopamine and Parkinson’s disease.

Datasets18
Size~515 MB
AssayVisium
Samplemouse · multiple
KindTime course
PMID:37667091 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse232910")
coll.ordered_artifacts.df()                 # the 18 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()}
Member datasets · 18
Open in Vitessce
Visium
Mouse caudate nucleus
GSM7392326
mouse caudate nucleus Parkinson disease 20 MB 4,984 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuecaudate nucleus
ConditionParkinson disease
Size20 MB
Obs4,984
Magnificationother · 3.545 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM7392317
mouse brain 35 MB 3,017 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size35 MB
Obs3,017
Magnificationother · 3.510 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM7392322
mouse brain 39 MB 3,617 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size39 MB
Obs3,617
Magnificationother · 3.542 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM7392310
mouse brain 27 MB 2,856 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size27 MB
Obs2,856
Magnificationother · 3.506 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM7392313
mouse brain 44 MB 2,913 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size44 MB
Obs2,913
Magnificationother · 3.504 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse caudate nucleus
GSM7392328
mouse caudate nucleus Parkinson disease 15 MB 4,633 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuecaudate nucleus
ConditionParkinson disease
Size15 MB
Obs4,633
Magnificationother · 3.545 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse caudate nucleus
GSM7392327
mouse caudate nucleus Parkinson disease 17 MB 4,868 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuecaudate nucleus
ConditionParkinson disease
Size17 MB
Obs4,868
Magnificationother · 3.544 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM7392312
mouse brain 43 MB 3,163 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size43 MB
Obs3,163
Magnificationother · 3.506 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse caudate nucleus
GSM7392325
mouse caudate nucleus Parkinson disease 16 MB 4,968 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuecaudate nucleus
ConditionParkinson disease
Size16 MB
Obs4,968
Magnificationother · 3.537 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse caudate nucleus
GSM7392324
mouse caudate nucleus Parkinson disease 13 MB 3,900 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuecaudate nucleus
ConditionParkinson disease
Size13 MB
Obs3,900
Magnificationother · 3.530 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM7392319
mouse brain 31 MB 3,357 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size31 MB
Obs3,357
Magnificationother · 3.507 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM7392321
mouse brain 39 MB 3,504 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size39 MB
Obs3,504
Magnificationother · 3.499 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM7392320
mouse brain 23 MB 3,601 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size23 MB
Obs3,601
Magnificationother · 3.511 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM7392311
mouse brain 28 MB 3,002 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size28 MB
Obs3,002
Magnificationother · 3.505 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM7392314
mouse brain 25 MB 2,675 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size25 MB
Obs2,675
Magnificationother · 3.487 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM7392316
mouse brain 28 MB 2,918 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size28 MB
Obs2,918
Magnificationother · 3.518 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM7392318
mouse brain 26 MB 2,964 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size26 MB
Obs2,964
Magnificationother · 3.507 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM7392323
mouse brain 47 MB 3,116 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size47 MB
Obs3,116
Magnificationother · 3.541 µm/px
bronze H&E Open in Vitessce

Cite this collection

No linked publication found — please cite the data source.