BrainImageRdata provides the brainmaps and gene expression data to be used with the companion package brainImager. BrainImageR will internally reference these datasets. They do not need to be accessed by the user directly.
To load the brainImageRdata datasets into your workspace:
hub <- ExperimentHub::ExperimentHub()
a <- list()
a[1] <- hub[["EH1434"]]
a[2] <- hub[["EH1435"]]
a[3] <- hub[["EH1436"]]
a[4] <- hub[["EH1437"]]
a[5] <- hub[["EH1438"]]
a[6] <- hub[["EH1439"]]
a[7] <- hub[["EH1440"]]
a[8] <- hub[["EH1441"]]
a[9] <- hub[["EH1442"]]
a[10] <- hub[["EH1443"]]
a[11] <- hub[["EH1444"]]
a[12] <- hub[["EH1445"]]
a[13] <- hub[["EH1446"]]
a[14] <- hub[["EH1447"]]
a[15] <- hub[["EH1448"]]
a[16] <- hub[["EH1449"]]
a[17] <- hub[["EH1450"]]
a[18] <- hub[["EH1451"]]For a full description of each object please run make-metadata.R. In brief:
EH1434:
Title: DevHum_low
For use with: BrainImageR Spatial Analysis (ie: SpatialEnrichment, CreateBrain, PlotBrain)
Developmental Timepoint: Prenatal
General Description: A list of low resolution image masks of the developing human brain. Each element in the list is a different section of the brain. Each matrix within a list element is a segment of the brain to be colored based on enrichment information.
EH1435:
Title: AdHum
For use with: BrainImageR Spatial Analysis (ie: SpatialEnrichment, CreateBrain, PlotBrain)
Developmental Timepoint: Adult
General Description: A list of low resolution image masks of the adult human brain. Each element in the list is a different section of the brain. Each matrix within a list element is a segment of the brain to be colored based on enrichment information.
EH1436:
Title: Dev_DIM
For use with: BrainImageR Spatial Analysis (ie: SpatialEnrichment, CreateBrain, PlotBrain)
Developmental Timepoint: prenatal
General Description: A list of the original dimensions of each image mask. Required to reconstruct the image.
EH1437:
Title: ad_DIM
For use with: BrainImageR Spatial Analysis (ie: SpatialEnrichment, CreateBrain, PlotBrain)
Developmental Timepoint: adult
General Description: A list of the original dimensions of each image mask. Required to reconstruct the image.
EH1438:
Title: dev_abrev
For use with: BrainImageR Spatial Analysis (ie: SpatialEnrichment, CreateBrain, PlotBrain)
Developmental Timepoint: prenatal
General Description: A list of the tissues in each brain section. Each element in the list corresponds to the same brain sections as in DevHum_low.
EH1439:
Title: ad_abrev
For use with: BrainImageR Spatial Analysis (ie: SpatialEnrichment, CreateBrain, PlotBrain)
Developmental Timepoint: adult
General Description: A list of the tissues in each brain section. Each element in the list corresponds to the same brain sections as in AdHum.
EH1440:
Title: dev_outline
For use with: BrainImageR Spatial Analysis (ie: SpatialEnrichment, CreateBrain, PlotBrain)
Developmental Timepoint: prenatal
General Description: A list of matrices containing the outline for each brain section. Each element in the list corresponds to the same brain sections as in DevHum_low.
EH1441:
Title: ad_outline
For use with: BrainImageR Spatial Analysis (ie: SpatialEnrichment, CreateBrain, PlotBrain)
Developmental Timepoint: adult
General Description: A list of matrices containing the outline for each brain section. Each element in the list corresponds to the same brain sections as in AdHum.
EH1442:
Title: ad_conversion
For use with: BrainImageR Spatial Analysis (ie: SpatialEnrichment, CreateBrain, PlotBrain)
Developmental Timepoint: adult
General Description: A matrix containing the conversion between microdissected brain regions and the more general brain regions that are plotted in the final heatmap.
EH1443:
Title: dev_slices
For use with: BrainImageR Spatial Analysis (ie: SpatialEnrichment, CreateBrain, PlotBrain)
Developmental Timepoint: prenatal
General Description: A vector of the different sections available for the prenatal brain
EH1444:
Title: ad_slices
For use with: BrainImageR Spatial Analysis (ie: SpatialEnrichment, CreateBrain, PlotBrain)
Developmental Timepoint: adult
General Description: A vector of the different sections available for the adult brain
EH1445:
Title: dev_abatissuesBygenes
For use with: BrainImageR Spatial Analysis (ie: SpatialEnrichment, CreateBrain, PlotBrain)
Developmental Timepoint: prenatal
General Description: Expression information for each microdissected region in the prenatal brain.
EH1446:
Title: ad_abatissuesBygenes
For use with: BrainImageR Spatial Analysis (ie: SpatialEnrichment, CreateBrain, PlotBrain)
Developmental Timepoint: adult
General Description: Expression information for each microdissected region in the adult brain.
EH1447:
Title: dev_colmeta
For use with: BrainImageR Spatial Analysis (ie: SpatialEnrichment, CreateBrain, PlotBrain)
Developmental Timepoint: prenatal
General Description: sample metadata provided by the Allen Brain Institute for the prenatal brain
EH1448:
Title: ad_colmeta
For use with: BrainImageR Spatial Analysis (ie: SpatialEnrichment, CreateBrain, PlotBrain)
Developmental Timepoint: adult
General Description: sample metadata provided by the Allen Brain Institute for the adult brain
EH1449:
Title: rowmeta
For use with: BrainImageR Spatial Analysis (ie: SpatialEnrichment, CreateBrain, PlotBrain)
Developmental Timepoint: prenatal and adult
General Description: gene metadata provided by the Allen Brain Institute
EH1450:
Title: alldev_colmeta
For use with: BrainImageR Temporal Analysis (ie: predict_time). T
Developmental Timepoint: 8 weeks post-conception - 40 years
General Description: sample metadata provided by the Allen Brain Institute
EH1451:
Title: alldev_scale
For use with: BrainImageR Temporal Analysis (ie: predict_time).
Developmental Timepoint: 8 weeks post-conception - 40 years
General Description: sample expression data for all timepoints provided by the Allen Brain Institute