add4ChannelImage: Add 4-channel image to SpatialOverlay from OME-TIFF. Allows...

In Nanostring-Biostats/SpatialOmicsOverlay: Spatial Overlay for Omic Data from Nanostring GeoMx Data

Add 4-channel image to SpatialOverlay from OME-TIFF. Allows for recoloring of image

Description

Add 4-channel image to SpatialOverlay from OME-TIFF. Allows for recoloring of image

Usage

add4ChannelImage(overlay, ometiff = NULL, res = NULL, ...)

Arguments

overlay	SpatialOverlay object
ometiff	File path to OME-TIFF. NULL indicates pull info from overlay
res	resolution layer, 1 = largest & higher values = smaller. The images increase in resolution and memory. The largest image your environment can hold is recommended. NULL indicates pull info from overlay
...	Extra variables

Value

SpatialOverlay object with image

Examples

muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

image <- downloadMouseBrainImage()

muBrain <- add4ChannelImage(overlay = muBrain, 
                            ometiff = image, res = 8)

dim(EBImage::imageData(showImage(muBrain)))

Nanostring-Biostats/SpatialOmicsOverlay documentation built on Dec. 18, 2024, 9:26 a.m.