Does any one know how to filter objects overlapping with another channel using EBImage? For example, I have red and green channels with the following code. Now how can I get the red cells that overlap with green cells? Thanks.

x <- readImage(system.file('images', 'nuclei.tif', package='EBImage'))
x <- thresh(x, w = 15, h = 15, offset = 0.1)
red <- x[,,1]
green <- x[,,2]

How about

overlap <- (red > 0) & (green > 0)

This finds overlapping pixels. If you want to look at cells, you'll need to segment the red image into cells, and subset those cells that overlap in a similar manner.