how do i loop through folders and apply a function on a file in these folders?

Make the path to read csv dynamic in your function

object_extraction<-function(x){ 
  image<-read.csv(paste0(x, '/image.csv'), header=T, sep=",") 
  #header = T and sep = ',' is default in read.csv so this should 
  #work without specifying them as well.
  cells<-read.csv(paste0(x, '/cells.csv'))
  object<-dplyr::inner_join(cells,image,by="ImageNumber")
  return(object)
}

and then apply the function to each folder.

dirs <- list.dirs(recursive=FALSE)
dirs <- grep('output', dirs, value = TRUE)
result <- lapply(dirs, object_extraction)

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