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Commit cf2e5b6d authored by Wayne Crismani's avatar Wayne Crismani
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Update auto_crop.R

parent 934bfa11
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1 merge request!1Update auto_crop.R
This commit is part of merge request !1. Comments created here will be created in the context of that merge request.
......@@ -121,12 +121,14 @@ keep_cells <- function(candidate){
# delete everything that's too small
colorimg<- colorLabels(candidate, normalize = TRUE)
x <- computeFeatures.shape(candidate)
x <- computeFeatures.shape(candidate) # uses function from ebimage. give output kind of related to how circular the object is, size, perimeter, radius average etc
x <- data.frame(x)
OOI <- width(x)
OOI <- width(x) #Object Of Interest
counter <- 0
removed <- candidate
# loops over each Object of Interest (OOI)
while(counter<OOI){
counter <- counter+1
pixel_area = x$s.area[counter]
......@@ -146,7 +148,7 @@ keep_cells <- function(candidate){
return(removed)
}
# function to help not count the same object twice
crop_single_object <- function(removed, OOI_final,counter_final,img_orig,img_orig_foci,file,cell_count){
tmp_img <- removed
## have a single object
......@@ -163,6 +165,7 @@ crop_single_object <- function(removed, OOI_final,counter_final,img_orig,img_ori
}
# put nucleus mask on original image of the axis-marker or foci channel. matrix stuff which crops it to a square
## function: remove noise
noise_gone <- bwlabel(tmp_img)*as.matrix(img_orig)
noise_gone_foci <- bwlabel(tmp_img)*as.matrix(img_orig_foci)
......
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