Update auto_crop.R

Hi Lucy. I put a couple of comments and queries. Let me know if this works and makes sense. Best, Wayne

source/auto_crop.R

@@ -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)