count_foci has crowded_foci option (TRUE/FALSE) which determines whether foci...

count_foci has crowded_foci option (TRUE/FALSE) which determines whether foci channel is smoothed (FALSE). Defaults to FALSE

DESCRIPTION

@@ -6,13 +6,12 @@ Authors@R:
     c(person(given = "Lucy",
              family = "McNeill",
              role = c("aut", "cre", "cph"),
-             email = "lucmcneill@gmail.com",
+             email = "luc.mcneill@gmail.com",
              comment = c(ORCID = "0000-0003-1752-4882")),
       person(given = "Wayne",
              family = "Crismani",
              role = c("rev", "ctb"),
              comment = c(ORCID = "0000-0003-0143-8293")))
-Maintainer: Lucy McNeill <lucmcneill@gmail.com>
 Description: Synapsis is a Bioconductor software package for automated (unbiased and reproducible) analysis of meiotic immunofluorescence datasets. The primary functions of the software can i) identify cells in meiotic prophase that are labelled by a synaptonemal complex axis or central element protein, ii) isolate individual synaptonemal complexes and measure their physical length, iii) quantify foci and co-localise them with synaptonemal complexes, iv) measure interference between synaptonemal complex-associated foci. The software has applications that extend to multiple species and to the analysis of other proteins that label meiotic prophase chromosomes. The software converts meiotic immunofluorescence images into R data frames that are compatible with machine learning methods. Given a set of microscopy images of meiotic spread slides, synapsis crops images around individual single cells, counts colocalising foci on strands on a per cell basis, and measures the distance between foci on any given strand.
 biocViews:
   Software,

R/count_foci.R

@@ -21,10 +21,11 @@
 #' @param watershed_stop Turn off default watershed method with "off"
 #' @param watershed_radius Radius (ext variable) in watershed method used in foci channel. Defaults to 1 (small)
 #' @param watershed_tol Intensity tolerance for watershed method. Defaults to 0.05.
+#' @param crowded_foci TRUE or FALSE, defaults to FALSE. Set to TRUE if you have foci > 100 or so.
 #' @return foci count per cell
 
 
-count_foci <- function(img_path, stage = "none", offset_px = 0.2, offset_factor = 2, brush_size = 3, brush_sigma = 3, foci_norm = 0.01, annotation = "off",channel2_string = "SYCP3", channel1_string = "MLH3",file_ext = "jpeg", KO_str = "--",WT_str = "++",KO_out = "-/-", WT_out = "+/+", watershed_stop = "off", watershed_radius = 1, watershed_tol = 0.05)
+count_foci <- function(img_path, stage = "none", offset_px = 0.2, offset_factor = 2, brush_size = 3, brush_sigma = 3, foci_norm = 0.01, annotation = "off",channel2_string = "SYCP3", channel1_string = "MLH3",file_ext = "jpeg", KO_str = "--",WT_str = "++",KO_out = "-/-", WT_out = "+/+", watershed_stop = "off", watershed_radius = 1, watershed_tol = 0.05, crowded_foci = TRUE)
 {
   cell_count <- 0
   image_count <-0
@@ -71,7 +72,7 @@ count_foci <- function(img_path, stage = "none", offset_px = 0.2, offset_factor
       # call functions: get
       antibody2_store <- 1
     }
-    if(  antibody1_store +antibody2_store == 2){
+    if(antibody1_store +antibody2_store == 2){
       antibody1_store <- 0
       antibody2_store <- 0
       cell_count <- cell_count + 1
@@ -99,7 +100,7 @@ count_foci <- function(img_path, stage = "none", offset_px = 0.2, offset_factor
 
       #### normalise the foci image
       offset <- offset_factor*bg
-      if(stage != "pachytene"){
+      if(crowded_foci == TRUE){
         foci_th <- foci_mask_crop > bg + offset
         #foci_th <- watershed(bwlabel(foci_th)*as.matrix(img_orig_foci),tolerance=0.05, ext=1)
       }

man/count_foci.Rd

@@ -22,7 +22,8 @@ count_foci(
   WT_out = "+/+",
   watershed_stop = "off",
   watershed_radius = 1,
-  watershed_tol = 0.05
+  watershed_tol = 0.05,
+  crowded_foci = TRUE
 )
 }
 \arguments{
@@ -61,6 +62,8 @@ count_foci(
 \item{watershed_radius}{Radius (ext variable) in watershed method used in foci channel. Defaults to 1 (small)}
 
 \item{watershed_tol}{Intensity tolerance for watershed method. Defaults to 0.05.}
+
+\item{crowded_foci}{TRUE or FALSE, defaults to FALSE. Set to TRUE if you have foci > 100 or so.}
 }
 \value{
 foci count per cell