diff --git a/DESCRIPTION b/DESCRIPTION index 8e45c8f..a6c8556 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: cellPixels Type: Package Title: Detect nuclei (and cells) and count pixel intensities in these regions -Version: 0.2.9 +Version: 0.2.10 Author: c(person("Kai", "Budde", email = "kai.budde@uni-rostock.de", role = c("aut", "cre")) Maintainer: Kai Budde diff --git a/R/cellPixels.R b/R/cellPixels.R index e787b31..4e0a340 100644 --- a/R/cellPixels.R +++ b/R/cellPixels.R @@ -10,6 +10,7 @@ #' @param apotome A boolean (TRUE if Apotome was used) #' @param apotome_section A boolean (TRUE is sectioned image shall be used) #' @param nucleus_color A character (color (layer) of nuclei) +#' @param min_nucleus_size A number (minimum size in pixels of nuclei to be kept) #' @param protein_in_nuc_color A character (color (layer) of protein #' expected in nucleus) #' @param protein_in_cytosol_color A character (color (layer) of protein @@ -40,6 +41,7 @@ cellPixels <- function(input_dir = NULL, apotome = FALSE, apotome_section = FALSE, nucleus_color = "blue", + min_nucleus_size = NULL, protein_in_nuc_color = "none", protein_in_cytosol_color = "none", protein_in_membrane_color = "none", @@ -776,7 +778,12 @@ cellPixels <- function(input_dir = NULL, # barplot(table(nmask)[-1]) table_nmask <- table(nmask) - nuc_min_size <- 0.2*stats::median(table_nmask[-1]) + if(is.null(min_nucleus_size)){ + nuc_min_size <- 0.2*stats::median(table_nmask[-1]) + }else{ + nuc_min_size <- min_nucleus_size + } + # remove objects that are smaller than min_nuc_size to_be_removed <- as.integer(names(which(table_nmask < nuc_min_size))) @@ -1683,6 +1690,7 @@ cellPixels <- function(input_dir = NULL, "apotome", "apotome_section", "nucleus_color", + "min_nucleus_size", "protein_in_nuc_color", "protein_in_cytosol_color", "protein_in_membrane_color", diff --git a/man/cellPixels.Rd b/man/cellPixels.Rd index 4cc6124..788cef1 100644 --- a/man/cellPixels.Rd +++ b/man/cellPixels.Rd @@ -11,6 +11,7 @@ cellPixels( apotome = FALSE, apotome_section = FALSE, nucleus_color = "blue", + min_nucleus_size = NULL, protein_in_nuc_color = "none", protein_in_cytosol_color = "none", protein_in_membrane_color = "none", @@ -38,6 +39,8 @@ cellPixels( \item{nucleus_color}{A character (color (layer) of nuclei)} +\item{min_nucleus_size}{A number (minimum size in pixels of nuclei to be kept)} + \item{protein_in_nuc_color}{A character (color (layer) of protein expected in nucleus)}