//
// *******************************************
// * *
// * Channel Merging Script *
// * made by Nicholas Condon *
// * contact n.condon@uq.edu.au *
// * *
// *******************************************
//
//AboutME:
//This script is written in the ImageJ Macro Language
//This script takes generates 2 or 3 channel images by merging single images into a composite .tif image.
//This script lets the user define the output LUTs for each channel (RGBCMYK)
//
//NOTE: Input image files should be in order, with no duplicate images (ie. Files should all be Red,Green,Blue,Red,Green,Blue...) and be within a single folder.
//Note: Output images (merged) must be placed in a seperate directory and not within the input folder.
//Currently 4-channel images are not being merged properly and this functionally has been disabled temporarily.
//IMB Splash screen
showMessage("Institue for Molecular Biosciences ImageJ Script", ""
+" ACRF: Cancer Biology Imaging Facility
+"The University of Queensland
+"ImageJ Script Macro: Channel Merging Script
"
+"Created by Nicholas Condon 2018
"
+"This script takes single images from a folder and merges them into user defined channels. Folders should contain only images in the correct order (ie. Red, Green, Blue, Red, Green, Blue...)
+" Directory structure should include a folder for Raw Images and one for merged images (not within the Raw Image Folder).
"
+""
+""
+" contact n.condon@uq.edu.au"
+"
"
+" "
+"");
//Selecting the number of channels for final output images
Dialog.create("Number of Channels");
Dialog.addMessage("Select the number of channels for your merged images")
Dialog.addMessage(" ")
// Dialog.addChoice("Number of channels:", newArray("2", "3", "4")); <------ //Blanked out as 4-channel not currently working
Dialog.addChoice("Number of channels:", newArray("2", "3"));Dialog.show();
numChen = Dialog.getChoice();
//print(numChen);
//Selecting the LUTs for each channel
//For 2 channel images
if (numChen=="2") {
Dialog.create("Select LUT for Channels");
Dialog.addMessage("Select the LUTs for your two channels")
Dialog.addMessage(" ")
Dialog.addChoice("Channel1:", newArray("Red", "Green", "Blue", "Grays", "Cyan", "Magenta", "Yellow"));
Dialog.addChoice("Chennel2:", newArray("Green", "Red", "Green", "Grays", "Cyan", "Magenta", "Yellow"));
Dialog.show();
Channel1 = Dialog.getChoice();
Channel2 = Dialog.getChoice();;
}
//For 3 channel images
else if (numChen=="3") {
Dialog.create("Select LUT for Channels");
Dialog.addMessage("Select the LUTs for your three channels")
Dialog.addMessage(" ")
Dialog.addChoice("Channel1:", newArray("Red", "Green", "Blue", "Grays", "Cyan", "Magenta", "Yellow"));
Dialog.addChoice("Chennel2:", newArray("Green", "Red", "Green", "Grays", "Cyan", "Magenta", "Yellow"));
Dialog.addChoice("Chennel3:", newArray("Blue", "Red", "Green", "Grays", "Cyan", "Magenta", "Yellow"));
Dialog.show();
Channel1 = Dialog.getChoice();
Channel2 = Dialog.getChoice();;
Channel3 = Dialog.getChoice();;
}
//For 4 channel images (Disabled)
else if (numChen=="4") {
Dialog.create("Select LUT for Channels");
Dialog.addMessage("Select the LUTs for your four channels")
Dialog.addMessage(" ")
Dialog.addChoice("Channel1:", newArray("Red", "Green", "Blue", "Grays", "Cyan", "Magenta", "Yellow"));
Dialog.addChoice("Chennel2:", newArray("Green", "Red", "Blue", "Grays", "Cyan", "Magenta", "Yellow"));
Dialog.addChoice("Chennel3:", newArray("Blue", "Red", "Green", "Grays", "Cyan", "Magenta", "Yellow"));
Dialog.addChoice("Chennel4:", newArray("Grays", "Red", "Green", "Blue", "Cyan", "Magenta", "Yellow"));
Dialog.show();
Channel1 = Dialog.getChoice();
Channel2 = Dialog.getChoice();;
Channel3 = Dialog.getChoice();;
Channel4 = Dialog.getChoice();;
}
//Prompt for user about directory structure
title = "Folder Selection Selections";
msg = "First Select Input Directory, then Output Directory (must be two different folders)";
waitForUser(title, msg);
//Directory selection
dir1 = getDirectory("Choose Source Directory ");
dir2 = getDirectory("Choose Destination Directory ");
list = getFileList(dir1);
setBatchMode(true);
n = list.length;
//2-channel merging section
if ((n%numChen)!=0)
exit("The number of files must be a multiple of "+numChen);
stack = 0;
first = 0;
if (numChen==2) {
for (i=0; i