//
// *******************************************
// * *
// * SDC Channel Flip Tool *
// * made by Nicholas Condon *
// * contact n.condon@uq.edu.au *
// * *
// *******************************************
//
//AboutME:
//This script is written in the ImageJ Macro Language
//This script takes .czi files from the spinning disk confocal (Zeiss) (Can be changed on line 52)
//
//The image is opened and one channel is flipped horizontally.
//
//The script prompts the user to select Green/Red or CFP/YFP image use, this is only applying it for the LUT.
//
//The ability to add in x/y translations is currently turned off in line 63
//
//Note: Output images (corrected) are saved into the same directory with the suffix _corrected.tif
//
//Currently 4-channel images are not being merged properly and this functionally has been disabled temporarily.
//IMB Splash screen (Do not remove this acknowledgement)
showMessage("Institue for Molecular Biosciences ImageJ Script", ""
+" ACRF: Cancer Biology Imaging Facility
+"The University of Queensland
+"ImageJ Script Macro: Spining Disc Confocal Dual Camera Channel transoformation
"
+"Created by Nicholas Condon 2018
"
+"This script takes dual channel images from the IMB Zeiss Spinning disc confoal and flips one channel horizontally and remerges them before saving with the suffix 'correct.'
"
+" "
+" contact n.condon@uq.edu.au"
+" "
+"");
//Dye selection pop-up window
Dialog.create("Select Dye Combination used");
Dialog.addChoice("Type:", newArray("GFP-RFP", "CFP-YFP"));
Dialog.show();
dye = Dialog.getChoice();
print(dye);
//Directory location dialogue box
path = getDirectory("Choose Source Directory ");
list = getFileList(path);
//Runs in the background, turn off if you want it to run in forground (opening windows etc)
setBatchMode(true);
//Loop for checking multiple files within directory
for (i=0; i