How to average all files within a folder by image j macro

Question

Hey I am new very new to programming in ImageJ macro, I would like to average all images in a folder, save that single average image in a separate folder

Answer 1

Presuming your images are logically ordered (e.g., image001, image002, image003 etc...) - try this:

setBatchMode(true);

//retrieve images from directory
dir = getDirectory("Choose a directory of images...");
list = getFileList(dir);

for (i=0; i <list.length; i++) {
    path = dir + list[i];
    open(path); 
}
run("Images to Stack", "name=Stack title=[] use");
stackImage = getTitle();

//make an average intensity image
run("Z Project...", "projection=[Average Intensity]");

//save out to new folder
outputPath = dir + File.separator + "separateFolder";
if (!File.exists(outputPath)) File.makeDirectory(outputPath);
newPath = outputPath + File.separator + "averagedImage";
run("Save","save=[newPath]");
close(stackImage);
close();

setBatchMode(false);