FIJI/ImageJ Macro not saving every analyze particles results and summary table

Question

I have a folder of multiple Tif images, that I wish to analyze the particles, using analyze particles function. I need one channel, with all of its z-stack slices to be analysed and saved into a folder. My problem is that only every second summary and results table is being saved. So if my image has 10 z-stack slices, it saves slice 1, 3, 5, 7 etc. I must just be missing something small! This is in the ImageJ macro language.

// Choose input and output folders
dir1 = getDirectory("Choose Source Directory ");
resultsDir = dir1+"results/";
File.makeDirectory(resultsDir);
dir2 = getDirectory("Choose Destination Directory ");
list = getFileList(dir1);

processFolder(dir1);
function processFolder(dir1){
    list = getFileList(dir1);
    list = Array.sort(list);
    for (i = 0; i < list.length; i++) {
        if(File.isDirectory(dir1 + File.separator + list[i]))
            processFolder(dir1 + File.separator + list[i]);
        if(endsWith(list[i], ".tif"))
            processFile(dir1, dir2, list[i]);
    }
}    

function processFile(dir1, dir2, file){
    open(dir1 + File.separator + file);
    
    
// Split channels and rename     
title = getTitle();
run("Split Channels");
selectWindow("C2-" + title);
rename("live");
selectWindow("C3-" + title);
rename("dead");
selectWindow("C4-" + title);
rename("total");



//Apply pre-processing filters and threshold live cells
selectWindow("live");
run("Duplicate...", "duplicate"); // Duplicates live channel so accurate thresholding can be done in the following step
rename("duplicate");
selectWindow("live");
run("Gaussian Blur...", "sigma=2 stack");
run("Threshold...");
waitForUser("Adjust threshold, press ok on this pop-up when the threshold has been set. Do not press anything on the threshold screen when finished. Just press ok on action required screen");
run("Make Binary", "method=Default background=Dark calculate black");
//run("Auto Local Threshold", "method=Phansalkar radius=8 parameter_1=0 parameter_2=0 white stack");
run("Fill Holes", "stack");
//run("Watershed", "stack");
run("Stack to Images"); //Makes z-slices individual images



//For every image that is binary, rename the slice and analyze particles
for(z=0; z<nImages; z++){
            selectImage(z+1);
        if(is("binary")){
            name = getTitle();
            rename(name + "_" + title);
            run("Analyze Particles...", "size=0.50-Infinity show=[Overlay Masks] display clear summarize overlay add");
            selectWindow("Summary");
            saveAs("Results", dir2 + "Live_Summary_" + z + "_" + title + ".csv");
            selectWindow("Results");
            saveAs("Results", dir2  + name +"_" + z + "_" + title + ".csv"); 
            close();
        }
    }       
        close("live*");
        close("duplicate");
        run("Close");
        close();
        // Leave the print statements until things work, then remove them.
    print("Processing: " + dir1 + File.separator + file);
    print("Saving to: " + dir2);
}

Answer 1

The problem is likely to be that you run close(); inside the loop and then evaluate nImages in the loop condition.

Example: If you had 3 images, and 1st is binary. The loop starts, 1st image is processed and removed. 2nd time through, i is incremented and second image from the window list is now evaluated, however, this will be your 3rd image, because 1st image was removed, so 2nd image has been skipped.

You would either need to close the image outside the loop, or descend the list of images using for (i = nImages; i > 0; i--) removing as you go.