I’m trying to quantify the holes in an image, and despite having used ImageJ on and off for 5 years, I can’t get this seemingly extremely simple procedure to work. My dataset consists of binary images such as the one in the top left frame in the montage below, and what I want to do is to count the number and measure the areas of all the white sections of the image, but the Analyze Particles function includes the black areas in the quantification (see top right frame), which I don’t want it to do. I tried skeletonizing the images (mid left frame), but this resulted in no counts being recognized at all (mid right frame), and if I dilate the skeletonized image (bottom left frame), the counts are recognized, but again it hollows out the skeleton and quantifies that as well (bottom right frame).
I’ve tried inverting the images at every step, I’ve tried using ROIs to include/exclude segments in the count, but I just can’t seem to get this work. Any suggestions?