The function “include holes” in “analyze particles” can dot work properly

Hi, I have struggled with a basic function of FIJI for several days. As described in the“Image J user guide”,when i do not choose “include holes”, the internal holes inside the particle can be recognized. Internal holes will be ignored only if “include holes” is chose.

But , whether I choose it or not, internal holes always were ignored. As show in the below image, same results was got. It confuses me.

Thanks very much if anyone can help.

Please compare the measurements. You will see that the results in the Results Table differ with or without holes (e.g., area measurements).
However in the “Show” method only the outlines (without the holes) are displayed.


As @Bio7 said, the measuremenets will differ but a nice way to visualise it is if you set Show to “Count Masks” you will see the resulting shapes with and without the holes between the two methods.


@Bio7 Thank you very much! Now,I can obtain “area” value with or without holes. I was so careless,did not notice the change of “Results Table” .
Besides, the “perim.” measurement result still unchanged, is it always the outlines‘ length to be measured?

@lmurphy Thanks very much for help. I try you adverse,but there are some proplems. As shows in the below picture, the interface is partially or completely black. Is there something wrong with my other settings?

Looking forward to your reply.

Hi @sunny,

The count mask creates an image with, every detected objets filled with a number (1 for the first object, 2 for the second…). In your image, you have 3 objects. So the resulting image has a max value of 3. With this display, you won’t see anything. Adjust the display to see well (Image>Adjust>Brigtness/Contrast).


1 Like

Amazing! I got it! @VirtualSlide Thanks for your kind help ~

Please read the documentation here:

If you would like to measure the perimeter of the holes you could easily extract the holes with a substraction of a before generated “Mask” and then analyze the holes (in this specific case).


run("Particles (75K)");
run("Analyze Particles...", "  show=Masks display exclude clear include");
imageCalculator("Subtract create", "Mask of particles.gif","particles.gif");
selectWindow("Result of Mask of particles.gif");

Thanks for sharing the links, the documentation is really helpful for me. @Bio7:grinning:

And, thanks for your case guidance, it works great.