Novice thresholding/counting

Hi all,

Apologies, I am a complete novice with ImageJ and whilst I would like to get to this stage eventually, my requirement I think will take a while to learn!

I am trying to count the amount of grains in a polycrystalline material, with the picture taken under a microscope. I am assuming that each grain has a peak, and each of these peaks has a reflection under microscope (broadly proven based on images I’ve seen so far).

To count the amount of grains, I am thinking of creating a threshold of colour, where a certain ‘whiteness’ would constitute a reflection and therefore a single grain. Then I need to create a script that will allow me to automatically count the number of these individual pockets of white for the whole picture.

If anyone can point me in the right direction I will be very appreciative. Thank you and I’m looking forward to learning more about this software.

Hello Adam and welcome here!
Your assumptions sound very reasonable for a novice :wink:

in the menu you can find the Threshold command (also Ctrl-Shft-T)
and then you would usually do a detection of bits:
Analyze>Analyze Particles…

If you run into problems, upload one of your sample images!

Good luck,

1 Like

If your image itself is RGB/color, you may also want to Image->Type->8bit as a first step if you want to simplify finding “light vs dark”

1 Like

Hi Daanb88,

Thanks for the response!

I have done the following:

Image>Adjust>Threshold (I’ve gone with auto values)
Analyze>Analyze particles (Showing Masks)

I’m finding it difficult to get a good threshold value - too low and I’m worried it will pick up insignificant parts (only the really white parts are ‘grains’ in the image attached), too high and I’m worried it will miss out some important parts of the image.

Any tips you could share?

Thank you


Thanks for the reply, that is very helpful!