How can I count the number of neurons that are in different brightness


I am new to imageJ and need help counting the number of neurons in this image.
I know I should find the threshold and do the “analyze particles”; but when I try doing it, it doesn’t accurately count the number of particles. Could you tell me the method so I can do it on my own next time thank you.



Welcome to the Forum and ImageJ in general. :slight_smile:

So looking at your image - you can see that your sample varies across the background… you have a brighter background on the left side which diminishes as you move towards the right side. That is why a simple threshold won’t really work across the entire image.

You’ll have to do some pre-processing to deal with that background variation. Take a look at these older forum posts - you might find helpful:

Here are some other helpful links that you can use to get you started in Segmenting those cells (though know that things won’t be ‘perfect’ because of this background issue - just clean it up as much as you can):