Threshold and area of particles

Hello everyone,

I have some pictures to analyse with “analyze particles” because I want to measure the area, area fraction, counting and etc. My problem stars when I choose the threshold ( I tried to take a pictures the most black background and same light intensity), but the problem follows when I run analyze particles (some ROI selection include non-interested particles, so the background).

At the end I get:

  • If I use “include holes” = a large ROI selection with some background places
    If I don’t use “include holes” = a large ROI selection sometimes without background places, sometimes a large Selection and another small included selection.
    I would like to have as result only one selection that takes the real particles and non the black background as another new included selection because this can be an error in measurements.

Thanks a lot for your help,


Ok. So perhaps it’s just me… but I am not quite understanding exactly what you want to measure in your image. Let’s start with a couple questions:

  1. Can you post an original image? And indicate exactly how you set your threshold, etc…
  2. What do you consider ‘background’ in your image?
  3. Is this what you want to do? : Measure the ‘small particles’ within the large circular object? If this is the case… you can write a script/macro to find region of the circle and then measure the small particles within… it’s doable via scripting.

Here are some helpful links if you want to look into Segmentation and Scripting in ImageJ/Fiji:

eta :slight_smile:

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