Fiji - mean intensity value

I would like to create a line scan or just try to have the mean intensity between two images.
I create new staining (black) on mitochondria in electron microscopy and i can see the difference when you look at them
And I also try to put manual threshold :

  • threshold 90: the mitochondrial mass is depicted by setting a higher threshold
  • threshold 50: the specific activity is depicted by setting a lower threshold and its working really well the images are great,

but I would like to have some value and show that the intensity is less on one image compare to the other one (one have the specific activity and the other one)
I know this is a stupid question but when I tried the histogram, it’s about grey value, its not what i want
I want to create this mean intensity between all the images (between the threshold images )
thank you so much in advance for your answer

I never use electron microscopy images but it’s always better to use automatic threshold compare to manual.

I think you can easily create a macro in fiji plugins > macro > record…

  1. duplicate your image
  2. apply your threshold and convert to mask
  3. set measurement to mean gray value
  4. analyze particles… and add to ROI
  5. Go to Image -> Overlay -> From ROI Manager
  6. Go to your ROI Manager (should be open)
    7)Click Measure
  7. save the Mean Intensity in csv or excel

Hi Alex thank you so much for you reply
that was really good
And it’s for my future paper. Is it a problem for you if I put your name in the acknowledgement?
because I think it’s normal so if you want me to put your name and institute ou something like that because at the moment I just have the username :slight_smile:

No problem it’s a pleasure :slight_smile:

cool perfect :slight_smile:
I find everything that’s great thank you:)