I’m using Fiji to analyze samples of microscopic geometric crystals for my undergraduate chemistry thesis. For this analysis I am attempting to obtain thickness measurements for these crystals based on the amount of light that passes through them. I am hoping that this is possible by measuring the average pixel intensity of each particle.
So far I have worked largely with the Analyze Particles tool to categorize each crystal based on their size and shape.
I am wondering if there is a way to obtain an average pixel intensity value for each of the particles?
It would be ideal to use a single measurement tool to obtain the same data as found in the Analyze Particles tool with the addition of this average pixel intensity per particle.
Here is an example of one of my samples. As you can see thicker particles will be nearly black with lower intensity values while thinner particles will have higher intensity values and appear almost transparent.
Thank you in advance for any help you can offer.