Particle analysis in ROI

Posted by ludwiczakagnieszka on
URL: http://imagej.273.s1.nabble.com/Particle-analysis-in-ROI-tp5008277.html

Cheers.
I'm trying to analyze the intramuscular fat particles on a cross-section of  a musce. I have already tried to apply "Analyze particles" but it refers to the whole image, not just the region of the muscle that I'm interested in. I want to analyze only the region within the boundary of the examined muscle - in order to get data on the distribution and shape of the fat particles as well as the percentage share of fat on the muscle cross-section surface. I suppose that I should use the ROI manager, but it doesn't offer an accurate particle anaysis. At least I can't find a way to link the ROI manager and the particle analysis.
I've attached an image (meat selected.png) after the muscle selection and using the "Clear outside" - as I've mentioned before, I'm interested in the muscle tissues only. I've also attached an image after convertion to 16-bit, thresholding, and "analyze particles" (particles.png). These particles are the subject of my research.
I will be gratefull for all guidelines.