How to measure average intensity of selected particles in the stack


Hello. How is it possible to measure average intensities of all labeled particle in the stack (average value for each slice per all particles per slice)? I have a stack and a binary image of a labeled particles. I can go to option of “Anazlyze particles” where I can label these particles and make them appear in the ROI manager, and then I can go to a stack and choose in ROI manager “Show All”. This operation shows all labeled particles appeared in a stack. Then in ROI manager I go to “More”, choose “Multi Measure”. Then I go to “Image”, “Stacks”, “Plot Z-axis Profile”. However this operation somehow shows me a plot average intensities per entire slice (not of labeled particles)? Is there a way how I can get plot with average intensities of labeled particles only?


Yes, this is possible however, only with a workaround using the macro language.

You can read the results you measured in the results table into an array
a1 = newArray();
for (i=0;i<nResults;i++){
a1 = Array.concat(a1,getResult(“Mean”, i));

and then using
Plot.create(“Title”, “X-axis Label”, “Y-axis Label”, xValues, yValues)
omitting the xValues will result in a plot you desire.

Plot.create(“Average intensity”, “ROI #”, “Means”, a1)

This should work