Analyze particles use without threshold images

Hi image J community,

I was wondering is it possible to use analyze particles tool with images that are not thresholded. I need to measure average pixel values in cells after background subtraction/masking and want to know to exact grey values in the ROIs. There are hundreds of cells in the image and analyze particle is the ideal tool for cell counting and finding out area of cells but I can’t retain the exact grey values within each cell that I would love to also get from “analyze particles” tool. Any help/suggestion would be really appreciated.


Hi NZ,

use a thresholded copy of your image to run the "Analyze particles" command, making sure the "Add to ROI Manager" option is ticked. Then, go back to your original image, click twice on the "Show all" option (to show the ROI’s on your original image), and finally hit the "Measure" button.

Your measurements will then be done on your original data.


1 Like

Analyze Particles can measure the grey value, you don’t need to apply the threshold on your image. See this macro:

run("Blobs (25K)");
run("Set Measurements...", "mean display redirect=None decimal=4");
run("Analyze Particles...", "display");

Does this do what you want?
I might have misunderstood your question though. If you have a binary image and want to measure intensities within its ROIs but from a different image, the Redirect to option in Analyze > Set Measurements… might be your friend:

run("Blobs (25K)"); // opens "blobs.gif"
run("Blobs (25K)"); // opens "blobs-1.gif"
setOption("BlackBackground", true);
run("Convert to Mask");
run("Set Measurements...", "mean display redirect=blobs.gif decimal=4");
run("Analyze Particles...", "display");