Restoring grayscale gradient after threshold and analyze particles?

Hello community! (This is my first post, redirect me if something is wrong)

I am trying to classify particles from SEM-images, using ImageJ. I have done so successfully with -thresholding and analyze particles, although a very important feature is lost in this process of making the image binary, the grayscale of the particle that i am trying to study. Is there some (automatic) way to retrieve the grayscale of particles after thresholding the image and analyzing the particles?

When using the ROI and measure i seem to recover some form of grayscale information as "“mean” and “StdDev”. What does this mean/represent?

How can i get a good representation of the grayscale of the particles?

I have included the original image and my current setup below.

Thank you!

setup%20and%20ROI

SA-2_m09.tif (1.2 MB)

Hello Senecai -

In short, apply the ROIs that you obtained from running
Analyze Particles... on your thresholded image (they’re in
the ROI Manager) to your original image, and then run Measure.

In more detail, one way to do this is open your original image,
duplicate it, do your thresholding procedure on the duplicate,
and run Analyze Particles.... Now close your thresholded
image, select your original image, and check the Show All and
Labels check-boxes at the bottom of the ROI Manager. You
should now see the ROI outlines (and labels) on your original
image. Now run Measure and the Results Table will contain
measurements for your original image, with its original grayscale
values.

The clue comes from the Min and Max values of 0 and 255 shown
in your Results Table. Your ROIs (after your thresholding procedure)
contain pixels whose values are either 0 or 255. (These match
your Mean and StdDev values for the appropriate mixture of 0’s
and 255’s.)

So the Mean and StdDev are not giving you grayscale information
for your original image – they are telling you how many 0 and 255
pixel values you have in each particle in your thresholded image.

Thanks, mm

1 Like

Thank you Mountain_Man!

Your feedback works excellent!

Looking forward to get to know this community more and one day contribute =)

Best regards!