Re: HELP!!!-segmentation and quantification of DIC images

Posted by Jim Peterson on Feb 27, 2020; 6:25pm
URL: http://imagej.273.s1.nabble.com/HELP-segmentation-and-quantification-of-DIC-images-tp5022977p5022982.html

Rather than trying to flatten the background, you can look at gradients.
This also takes care of the light and shadow of each droplet.  The following
script fragment will do this:

run("8-bit");
run("Find Edges");
run("Despeckle");
run("Gaussian Blur...", "sigma=2");
setAutoThreshold("Otsu dark no-reset");
setOption("BlackBackground", true);
run("Convert to Mask");

Or you can run the commands from the interface:
Image/Type/8-bit
Process/Find Edges
Process/Filter/Gaussian Blur...  (sigma=2)
Image/Adjust/Threshold... (I used Otsu - you can try other methods, or set
the threshold manually)
    Then hit Apply.

The result is here:
<http://imagej.1557.x6.nabble.com/file/t381520/mask.png>

- Jim




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