Re: Define edges

Posted by Joel Sheffield on Apr 04, 2019; 6:49pm
URL: http://imagej.273.s1.nabble.com/Define-edges-tp5021980p5021981.html

I took the image you posted, and ran the following:

run("8-bit");
setAutoThreshold("Default");
//run("Threshold...");
run("Create Mask");
run("Fill Holes");
run("Watershed");
selectWindow("Clipboard");
run("Restore Selection");
run("Analyze Particles...", "size=500-Infinity show=Outlines display
include summarize");

The problem with this sample is that the central portion of each object is
bright, and so you can't threshold the entire particle. Each particle is
thresholded with a hole.   Instead, you can convert to a mask, and then use
the Binary options to (a) fill holes, and (b) watershed, to isolate
particles that touch.  Then you create a selection around the masked
particles, and restore it to your original image.  then you can run Analyze
particles, and check "includeholes" in the options.  You also have to set a
lower bound for the particles so that you don't pick up the small
detritus.  It's not perfect --note the cluster at 8 o'clock, but it's
pretty good.  How much precision do you need?

[image: image.png]

Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
Office:  Biolife 311
URL:  *https://bio.cst.temple.edu/~jbs/ <https://bio.cst.temple.edu/~jbs/>
<http://tinyurl.com/khbouft>*


On Thu, Apr 4, 2019 at 1:24 PM retgar <[hidden email]> wrote:

> Hello, i`m requesting some help please!
> Cant find the way to define the edges, so that imageJ "analyze particles"
> can analyze each separate particle.
> "find edges' and threshold doesnt seem to help. also tried 'FeatureJ' and
> 'image edge' plugins
> https://imgur.com/a/dE26Zcj
>
>
>
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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