RE: IJ Color Thresholding in Macro

Posted by Steve R on Dec 04, 2014; 8:58pm
URL: http://imagej.273.s1.nabble.com/IJ-Color-Thresholding-in-Macro-tp5010727p5010772.html

Hi Gabriel,

One thing I just noticed is the Overlay Outlines created in Analyze Particles doesn’t transfer to the combined image after the Image Calculator routine. (see attached pics)

Is there any way to combine them & keep the outline overlay? like with ImagePro you can burn the overlay into the image so it’s part of the picture.

 

Reason this is important is the black Areas highlight everything thresholded, but if I don’t want to include very small voids in the data analysis, I set the filter range in the analyze particles routine to exclude the smaller voids, so after analyze particles routine it only outlines the voids in the Area range I’ve selected. Which is what the operators need to see to confirm the analysis has correctly chosen voids.

Let me know, thanks Steve

 

From: Steve Roach
Sent: Thursday, December 4, 2014 1:07 PM
To: 'Gabriel Landini [via ImageJ]'
Subject: RE: IJ Color Thresholding in Macro

 

 

Gabriel, Thanks so much! I have it working now. I had an error at first when I ran the macro saying the image must be color thresholded before doing an Analyze Particles.

So I moved the ImageCalculator string down after the Analyze Particles routine in the macro & it worked.

Again appreciate your  help, wouldn’t have been able to even come close if it wasn’t for your help.

 

Oh yeah, one more quick question, is there not a way to save all the settings in ImageJ, like a configuration file or something, so that next time you open ImageJ & run things like Color Threshold, the default starting settings come up with what you had saved?

Let me know,

Thanks,

Steve

 

 

From: Gabriel Landini [via ImageJ] [[hidden email]]
Sent: Thursday, December 4, 2014 9:18 AM
To: Steve Roach
Subject: Re: IJ Color Thresholding in Macro

 

On Thursday 04 Dec 2014 07:59:50 Steve R <[hidden email]> wrote:
> Sorry, still a little confused with this:

This should explain it.

run("Clown (14K)");
n1=getTitle();
run("Duplicate...", " ");
n2=getTitle();
selectImage(n1);
// include the the thresholding macro code here
// it will threshold the selected image n1
imageCalculator("AND create", n2, n1);

Cheers
Gabriel

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