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Re: particle analysis within region of interest

Posted by spt on Jul 26, 2015; 6:17pm
URL: http://imagej.273.s1.nabble.com/particle-analysis-within-region-of-interest-tp5013741p5013745.html

Dear Avital,
Thanks for the tip. It should work, but the problem is that even when I select an ROI, the threshold is applied to the entire image.  This is despite the fact that the ROI is effective for other operations like adjusting brightness and contrast.  And the solution that was proposed by Jens yesterday (ie duplicating an ROI then thresholding) works, but only if the ROI is a rectangular shape... so, I still don't have a solution and I'm suspicious that a default is set up wrong somewhere in my program.  

Thanks for any insights!

Susan Travers
Professor, Biosciences
Division of Biosciences, College of Dentistry
The Ohio State University
305 West 12th Avenue
Columbus, Ohio  43210
[hidden email]
(614)361-0800 (cell)
(614)292-6366 (work)

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Avital Steinberg
Sent: Sunday, July 26, 2015 3:21 AM
To: [hidden email]
Subject: Re: particle analysis within region of interest

Dear Susan,
You can select a ROI, then image, adjust, threshold - and set it to the value you would like. Then, analyze, particles only segments what's in the ROI. You can go back to image, adjust, threshold, click on reset, and then the image looks normal again. (but the segmented ROIs are still there)

I hope this helps,

Avital

On Sat, Jul 25, 2015 at 9:58 PM, Travers, Susan <[hidden email]> wrote:

> This should be simple but somehow I can't get it to work. I want to
> count particles in a specific region of interest. I have:
> Thresholded the image (using, threshold or color threshold-the
> particle analysis works correctly on the thresholded image) But when I
> try to count particles in a subregion, either by using the ROI manager
> or "selection" "specify", I still get the count that corresponds to
> ALL the particles in the image.
> At the same time, if I use the ROI manager and then the "measure"
> command, the measurements correspond to the ROI's that I've defined.
> Does anyone have a suggestion?  Thanks so much.
>
> Susan
>
> Susan Travers
> Professor
> Division of Biosciences
> College of Dentistry
> The Ohio State University
>
> 305 West 12th Avenue
> Columbus, Ohio  43210
>
> 614-292-6366 (office)
> 614-457-6945 (fax)
> 614-361-0800 (cell)
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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