particle analysis within region of interest

[spt]

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)


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[jerie]

Dear Susan,

could it be a simple as using the command 'duplicate' after ROI selection
and applying thus the thresholded  measurement only at the copied subregion
of the image?

Good luck,  Jens

Visiting Scientist
Fundação Oswaldo Cruz - Ministério da Saúde, Centro de Desenvolvimento
Tecnológico em Saúde (CDTS)
Am 25.07.2015 16:23 schrieb "Travers, Susan" <[hidden email]>:

> 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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[spt]

Thanks Jens, that does work and I imagine I could write a macro to do several ROIs at a time, but it puzzles me that it would require the duplication b/c the manual implies otherwise. So, I'm still thinking that I may be  missing something fundamental. Very helpful nonetheless.

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of jens rietdorf
Sent: Saturday, July 25, 2015 7:01 PM
To: [hidden email]
Subject: Re: particle analysis within region of interest

Dear Susan,

could it be a simple as using the command 'duplicate' after ROI selection and applying thus the thresholded  measurement only at the copied subregion of the image?

Good luck,  Jens

Visiting Scientist
Fundação Oswaldo Cruz - Ministério da Saúde, Centro de Desenvolvimento Tecnológico em Saúde (CDTS) Am 25.07.2015 16:23 schrieb "Travers, Susan" <[hidden email]>:

> 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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[Avital Steinberg]

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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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[spt]

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]
[phone] (cell)
[phone] (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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[Peterbauer Thomas]

On 2015-07-26 20:18, Travers, Susan wrote:
> 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.

Rather than duplicating the image, you can copy selections of arbitrary
shape into a new image (either black or white, depending on the
background of your objects), and do the thresholding and particle
analysis there.

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[Avital Steinberg]

Dear Susan,
I also thought that the threshold is applied to the entire image, but Wayne
said that in spite of the fact that it looks like that, the threshold is
applied only to the pixels of the selection. And indeed, after I set the
threshold, when I did analyze, particles, it segmented only the particles
that I wanted - within the ROI.

It worked for me.

I hope it works also for you,
Avital

On Sun, Jul 26, 2015 at 9:18 PM, Travers, Susan <[hidden email]> wrote:

> 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]
> [phone] (cell)
> [phone] (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
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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