Getting greyscale data from thresholded image

[Adam Hughes]

Hi guys,

I'm looking at the information about the analyze particles
<http://rsbweb.nih.gov/ij/docs/menus/analyze.html>macro in ImageJ, and I
noticed there are several fields that have to do with the greyscale value
of the particles.  For example, the mean and modal grey value fields.
Whenever one uses analyze particles, one must always threshold the image,
which converts it to black and white.  Therefore, the greyscale values of
the particles in my results are always 255.  Is it possible to retain the
greyscale information from the real image before thresholding?  This would
be super important information for me.

Thanks.

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[Tiago Ferreira-2]

Hi Adam,

On 2012.10.08, at 20:49 , Adam Hughes wrote:
> Whenever one uses analyze particles, one must always threshold the image,
> which converts it to black and white.

This is only the case if you press "Apply" in the Threshold widget. Just set
threshold levels on the grayscale image (without pressing "Apply") before
running the ParticleAnalyzer and you will have access to the original values.

Alternatively, you can use the "Add to Manager" option, that will allow you to
measure the resulting ROIs on any image.

HTH,
-tiago

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[Jacqueline Ross]

Hi Adam,

Further to Tiago's explanation, you also need to make sure that you select "Limit to Threshold" in the "Set Measurements window". Then it all should work well.

Kind regards,

Jacqui

Jacqueline Ross
Biomedical Imaging Microscopist
Biomedical Imaging Research Unit 
School of Medical Sciences 
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland 1142, NEW ZEALAND

Tel: [phone]
Fax: [phone]

http://www.fmhs.auckland.ac.nz/sms/biru/


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Tiago Ferreira
Sent: Tuesday, 9 October 2012 4:52 p.m.
To: [hidden email]
Subject: Re: Getting greyscale data from thresholded image

Hi Adam,

On 2012.10.08, at 20:49 , Adam Hughes wrote:
> Whenever one uses analyze particles, one must always threshold the
> image, which converts it to black and white.

This is only the case if you press "Apply" in the Threshold widget. Just set threshold levels on the grayscale image (without pressing "Apply") before running the ParticleAnalyzer and you will have access to the original values.

Alternatively, you can use the "Add to Manager" option, that will allow you to measure the resulting ROIs on any image.

HTH,
-tiago

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[Krs5]

Hi Adam,

And as 3rd option you can duplicate your image, do any processing you want, threshold and select in the "Set Measurements" menu the image you did not changed from the dropdown menu "Redirect to:". This will also work when using a macro.

Best wishes

Kees

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Jacqui Ross
Sent: 09 October 2012 05:15
To: [hidden email]
Subject: Re: Getting greyscale data from thresholded image

Hi Adam,

Further to Tiago's explanation, you also need to make sure that you select "Limit to Threshold" in the "Set Measurements window". Then it all should work well.

Kind regards,

Jacqui

Jacqueline Ross
Biomedical Imaging Microscopist
Biomedical Imaging Research Unit 
School of Medical Sciences 
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland 1142, NEW ZEALAND

Tel: [phone]
Fax: [phone]

http://www.fmhs.auckland.ac.nz/sms/biru/


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Tiago Ferreira
Sent: Tuesday, 9 October 2012 4:52 p.m.
To: [hidden email]
Subject: Re: Getting greyscale data from thresholded image

Hi Adam,

On 2012.10.08, at 20:49 , Adam Hughes wrote:
> Whenever one uses analyze particles, one must always threshold the
> image, which converts it to black and white.

This is only the case if you press "Apply" in the Threshold widget. Just set threshold levels on the grayscale image (without pressing "Apply") before running the ParticleAnalyzer and you will have access to the original values.

Alternatively, you can use the "Add to Manager" option, that will allow you to measure the resulting ROIs on any image.

HTH,
-tiago

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[Adam Hughes]

Thanks for all the help guys.  I did end up getting it to work, using the
limit set threshold command, so thanks especially for pointing that out.

Cheers.

On Tue, Oct 9, 2012 at 4:19 AM, Straatman, Kees R. (Dr.) <
[hidden email]> wrote:

> Hi Adam,
>
> And as 3rd option you can duplicate your image, do any processing you
> want, threshold and select in the "Set Measurements" menu the image you did
> not changed from the dropdown menu "Redirect to:". This will also work when
> using a macro.
>
> Best wishes
>
> Kees
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Jacqui Ross
> Sent: 09 October 2012 05:15
> To: [hidden email]
> Subject: Re: Getting greyscale data from thresholded image
>
> Hi Adam,
>
> Further to Tiago's explanation, you also need to make sure that you select
> "Limit to Threshold" in the "Set Measurements window". Then it all should
> work well.
>
> Kind regards,
>
> Jacqui
>
> Jacqueline Ross
> Biomedical Imaging Microscopist
> Biomedical Imaging Research Unit
> School of Medical Sciences
> Faculty of Medical & Health Sciences
> The University of Auckland
> Private Bag 92019
> Auckland 1142, NEW ZEALAND
>
> Tel: [phone]
> Fax: [phone]
>
> http://www.fmhs.auckland.ac.nz/sms/biru/
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Tiago Ferreira
> Sent: Tuesday, 9 October 2012 4:52 p.m.
> To: [hidden email]
> Subject: Re: Getting greyscale data from thresholded image
>
> Hi Adam,
>
> On 2012.10.08, at 20:49 , Adam Hughes wrote:
> > Whenever one uses analyze particles, one must always threshold the
> > image, which converts it to black and white.
>
> This is only the case if you press "Apply" in the Threshold widget. Just
> set threshold levels on the grayscale image (without pressing "Apply")
> before running the ParticleAnalyzer and you will have access to the
> original values.
>
> Alternatively, you can use the "Add to Manager" option, that will allow
> you to measure the resulting ROIs on any image.
>
> HTH,
> -tiago
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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