JACOP - macro - changing thresholds

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JACOP - macro - changing thresholds

Jacqui Ross
Hi everyone,

I'm working on a macro for colocalisation analysis and it's working OK except that I have to manually change the threshold values.

Does anyone know if it's possible to add something into the macro that does a "refresh" of the threshold step so that each new image has a new automatic threshold set?

I also thought of a "Wait for user" step so that the values could be changed as the macro progresses but that doesn't seem possible either.

Cheers,

Jacqui

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

Telephone: Ext 87438; DDI:  +64 9 923 7438

Website:    http://www.auckland.ac.nz/biru




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Re: JACOP - macro - changing thresholds

Gabriel Landini
On Friday, 13 October 2017 02:51:22 BST [hidden email] wrote:
> Does anyone know if it's possible to add something into the macro that does
> a "refresh" of the threshold step so that each new image has a new
> automatic threshold set?
>
> I also thought of a "Wait for user" step so that the values could be changed
> as the macro progresses but that doesn't seem possible either.

Hi Jacqui,

Would this work:

selectImage(Your_image);
setAutoThreshold("Default");

(or any other AutoThresh method)?
Sorry if I misunderstood the question?

Cheers

Gabriel

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Re: JACOP - macro - changing thresholds

Jacqui Ross
Hi Gabriel,

Thanks for your reply. Thanks also to Volko who replied and has suggested a similar approach.

The problem is that the JACOP plugin has its own automatic threshold built-in so I can't run the command separately.

What I thought might work is to ask the JACOP window to close and then re-open for each image. However, I don't know how to do that and the macro code includes specific values for each image threshold. If I can determine values for all of the images, then it's OK because I just populate with that but it would be nice if I could have the automatic threshold applied. The upper limit is easy but it's the lower limit that I want the macro to automatically populate.

This is the relevant line of code.

run("JACoP ", "imga=[C1] imgb=[C3] thra=2591 thrb=912 pearson mm");

Cheers,

Jacqui

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Gabriel Landini
Sent: Friday, 13 October 2017 9:11 p.m.
To: [hidden email]
Subject: Re: JACOP - macro - changing thresholds

On Friday, 13 October 2017 02:51:22 BST [hidden email] wrote:
> Does anyone know if it's possible to add something into the macro that
> does a "refresh" of the threshold step so that each new image has a
> new automatic threshold set?
>
> I also thought of a "Wait for user" step so that the values could be
> changed as the macro progresses but that doesn't seem possible either.

Hi Jacqui,

Would this work:

selectImage(Your_image);
setAutoThreshold("Default");

(or any other AutoThresh method)?
Sorry if I misunderstood the question?

Cheers

Gabriel

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Re: JACOP - macro - changing thresholds

Aryeh Weiss
Hi Jacqui

On 16/10/2017 0:02, Jacqui Ross wrote:

> Hi Gabriel,
>
> Thanks for your reply. Thanks also to Volko who replied and has suggested a similar approach.
>
> The problem is that the JACOP plugin has its own automatic threshold built-in so I can't run the command separately.
>
> What I thought might work is to ask the JACOP window to close and then re-open for each image. However, I don't know how to do that and the macro code includes specific values for each image threshold. If I can determine values for all of the images, then it's OK because I just populate with that but it would be nice if I could have the automatic threshold applied. The upper limit is easy but it's the lower limit that I want the macro to automatically populate.
>
> This is the relevant line of code.
>
> run("JACoP ", "imga=[C1] imgb=[C3] thra=2591 thrb=912 pearson mm");
I you determine the parameters externally, you should be able to include
them in your cammand using either of two possibilities:


1.  thra = 2591;
      thrb = 912;
      run("JACoP ", "imga=[C1] imgb=[C3] thra=&thra thrb=&thrb pearson
mm");

or

2.  thra = 2591;
      thrb = 912;
      run("JACoP ", "imga=[C1] imgb=[C3] thra="+d2s(thra,0)+"
thrb="+d2s(thrb,0)+" pearson mm");


either way, the idea is to embed your value into the argument string.

Hope that helps.
--aryeh



> Cheers,
>
> Jacqui
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Gabriel Landini
> Sent: Friday, 13 October 2017 9:11 p.m.
> To: [hidden email]
> Subject: Re: JACOP - macro - changing thresholds
>
> On Friday, 13 October 2017 02:51:22 BST [hidden email] wrote:
>> Does anyone know if it's possible to add something into the macro that
>> does a "refresh" of the threshold step so that each new image has a
>> new automatic threshold set?
>>
>> I also thought of a "Wait for user" step so that the values could be
>> changed as the macro progresses but that doesn't seem possible either.
> Hi Jacqui,
>
> Would this work:
>
> selectImage(Your_image);
> setAutoThreshold("Default");
>
> (or any other AutoThresh method)?
> Sorry if I misunderstood the question?
>
> Cheers
>
> Gabriel
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: 972-3-7384051

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Re: JACOP - macro - changing thresholds

Jacqui Ross
Hi Aryeh,

Thank you so much! The second suggestion is working! I am very happy.

I just added in the getThreshold command and made thrb the lower one.

This is the code in case someone else has the same issue.

setAutoThreshold("Default dark");
getThreshold(lower,upper);
thrb = (lower);
run("JACoP ", "imga=[C1] imgb=[C3] thra="+d2s(thra,0)+" thrb="+d2s(thrb,0)+" pearson overlap mm");

Cheers,

Jacqui



Kind regards,

Jacqui

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Aryeh Weiss
Sent: Monday, 16 October 2017 3:22 p.m.
To: [hidden email]
Subject: Re: JACOP - macro - changing thresholds

Hi Jacqui

On 16/10/2017 0:02, Jacqui Ross wrote:

> Hi Gabriel,
>
> Thanks for your reply. Thanks also to Volko who replied and has suggested a similar approach.
>
> The problem is that the JACOP plugin has its own automatic threshold built-in so I can't run the command separately.
>
> What I thought might work is to ask the JACOP window to close and then re-open for each image. However, I don't know how to do that and the macro code includes specific values for each image threshold. If I can determine values for all of the images, then it's OK because I just populate with that but it would be nice if I could have the automatic threshold applied. The upper limit is easy but it's the lower limit that I want the macro to automatically populate.
>
> This is the relevant line of code.
>
> run("JACoP ", "imga=[C1] imgb=[C3] thra=2591 thrb=912 pearson mm");
I you determine the parameters externally, you should be able to include them in your cammand using either of two possibilities:


1.  thra = 2591;
      thrb = 912;
      run("JACoP ", "imga=[C1] imgb=[C3] thra=&thra thrb=&thrb pearson
mm");

or

2.  thra = 2591;
      thrb = 912;
      run("JACoP ", "imga=[C1] imgb=[C3] thra="+d2s(thra,0)+"
thrb="+d2s(thrb,0)+" pearson mm");


either way, the idea is to embed your value into the argument string.

Hope that helps.
--aryeh



> Cheers,
>
> Jacqui
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Gabriel Landini
> Sent: Friday, 13 October 2017 9:11 p.m.
> To: [hidden email]
> Subject: Re: JACOP - macro - changing thresholds
>
> On Friday, 13 October 2017 02:51:22 BST [hidden email] wrote:
>> Does anyone know if it's possible to add something into the macro that
>> does a "refresh" of the threshold step so that each new image has a
>> new automatic threshold set?
>>
>> I also thought of a "Wait for user" step so that the values could be
>> changed as the macro progresses but that doesn't seem possible either.
> Hi Jacqui,
>
> Would this work:
>
> selectImage(Your_image);
> setAutoThreshold("Default");
>
> (or any other AutoThresh method)?
> Sorry if I misunderstood the question?
>
> Cheers
>
> Gabriel
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: 972-3-7384051

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

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