How to order images within a stack

[Theodoric]

Hi all,

Presumably an easily solved problem (sorry, i'm still not very familiar with imageJ)

I'm trying to make a stack from about 30 images. Unfortunately, the images are never in the order I'd like to have.
Is there any possibility to change the position of an image in an already built stack? Or is it at least possible to influence the order while building the stack?

Thank you a lot for your help!

Jan Bandemer,
FSU Jena, Germany

[gabibau]

Hi, Theodoric

You can influence the order by opening (or creating) the images in the order
you want to have them. It always works for me.

Gabriela Bauermann
Santa Maria /RS /Brasil
Processamento e Análise de Imagens
www.imagesurvey.com.br


On Thu, May 7, 2009 at 8:09 PM, Theodoric <[hidden email]> wrote:

> Hi all,
>
> Presumably an easily solved problem (sorry, i'm still not very familiar
> with
> imageJ)
>
> I'm trying to make a stack from about 30 images. Unfortunately, the images
> are never in the order I'd like to have.
> Is there any possibility to change the position of an image in an already
> built stack? Or is it at least possible to influence the order while
> building the stack?
>
> Thank you a lot for your help!
>
> Jan Bandemer,
> FSU Jena, Germany
> --
> View this message in context:
> http://n2.nabble.com/How-to-order-images-within-a-stack-tp2840732p2840732.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>

[lechristophe]

Theodoric,

You can use the Stack Sorter plugin by Bob Dougherty :
http://www.optinav.com/Stack-Sorter.htm

It allows you to manually sort images in a stack

Christophe

On Fri, May 8, 2009 at 12:53 PM, Gabriela Bauermann <[hidden email]> wrote:

>
> Hi, Theodoric
>
> You can influence the order by opening (or creating) the images in the order
> you want to have them. It always works for me.
>
> Gabriela Bauermann
> Santa Maria /RS /Brasil
> Processamento e Análise de Imagens
> www.imagesurvey.com.br
>
>
> On Thu, May 7, 2009 at 8:09 PM, Theodoric <[hidden email]> wrote:
>
> > Hi all,
> >
> > Presumably an easily solved problem (sorry, i'm still not very familiar
> > with
> > imageJ)
> >
> > I'm trying to make a stack from about 30 images. Unfortunately, the images
> > are never in the order I'd like to have.
> > Is there any possibility to change the position of an image in an already
> > built stack? Or is it at least possible to influence the order while
> > building the stack?
> >
> > Thank you a lot for your help!
> >
> > Jan Bandemer,
> > FSU Jena, Germany
> > --
> > View this message in context:
> > http://n2.nabble.com/How-to-order-images-within-a-stack-tp2840732p2840732.html
> > Sent from the ImageJ mailing list archive at Nabble.com.
> >

[Theodoric]

Hi Christophe,

That's perfect. Exactly what I've looked for!
Thank you very much for the link.

Best wishes!

-------- Original-Nachricht --------
> Datum: Fri, 8 May 2009 04:15:34 -0700 (PDT)
> Von: "lechristophe (via Nabble)" <[hidden email]>
> An: Theodoric <[hidden email]>
> Betreff: Re: How to order images within a stack

>
>
>
> Theodoric,
>
> You can use the Stack Sorter plugin by Bob Dougherty :
> http://www.optinav.com/Stack-Sorter.htm
>
> It allows you to manually sort images in a stack
>
> Christophe
>
> On Fri, May 8, 2009 at 12:53 PM, Gabriela Bauermann <[hidden email]>
> wrote:
> >
> > Hi, Theodoric
> >
> > You can influence the order by opening (or creating) the images in the
> order
> > you want to have them. It always works for me.
> >
> > Gabriela Bauermann
> > Santa Maria /RS /Brasil
> > Processamento e Análise de Imagens
> > www.imagesurvey.com.br
> >
> >
> > On Thu, May 7, 2009 at 8:09 PM, Theodoric <[hidden email]> wrote:
> >
> > > Hi all,
> > >
> > > Presumably an easily solved problem (sorry, i'm still not very
> familiar
> > > with
> > > imageJ)
> > >
> > > I'm trying to make a stack from about 30 images. Unfortunately, the
> images
> > > are never in the order I'd like to have.
> > > Is there any possibility to change the position of an image in an
> already
> > > built stack? Or is it at least possible to influence the order while
> > > building the stack?
> > >
> > > Thank you a lot for your help!
> > >
> > > Jan Bandemer,
> > > FSU Jena, Germany
> > > --
> > > View this message in context:
> > >
> http://n2.nabble.com/How-to-order-images-within-a-stack-tp2840732p2840732.html
> > > Sent from the ImageJ mailing list archive at Nabble.com.
> > >
>
>
> ______________________________________
>
> View message @
> http://n2.nabble.com/How-to-order-images-within-a-stack-tp2840732p2844741.html
> To start a new topic under ImageJ, email
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> To unsubscribe from ImageJ, click
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[mmettlen]

I have a somewhat related questions (I'm new to writing macros). Currently, I have a macro that generates and saves 4 images called red.jpg, green.jpg, far red.jpg and RGB.jpg. In order to automatically make a montage, I'm trying to built a stack that includes these 4 images in the listed order (which is of course not alphabetical). What commands do I have to include in my macro to do so? Is there something similar to the Color=>Merge Channels functions where I can define what image corresponds to what channel?
Thx

[Lachlan Whitehead]

There may be other ways to do this, but I've used the concatenate stacks command in the past.

run("Concatenate...", "  title=[Stack] image1=[red.jpg] image2=[green.jpg] image3=[far red.jpg] image4=[RGB.jpg]")

This should work so long as your filenames don't change, otherwise you'll have to make them variables to get them in there.
(eg red_image = "red.jpg"; then in your concatenate command replace the filenames: image1=["+red_image+"] etc)

Hope this helps.
-Lachie


----- Original Message -----
From: "mmettlen" <[hidden email]>
To: [hidden email]
Sent: Wednesday, 6 November, 2013 5:59:27 AM
Subject: Re: How to order images within a stack

I have a somewhat related questions (I'm new to writing macros). Currently, I
have a macro that generates and saves 4 images called red.jpg, green.jpg,
far red.jpg and RGB.jpg. I'm trying to built a stack that includes these 4
images in the listed order (which is of course not alphabetical). What
commands do I have to include in my macro to do so?
Thx!



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[mmettlen]

Thanks Lachie - that works. As I've now lost the title of my slices and the montage is labelled image1, etc., I applied the following to get it right again:
setSlice(1)
string1 = "Alexa561"
setMetadata("Label", string1)
setSlice(2)
string2 = "Alexa488"
setMetadata("Label", string2)
setSlice(3)
string3= "Alexa647"
setMetadata("Label", string3)
setSlice(4)
string4 = "merge"
setMetadata("Label", string4)

[Lachlan Whitehead]

Hi Marcel,

Ahh, apparently concatenate doesn't preserve the image names in the metadata. Easiest fix is to put this after you've made the stack but before the montage:

setSlice(1);
setMetadata("Label","Image Label 1");
setSlice(2);
setMetadata("Label","Image Label 2");
setSlice(3);
setMetadata("Label","Image Label 3");
setSlice(4);
setMetadata("Label","Image Label 4");

And just change the second argument in each of the setMetadata commands. If you've gone down the route of making the image filenames into variables, you can just put the variable in there without the quotes. eg:

fname1="red.jpg";
setSlice(1);
setMetadata("Label",fname1);

There are probably more elegant solutions, but this is quick and easy to implement.

Thanks,
-Lachie



----- Original Message -----
From: "mmettlen" <[hidden email]>
To: [hidden email]
Sent: Wednesday, 6 November, 2013 10:31:08 PM
Subject: Re: How to order images within a stack

Thanks Lachie - that works. However, now I've lost the title of my slices and
the montage is now labelled  image1, etc.



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