How to combine more than two stacks?

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How to combine more than two stacks?

Brian Grabiner
Hi,

I have 9 time-lapse stacks (1 channel only), with 13 timepoints (slices) per stack, taken from 9 separate fields. I'd like to make a larger 'mega-stack' with the 9 stacks stitched together (NOT concatenated). Right now, I use the Image->Stacks->Tools->Combine function to combine two of these stacks into one, then save that one, then do it again and again and again... There must be a faster/easier way to do this. Any help would be greatly appreciated.

Thanks!

Brian

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Re: How to combine more than two stacks?

CARL Philippe (LBP)
Dear Brian,
Why aren't you using Image>Stacks>Tools>Concatenete?
This method able to combine 4 stacks in one shot.
And for further automatization you should use the Plugins>Macros>Record... on one concatenation and then use macros.
My best regards,
Philippe


Philippe CARL
Laboratoire de Bioimagerie et Pathologies
UMR 7021 CNRS - Université de Strasbourg
Faculté de Pharmacie
74 route du Rhin
67401 ILLKIRCH
Tel : +33(0)3 68 85 41 84

----- Mail original -----
De: "Brian Grabiner" <[hidden email]>
À: "imagej" <[hidden email]>
Envoyé: Mercredi 9 Octobre 2019 19:33:50
Objet: How to combine more than two stacks?

Hi,

I have 9 time-lapse stacks (1 channel only), with 13 timepoints (slices) per stack, taken from 9 separate fields. I'd like to make a larger 'mega-stack' with the 9 stacks stitched together (NOT concatenated). Right now, I use the Image->Stacks->Tools->Combine function to combine two of these stacks into one, then save that one, then do it again and again and again... There must be a faster/easier way to do this. Any help would be greatly appreciated.

Thanks!

Brian

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Re: How to combine more than two stacks?

Brian Grabiner
Hi,

So Concatenate just puts the images at the end of one another, which doesn't help. Unless I'm misunderstanding your point.

Brian

On 10/9/19, 4:06 PM, "ImageJ Interest Group on behalf of CARL Philippe (LBP)" <[hidden email] on behalf of [hidden email]> wrote:

    *** EXTERNAL EMAIL: Use caution before replying, clicking links, and opening attachments ***
   
    Dear Brian,
    Why aren't you using Image>Stacks>Tools>Concatenete?
    This method able to combine 4 stacks in one shot.
    And for further automatization you should use the Plugins>Macros>Record... on one concatenation and then use macros.
    My best regards,
    Philippe
   
   
    Philippe CARL
    Laboratoire de Bioimagerie et Pathologies
    UMR 7021 CNRS - Université de Strasbourg
    Faculté de Pharmacie
    74 route du Rhin
    67401 ILLKIRCH
    Tel : +33(0)3 68 85 41 84
   
    ----- Mail original -----
    De: "Brian Grabiner" <[hidden email]>
    À: "imagej" <[hidden email]>
    Envoyé: Mercredi 9 Octobre 2019 19:33:50
    Objet: How to combine more than two stacks?
   
    Hi,
   
    I have 9 time-lapse stacks (1 channel only), with 13 timepoints (slices) per stack, taken from 9 separate fields. I'd like to make a larger 'mega-stack' with the 9 stacks stitched together (NOT concatenated). Right now, I use the Image->Stacks->Tools->Combine function to combine two of these stacks into one, then save that one, then do it again and again and again... There must be a faster/easier way to do this. Any help would be greatly appreciated.
   
    Thanks!
   
    Brian
   
    --
    ImageJ mailing list: https://urldefense.proofpoint.com/v2/url?u=http-3A__imagej.nih.gov_ij_list.html&d=DwIFaQ&c=n7UHtw8cUfEZZQ61ciL2BA&r=7C4mch1z_0t6vqo_E57lqOB8-RTaFgq8JftoJAuR3qo&m=oE8VLJBnlfhLsXT6MUq_VC59LMf0QCmu6IUsk7GnkBA&s=jsPR_vNxhDV295Y-kFpamILhz9oHz6CZh5RUMLb49fA&e= 
   
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Re: How to combine more than two stacks?

Curtis Rueden-2
Hi Brian,

Have a look at the "Multi Stack Montage" plugin:
  https://imagej.net/Multi_Stack_Montage

Regards,
Curtis

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ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Have you tried the Image.sc Forum? https://forum.image.sc/



On Wed, Oct 9, 2019 at 4:06 PM Brian Grabiner <[hidden email]>
wrote:

> Hi,
>
> So Concatenate just puts the images at the end of one another, which
> doesn't help. Unless I'm misunderstanding your point.
>
> Brian
>
> On 10/9/19, 4:06 PM, "ImageJ Interest Group on behalf of CARL Philippe
> (LBP)" <[hidden email] on behalf of [hidden email]> wrote:
>
>     *** EXTERNAL EMAIL: Use caution before replying, clicking links, and
> opening attachments ***
>
>     Dear Brian,
>     Why aren't you using Image>Stacks>Tools>Concatenete?
>     This method able to combine 4 stacks in one shot.
>     And for further automatization you should use the
> Plugins>Macros>Record... on one concatenation and then use macros.
>     My best regards,
>     Philippe
>
>
>     Philippe CARL
>     Laboratoire de Bioimagerie et Pathologies
>     UMR 7021 CNRS - Université de Strasbourg
>     Faculté de Pharmacie
>     74 route du Rhin
>     67401 ILLKIRCH
>     Tel : +33(0)3 68 85 41 84
>
>     ----- Mail original -----
>     De: "Brian Grabiner" <[hidden email]>
>     À: "imagej" <[hidden email]>
>     Envoyé: Mercredi 9 Octobre 2019 19:33:50
>     Objet: How to combine more than two stacks?
>
>     Hi,
>
>     I have 9 time-lapse stacks (1 channel only), with 13 timepoints
> (slices) per stack, taken from 9 separate fields. I'd like to make a larger
> 'mega-stack' with the 9 stacks stitched together (NOT concatenated). Right
> now, I use the Image->Stacks->Tools->Combine function to combine two of
> these stacks into one, then save that one, then do it again and again and
> again... There must be a faster/easier way to do this. Any help would be
> greatly appreciated.
>
>     Thanks!
>
>     Brian
>
>     --
>     ImageJ mailing list:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__imagej.nih.gov_ij_list.html&d=DwIFaQ&c=n7UHtw8cUfEZZQ61ciL2BA&r=7C4mch1z_0t6vqo_E57lqOB8-RTaFgq8JftoJAuR3qo&m=oE8VLJBnlfhLsXT6MUq_VC59LMf0QCmu6IUsk7GnkBA&s=jsPR_vNxhDV295Y-kFpamILhz9oHz6CZh5RUMLb49fA&e=
>
>     --
>     ImageJ mailing list:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__imagej.nih.gov_ij_list.html&d=DwIFaQ&c=n7UHtw8cUfEZZQ61ciL2BA&r=7C4mch1z_0t6vqo_E57lqOB8-RTaFgq8JftoJAuR3qo&m=oE8VLJBnlfhLsXT6MUq_VC59LMf0QCmu6IUsk7GnkBA&s=jsPR_vNxhDV295Y-kFpamILhz9oHz6CZh5RUMLb49fA&e=
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: How to combine more than two stacks?

CARL Philippe (LBP)
In reply to this post by Brian Grabiner
Dear Brian,

> So Concatenate just puts the images at the end of one another, which doesn't help.

Sorry if I was too fast within my explanations and thus let me go a little bit further.
So for your applications I see 3 ways to come out (at least frol your description)
1) You stay with the Image->Stacks->Tools->Combine method you described and to make things faster you create a macro by using the macro recorder as a guide.
2) You use the Concatenate method I described which will then indeed "put the images at the end of one another".
And once done, you use an "ad hoc" Image>Hyperstacks>Stack_to_hyperstack... method (i.e. you have to set the hyperstack order depending on how your data are formated, xyczt is by default) where the channel input will be your 9 separatly acquired fields.
3) You open different stacks of your separatly acquired fields and by using Analyze>Tools>Synchronize_windows you look at similarities in the different pictures windows.
So hoping I made you move further now I wish you a nice day (and night for me).
My best regards,
Philippe


Philippe CARL
Laboratoire de Bioimagerie et Pathologies
UMR 7021 CNRS - Université de Strasbourg
Faculté de Pharmacie
74 route du Rhin
67401 ILLKIRCH
Tel : +33(0)3 68 85 41 84

----- Mail original -----
De: "Brian Grabiner" <[hidden email]>
À: "imagej" <[hidden email]>
Envoyé: Mercredi 9 Octobre 2019 23:05:14
Objet: Re: How to combine more than two stacks?

Hi,

So Concatenate just puts the images at the end of one another, which doesn't help. Unless I'm misunderstanding your point.

Brian

On 10/9/19, 4:06 PM, "ImageJ Interest Group on behalf of CARL Philippe (LBP)" <[hidden email] on behalf of [hidden email]> wrote:

    *** EXTERNAL EMAIL: Use caution before replying, clicking links, and opening attachments ***
   
    Dear Brian,
    Why aren't you using Image>Stacks>Tools>Concatenete?
    This method able to combine 4 stacks in one shot.
    And for further automatization you should use the Plugins>Macros>Record... on one concatenation and then use macros.
    My best regards,
    Philippe
   
   
    Philippe CARL
    Laboratoire de Bioimagerie et Pathologies
    UMR 7021 CNRS - Université de Strasbourg
    Faculté de Pharmacie
    74 route du Rhin
    67401 ILLKIRCH
    Tel : +33(0)3 68 85 41 84
   
    ----- Mail original -----
    De: "Brian Grabiner" <[hidden email]>
    À: "imagej" <[hidden email]>
    Envoyé: Mercredi 9 Octobre 2019 19:33:50
    Objet: How to combine more than two stacks?
   
    Hi,
   
    I have 9 time-lapse stacks (1 channel only), with 13 timepoints (slices) per stack, taken from 9 separate fields. I'd like to make a larger 'mega-stack' with the 9 stacks stitched together (NOT concatenated). Right now, I use the Image->Stacks->Tools->Combine function to combine two of these stacks into one, then save that one, then do it again and again and again... There must be a faster/easier way to do this. Any help would be greatly appreciated.
   
    Thanks!
   
    Brian
   
    --
    ImageJ mailing list: https://urldefense.proofpoint.com/v2/url?u=http-3A__imagej.nih.gov_ij_list.html&d=DwIFaQ&c=n7UHtw8cUfEZZQ61ciL2BA&r=7C4mch1z_0t6vqo_E57lqOB8-RTaFgq8JftoJAuR3qo&m=oE8VLJBnlfhLsXT6MUq_VC59LMf0QCmu6IUsk7GnkBA&s=jsPR_vNxhDV295Y-kFpamILhz9oHz6CZh5RUMLb49fA&e= 
   
    --
    ImageJ mailing list: https://urldefense.proofpoint.com/v2/url?u=http-3A__imagej.nih.gov_ij_list.html&d=DwIFaQ&c=n7UHtw8cUfEZZQ61ciL2BA&r=7C4mch1z_0t6vqo_E57lqOB8-RTaFgq8JftoJAuR3qo&m=oE8VLJBnlfhLsXT6MUq_VC59LMf0QCmu6IUsk7GnkBA&s=jsPR_vNxhDV295Y-kFpamILhz9oHz6CZh5RUMLb49fA&e= 
   


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Re: How to combine more than two stacks?

Straub, Volko A. (Dr.)
Hi Brian,

I just want to add one more suggestion to the list of previous suggestions. I might have misunderstood you, but I had the impression that you wanted to create a stack of 13 images (one fore each time point), where each image shows a 3x3 montage of one time point.
If that is what you are aiming for, I would start by concatenating your 9 stacks. Then you can make a 3x3 montage, but set the increment to 13. Repeat, but set the start slice ('First slice') to 2, and so on until you have a montage for each time point. You can then combine the 13 montages into a single stack.
Doing this would certainly being much quicker by writing a little macro.
The code below should do it:

imageTitle=getTitle();
for (i = 0; i < 14; i++) {
selectWindow(imageTitle);
run("Make Montage...", "columns=3 rows=3 scale=0.25 first="+i);
};
run("Images to Stack", "name=Stack title=[] use");

Hope this helps,
Volko

________________________________
From: CARL Philippe (LBP) <[hidden email]>
Sent: 09 October 2019 22:32
To: [hidden email] <[hidden email]>
Subject: Re: How to combine more than two stacks?

Dear Brian,

> So Concatenate just puts the images at the end of one another, which doesn't help.

Sorry if I was too fast within my explanations and thus let me go a little bit further.
So for your applications I see 3 ways to come out (at least frol your description)
1) You stay with the Image->Stacks->Tools->Combine method you described and to make things faster you create a macro by using the macro recorder as a guide.
2) You use the Concatenate method I described which will then indeed "put the images at the end of one another".
And once done, you use an "ad hoc" Image>Hyperstacks>Stack_to_hyperstack... method (i.e. you have to set the hyperstack order depending on how your data are formated, xyczt is by default) where the channel input will be your 9 separatly acquired fields.
3) You open different stacks of your separatly acquired fields and by using Analyze>Tools>Synchronize_windows you look at similarities in the different pictures windows.
So hoping I made you move further now I wish you a nice day (and night for me).
My best regards,
Philippe


Philippe CARL
Laboratoire de Bioimagerie et Pathologies
UMR 7021 CNRS - Université de Strasbourg
Faculté de Pharmacie
74 route du Rhin
67401 ILLKIRCH
Tel : +33(0)3 68 85 41 84

----- Mail original -----
De: "Brian Grabiner" <[hidden email]>
À: "imagej" <[hidden email]>
Envoyé: Mercredi 9 Octobre 2019 23:05:14
Objet: Re: How to combine more than two stacks?

Hi,

So Concatenate just puts the images at the end of one another, which doesn't help. Unless I'm misunderstanding your point.

Brian

On 10/9/19, 4:06 PM, "ImageJ Interest Group on behalf of CARL Philippe (LBP)" <[hidden email] on behalf of [hidden email]> wrote:

    *** EXTERNAL EMAIL: Use caution before replying, clicking links, and opening attachments ***

    Dear Brian,
    Why aren't you using Image>Stacks>Tools>Concatenete?
    This method able to combine 4 stacks in one shot.
    And for further automatization you should use the Plugins>Macros>Record... on one concatenation and then use macros.
    My best regards,
    Philippe


    Philippe CARL
    Laboratoire de Bioimagerie et Pathologies
    UMR 7021 CNRS - Université de Strasbourg
    Faculté de Pharmacie
    74 route du Rhin
    67401 ILLKIRCH
    Tel : +33(0)3 68 85 41 84

    ----- Mail original -----
    De: "Brian Grabiner" <[hidden email]>
    À: "imagej" <[hidden email]>
    Envoyé: Mercredi 9 Octobre 2019 19:33:50
    Objet: How to combine more than two stacks?

    Hi,

    I have 9 time-lapse stacks (1 channel only), with 13 timepoints (slices) per stack, taken from 9 separate fields. I'd like to make a larger 'mega-stack' with the 9 stacks stitched together (NOT concatenated). Right now, I use the Image->Stacks->Tools->Combine function to combine two of these stacks into one, then save that one, then do it again and again and again... There must be a faster/easier way to do this. Any help would be greatly appreciated.

    Thanks!

    Brian

    --
    ImageJ mailing list: https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__imagej.nih.gov_ij_list.html%26d%3DDwIFaQ%26c%3Dn7UHtw8cUfEZZQ61ciL2BA%26r%3D7C4mch1z_0t6vqo_E57lqOB8-RTaFgq8JftoJAuR3qo%26m%3DoE8VLJBnlfhLsXT6MUq_VC59LMf0QCmu6IUsk7GnkBA%26s%3DjsPR_vNxhDV295Y-kFpamILhz9oHz6CZh5RUMLb49fA%26e&amp;data=02%7C01%7Cvs64%40leicester.ac.uk%7C922c555b06a04e26e85b08d74d003f2d%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C637062535763365721&amp;sdata=6v7HNfObWJYF8gxDlAvUR71wlx5GsWeSd5AbPP0QMAc%3D&amp;reserved=0=

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