add x number of stacks

[fabrice senger-2]

Hello,

is there a way to add  all the stacks in a folder ?
In other words is it possible to use imageCalculator in batch mode ?

Thank you ,

Fabrice.

[ved sharma-2]

Hi Fabrice,

I am not sure what you want to do. Do you want to concatenate all of your stacks (which are in a folder) one after the other, and make one large stack? If so, then I have a macro to do this. Let me know if you want to use it?

Ved

[fabrice senger-2]

Hello,

and thank you for your answer.

Actually if there are 10 stacks with 3 images(01,02,03) , I want to add all
together so that all 01 are added, all 02 are added and all 03 are added and
so I get a new stack with 3 images.

Concatenate thus not help as this produces a new stack but one stack after
another.

Ther several ways to sum stacks but it is always one to another, and I would
like to automate this, maybe in batch mode...

2010/9/8 Ved Sharma <[hidden email]>

> Hi Fabrice,
>
> I am not sure what you want to do. Do you want to concatenate all of your
> stacks (which are in a folder) one after the other, and make one large
> stack? If so, then I have a macro to do this. Let me know if you want to use
> it?
>
> Ved
>
>
>

[Rasband, Wayne (NIH/NIMH) [E]]

On Sep 8, 2010, at 2:33 AM, fabrice senger wrote:

> Hello,
>
> and thank you for your answer.
>
> Actually if there are 10 stacks with 3 images(01,02,03) , I want to add all
> together so that all 01 are added, all 02 are added and all 03 are added and
> so I get a new stack with 3 images.
>
> Concatenate thus not help as this produces a new stack but one stack after
> another.
>
> Ther several ways to sum stacks but it is always one to another, and I would
> like to automate this, maybe in batch mode...

Here is an easy way to do this:

1. Use File>Import>Raw to Open the 10 stacks as a single 30 image stack.
2. Use Image>Hyperstacks>Stack to Hyperstack to convert the stack to
a 10 slice, 3 frame hyperstack (Order="xyctz", c=1, z=10, t=3, display mode="Grayscale").
3. Use Image>Stack>Z Project (Projection type = "Sum Slices").

Use the command recorder (Plugins>Macros>Record) to generate a macro. It will look something like this:

run("Image Sequence...", "open=/Users/wayne/stack/stack01.tif sort");
run("Stack to Hyperstack...", "order=xyctz channels=1 slices=4 frames=3 display=Grayscale");
run("Z Project...", "projection=[Sum Slices] all");

-wayne

[fabrice senger-2]

Hi there, this is what I was looking for...
In any case I attach the code I was working on.

Thank you,

Fabrice.



dir = getDirectory("Choose a Directory ");
      list = getFileList(dir);



run(dir+list[0]);
id1 = getImageID;

run(dir+list[1]);
id2 = getImageID;




imageCalculator("Add create stack", id1,id2);

rename("test");

waitForUser("checkpoint");

 for (i=0; i<list.length-2; i++) {
     showProgress(i, list.length);

run(dir+list[i+2]);
id3=getImageID;

imageCalculator("Add create stack", "test",id3);

rename("test");

}





2010/9/8 Rasband, Wayne (NIH/NIMH) [E] <[hidden email]>

> On Sep 8, 2010, at 2:33 AM, fabrice senger wrote:
>
> > Hello,
> >
> > and thank you for your answer.
> >
> > Actually if there are 10 stacks with 3 images(01,02,03) , I want to add
> all
> > together so that all 01 are added, all 02 are added and all 03 are added
> and
> > so I get a new stack with 3 images.
> >
> > Concatenate thus not help as this produces a new stack but one stack
> after
> > another.
> >
> > Ther several ways to sum stacks but it is always one to another, and I
> would
> > like to automate this, maybe in batch mode...
>
> Here is an easy way to do this:
>
> 1. Use File>Import>Raw to Open the 10 stacks as a single 30 image stack.
> 2. Use Image>Hyperstacks>Stack to Hyperstack to convert the stack to
> a 10 slice, 3 frame hyperstack (Order="xyctz", c=1, z=10, t=3, display
> mode="Grayscale").
> 3. Use Image>Stack>Z Project (Projection type = "Sum Slices").
>
> Use the command recorder (Plugins>Macros>Record) to generate a macro. It
> will look something like this:
>
> run("Image Sequence...", "open=/Users/wayne/stack/stack01.tif sort");
> run("Stack to Hyperstack...", "order=xyctz channels=1 slices=4 frames=3
> display=Grayscale");
> run("Z Project...", "projection=[Sum Slices] all");
>
> -wayne
>

[ved sharma-2]

Hi Fabrice,

I think it will also work your way. See the code below:

---------------------
dir = getDirectory("Choose a Directory ");
list = getFileList(dir);
open(dir+list[0]);
rename("combined");

for (i=1; i<list.length; i++) {
        showProgress(i, list.length);
        open(dir+list[i]);
        current = getTitle();
        imageCalculator("Add stack", "combined",current);
        selectWindow(current);
        close();
}
----------------------

Ved

[fabrice senger-2]

nice !

2010/9/8 Ved Sharma <[hidden email]>

> Hi Fabrice,
>
> I think it will also work your way. See the code below:
>
> ---------------------
> dir = getDirectory("Choose a Directory ");
> list = getFileList(dir);
> open(dir+list[0]);
> rename("combined");
>
> for (i=1; i<list.length; i++) {
>        showProgress(i, list.length);
>        open(dir+list[i]);
>        current = getTitle();
>        imageCalculator("Add stack", "combined",current);
>        selectWindow(current);
>        close();
> }
> ----------------------
>
> Ved
>