Re: XYZT visualization

Posted by Philip Ershler on Jan 20, 2009; 7:07pm
URL: http://imagej.273.s1.nabble.com/Copy-volume-from-within-stack-to-new-stack-tp3693965p3693976.html

Hi,
        Here is a macro although fairly basic, does the job. It takes a stack  
of images and creates a stack of 3D images. Just setup the Interactive  
3D viewer with the view and other settings that you want. Then execute  
this macro.

   n = nSlices;
   if (n==1) exit("Stack required");
   stack1 = getImageID;
   stack2 = 0;
   setBatchMode(true);
   for (i=1; i<=n; i++) {
     showProgress(i, n);
     selectImage(stack1);
     setSlice(i);
     run("Duplicate...", "title=temp");
     temp = getImageID;
     run("Interactive 3D Surface Plot", "snapshot=1");
     run("Copy");
     w = getWidth; h = getHeight;
     close;
     selectImage(temp);
     close;
     if (stack2==0) {
      newImage("Plots", "RGB", w, h, 1);
      stack2 = getImageID;
     } else {
      selectImage(stack2);
      run("Add Slice");
     }
     run("Paste");
   }
   setSlice(1);
   run("Select None");
   setBatchMode(false);

HTH,

Phil

On Jan 20, 2009, at 10:30 AM, Benjamin Schmid wrote:

> Hi Aryeh,
>
> The 3D Viewer has the capability to load 4D data. You get a small
> dialog, with which you can go to certain timepoints, or you can
> animate it. However, it is some time ago that I worked on this, and
> it might not fully work as you expect. But in case you want to
> use it and have problems / find bugs, I have motivation again to
> improve this ;-)
>
> Wishes,
> Benjamin
>
> PS: -> You start the 4D Viewer by clicking on -> File -> Load 4D  
> data in
> the 3D viewer's menu bar.
>
>
> On 21:07 Mon 19 Jan     , Aryeh Weiss wrote:
>> Is there a volume viewer in ImageJ that can display a time series  
>> of volumes?
>> Something like the 3D-viewer, but with a slider on the bottom that  
>> would
>> allow one to select the volume at any given time point?
>>
>> --aryeh
>> --
>> Aryeh Weiss
>> School of Engineering
>> Bar Ilan University
>> Ramat Gan 52900 Israel
>>
>> Ph:  972-3-5317638
>> FAX: [phone]