Re: ImageJ projection of 4D stack

Posted by Joachim Walter on May 14, 2007; 10:38am
URL: http://imagej.273.s1.nabble.com/Re-ImageJ-projection-of-4D-stack-tp3690178p3690179.html

Aryeh,

here is a short macro to do this with the "Stack Focuser", which also
does Extended Depht of Field. The EPFL Extended Depht of Field Plugin is
not macro scriptable.

Wayne, there is currently no way to retrieve the number of channels or
frames of an Image in a macro. Could you add "nChannels" and "nFrames"
commands similar to the "nSlices" command?

Best wishes,
Joachim



// Macro start
idOrig = getImageID();
name = getTitle();
nFrames = 7;

run("New Image5D", "name="+name+"-ExtDepth type=8-bit fill=Black
width=256 height=256 channels=1 slices=1 frames="+nFrames);
idExtDepth = getImageID();

for (i=1; i<=nFrames; i++) {
  selectImage(idOrig);
  run("Set Position", "frame="+i);
  run("Stack Focuser ", "enter=11");
  run("Select All");
  run("Copy");
  run("Close");
  selectImage(idExtDepth);
  run("Set Position", "frame="+i);
  run("Paste");
}

Aryeh Weiss schrieb:

> I have a question about Image5D similar to the question below. I want to
> take an XYZT series, and reduce it to XYT by running the extended depth
> of field plugin on the z-stacks. Can this be done in Image5D, of has
> someone done something similar?
>
> --aryeh
>
> On Sat, 9 Dec 2006 18:15:53 +0100, Joachim Walter <[hidden email]-
> MUENCHEN.DE> wrote:
>
>  
>> You can use the Image5D plugin.
>> - If you have your data as separate 2D TIFF images all in one directory,
>> you open them with the Virtual Image5D opener.
>> - Click on the "Color" button and assign a color to each channel (not
>> limited to RGB)
>> - Use "Z Project" of the Image5D plugins. In the window that pops up you
>> have to select "All Time Frames".
>> The resulting series of projections has to fit in memory, though.
>>
>>
>> Rainer Kohler schrieb:
>>    
>>> Hi,
>>>
>>> I have a time series of image stacks with three channels from
>>> FluoView. Size 1 GB.
>>> How can I project the z-stacks to create a time series of the
>>> projections of merged images as well as of the separate channels.
>>> Because of memory restrictions it seems not to work in FluoView.
>>> Could I do it in ImageJ?
>>>      

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