Fwd: ImageJ projection of 4D stack

Posted by Knecht, David on Dec 08, 2009; 2:30pm
URL: http://imagej.273.s1.nabble.com/Re-ImageJ-projection-of-4D-stack-tp3690178p3690180.html

I am trying to do an extended depth of focus on a stack.  I found this  
macro from Joachim to do the job, but it is set for 256x256 and 7  
frames.  Is there a way to make this general or another way to do EDF  
on a stack?  Thanks- Dave

Begin forwarded message:

> From: Joachim Walter <[hidden email]>
> Date: May 14, 2007 5:38:09 AM EDT
> To: [hidden email]
> Subject: Re: ImageJ projection of 4D stack
> Reply-To: ImageJ Interest Group <[hidden email]>
>
> 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?
>>>>
>
>
> --
> -----------------------------------------------
> Dr. Joachim Walter
>
> TILL I.D. GmbH
> c\o BioImaging Zentrum
> Großhaderner Str. 2
> D-82152 Martinsried
>
> Tel.: [phone]
> Fax:  [phone]
> Geschäftsführer: Dr. Rainer Uhl
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Dr. David Knecht
Department of Molecular and Cell Biology
Co-head Flow Cytometry and Confocal Microscopy Facility
U-3125
91 N. Eagleville Rd.
University of Connecticut
Storrs, CT 06269
860-486-2200
860-486-4331 (fax)