Re: Deconvolve 3D plugin problem

Posted by Joel Sheffield on Jul 05, 2007; 3:42pm
URL: http://imagej.273.s1.nabble.com/Workflow-for-importing-DV-video-tp3698931p3698938.html

See what happens if you make a smaller psf.  my guess is that even
for a single image, you are creating a volume of at least 64 times
the 2D volume based on the need for a power of 2 in the z dimension..
So, if your original image were 1000x1000, that would be padded in
the x,y dimension to 2048x2048 (i.e. approx 4 mb).  This would then
have to be multiplied by 64, yielding a minimum of 266 mb.  If the
volume needs to be a cube (I don't know the algorithm well enough),
you need even more.

Re the 300x300 success, can you extract that sized subset from your
original image, and not have to scale it?

Joel


Date sent:       Thu, 5 Jul 2007 16:23:38 +0200
Send reply to:   ImageJ Interest Group <[hidden email]>
From:           Przemko <[hidden email]>
Subject:         Re: Deconvolve 3D plugin problem
To:             [hidden email]

> Joel Sheffield wrote:
> > How many images are you trying to process at once?  Similarly, how
> > many slices are taken up by the 3D psf?  You might be able to get the
> > result you want by defining the psf in fewer slices.
> >  
>
> I started with one and never moved to more because of the crash. My PSF
> has 34 slices. Interestingly I looked into the task manager. When I run
> Diffraction Limit PSF and then Iterative Deconvolution the memory usage
> was around 1G but when I do the 3D the memory usage goes above the magic
> value of 1.7.
> Another thing that I noticed was that I could the 3D plugin to work on
> an image of 300x300 pixels. This however is way too small for my
> applications.
>
> Przemko
>
>
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--
Joel B. Sheffield, Ph.D.
Biology Department, Temple University
1900 North 12th Street
Philadelphia, PA 19122
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