Re: Deconvolve 3D plugin problem

Posted by Joel Sheffield on Jul 05, 2007; 3:09pm
URL: http://imagej.273.s1.nabble.com/Workflow-for-importing-DV-video-tp3698931p3698936.html

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.

Joel


Date sent:       Thu, 5 Jul 2007 11:20:40 +0200
Send reply to:   ImageJ Interest Group <[hidden email]>
From:           Przemko <[hidden email]>
Subject:         Re: Deconvolve 3D plugin problem
To:             [hidden email]

> Gentlemen, thank you for the prompt response. Here is some more info
> about my images and what happens. So, first of all I am not doing a 3D
> medical imaging but immunofluorescence. Normally I use the Iterative
> Deconvolve plugin and it works on my images rather well. I have decided
> however to give it a try with Deconvolve 3D because some of my images
> would not be processed to the point that I was happy with them. Namely,
> I am looking at the colocalization of two proteins and sometimes, with
> insufficient deconvolution, I had troubles deciding if the two proteins
> colocalized or not.
> My images are 1315x1033 pixels. If I do Diffraction Limit PSF and then
> Iterative Deconvolution, the rpogram works and on my machine it takes
> about 60 seconds to 5 rounds of deconvolution. Now if I go with the same
> file to Diffraction PSF 3D and Iterative Deconvolution 3D, I get the
> crash as described before. If I decrease the number of pixel by half
> (loosing some of the resolution which I need), it seems that the program
> goes a bit longer (2-3 min) before crashing as mentioned earlier. The
> reason to go for the 3D plugin comes from the info on the plugin site
> stating "This plugin is intended to replace both the Iterative
> Deconvolution and Iterative Deconvolution 2 plugins for 2D applications,
> as well as extending the function to 3D"
>
> So, here I am. What I wonder is, as one of you suggested, so do the
> processing in parts so that the memory usage is better controlled. Would
> that be somehow possible?
>
> Again, thank you for your help!
>
> 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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