Re: Deconvolution on MacBook?

Posted by Daniel James White on Mar 09, 2011; 10:16am
URL: http://imagej.273.s1.nabble.com/Deconvolution-on-MacBook-tp3685439p3685440.html

Hi Mark,

On Mar 9, 2011, at 6:00 AM, IMAGEJ automatic digest system wrote:

> Date:    Tue, 8 Mar 2011 11:42:17 -0500
> From:    "Mark Adelman (Work)" <[hidden email]>
> Subject: Deconvolution on MacBook?
>
> Is it realistic to attempt to do a limited number of wide field  
> deconvolutions using ImageJ on a MacBook?

Yes, so long as the images are small enough to fit in your RAM with a copy or two also in RAM...
So RAM needs to be a few times larger than the size of the image.

>  My MacBook has a 2.13 GHz  
> Intel Core 2 Duo Processor and Memory of 2 GB 800 MHz DDR2 SDRAM.

so the biggest image you could probably try and deconvolve in imageJ is limited by the
2GB ram, less whatever the MacOSX is usiung for itself...in the ideal case.

Close all other applications and reboot the computer,
and only open imageJ or Fiji,
so the java VM can get that whole nearly 2GB  RAM in a single continuous chunk.

If the memory is already fragmented in to smaller bits, you will struggle.

Try DeconvolutionLab plugin from the BIG group in lausanne.
Its very good.
http://bigwww.epfl.ch/algorithms/deconvolutionlab/

Use a measured PSF (image og a 100 nm bead z stack)
or use Bob's Diffraction PSF 3D plugin to calculate a pretend 3D widefield PSF
and use that in the deconvolution.

http://www.optinav.com/Diffraction-PSF-3D.htm


>  I  
> am running Leopard (OS 10.5.8).  I have the ability to capture Z  
> series fluorescence microscopy data sets (Zeiss Photomicroscope III  

thats a very cool old microscope!
http://www.microscopy-uk.org.uk/mag//artnov07/dw-pm3.html

How are you doing fluorescence  on it? II dint see where the filter sets go? Do you have the epi accessories?

Deconvolution doesnt really work on transmitted light images... there are approaches for that... but
the tools above are strictly for fluorescence.


> with a Focus Controller and a digital camera), under the control of an  
> iMac (running under 10.4.11).  I already know the iMac does not have  
> enough computing power.  If anyone has suggestions regarding  
> possibilities using the MacBook, please contact me offline (unless you  
> think others would be interested).

the mac book will work fine... so long as the java VM doesnt run out of RAM.

so for small images (say 256x256x20) you might be fine,
but large images, eg full camera chip image and many z slices you will be in trouble...

then the only solution is a powerful 64 bit workstation with tens of GB or ram and multiple processors.

you need to make sure that the magnification is matched to the camera xy pixel spacing so that you
fulfill the Nyquist  sampling criterion, and that you z slice separation is also fulfilling that criterion, and its precise.

What objective are you using?

you can calculate the xyz pixel sizes needed to get data suitable doe deconvolution here:
http://www.svi.nl/NyquistCalculator
and read up more on that wiki, it is excellent for understanding how to do deconvolution microscopy.


>
> Thanks in advance!!

but I didn't help you before I wrote this email...

if you like you can retract the premature felicitations, and thank me now instead!!

cheers

Dan

>
> Mark R. Adelman
> [hidden email]

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

[phone] (German Mobile)
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[phone] (Fax MPI-CBG LMF)

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