Computer for high resolution image stack analysis

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Computer for high resolution image stack analysis

Abigail Nunn
Hi,

I wondered if anyone could provide me with some advice about how to choose
a new computer for use in imaging.  I have some experience of using Fiji to
process nonlinear microscopy image stacks, and I have noticed that the 3D
Object Counter does not run on most of the computers I have tried,
including a 16 GB RAM computer, for high resolution stacks (2048x2048x30).
I have also had problems running the PureDenoise plugin with stacks of this
size. I need to purchase a new computer for image processing and analysis
if these image stacks, and I wondered if anyone could provide any advice on
specifications I should look for.

Many thanks,

Abigail

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Re: Computer for high resolution image stack analysis

José María Mateos
On 31/05/2013 13:07, Abigail Nunn wrote:
> I wondered if anyone could provide me with some advice about how to choose
> a new computer for use in imaging.  I have some experience of using Fiji to
> process nonlinear microscopy image stacks, and I have noticed that the 3D
> Object Counter does not run on most of the computers I have tried,
> including a 16 GB RAM computer, for high resolution stacks (2048x2048x30).
> I have also had problems running the PureDenoise plugin with stacks of this
> size.

Have you tried processing your data as a Virtual Stack? I understand
that this option allows ImageJ to open very big stacks but does not need
to store all the data into memory.

Best,

José María Mateos.

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Re: Computer for high resolution image stack analysis

Glen MacDonald-2
In reply to this post by Abigail Nunn
Hello,
Did you increase the memory allocation to FIJI?  The default allocation is probably not enough for a 2kX2k image.  
instructions are in these 2 places.

http://imagej.nih.gov/ij/docs/install/index.html
        select your operating system
http://imagej.nih.gov/ij/docs/guide/146-27.html#toc-Subsection-27.13
        Scroll to section 27.13.12 Memory & Threads…

Glen MacDonald
        Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
        Cellular Morphology Core
Center on Human Development and Disability
Box 357923
University of Washington
Seattle, WA 98195-7923  USA
(206) 616-4156
[hidden email]







On May 31, 2013, at 4:07 AM, Abigail Nunn <[hidden email]> wrote:

> Hi,
>
> I wondered if anyone could provide me with some advice about how to choose
> a new computer for use in imaging.  I have some experience of using Fiji to
> process nonlinear microscopy image stacks, and I have noticed that the 3D
> Object Counter does not run on most of the computers I have tried,
> including a 16 GB RAM computer, for high resolution stacks (2048x2048x30).
> I have also had problems running the PureDenoise plugin with stacks of this
> size. I need to purchase a new computer for image processing and analysis
> if these image stacks, and I wondered if anyone could provide any advice on
> specifications I should look for.
>
> Many thanks,
>
> Abigail
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html