Memory size for large images

[Phase GmbH]

Hi,

sometimes I have to process large single images with up to 300 MB per image. What would be the recommended memsize parameter for ImageJ?

Thanks

Christian Kreutzfeldt

[Sami Badawi-2]

Hi Christian,

If you have very large images you might consider looking at JAI, Java
Advanced Imaging, from Sun. I think that ImageJ is simpler to work with, but
JAI can work on tiled images and you can set up a pipeline of the image
operations that you want to preform.

You could possibly do some work in JAI and some in ImageJ. I am using Sun's
Java2D and ImageJ together without any problems.

The JAI community does not seem to be as active as ImageJ. Here are a few links:

http://java.sun.com/products/java-media/jai/forDevelopers/jai1_0_1guide-unc/
http://java.sun.com/products/java-media/jai/collateral/datasheet.html
http://java.sun.com/developer/onlineTraining/javaai/jai/index.html
http://java.sun.com/products/java-media/jai/forDevelopers/jaifaq.html

-Sami Badawi
http://www.shapelogic.org

[Mark J. Chopping]

Hi Christian,

If you do not need to access the entire image, I would advise looking at
the Virtual Stack functionality in 1.39. I use this to access a large
image (much larger than memory) and extract manageable slices to work on.
Many thanks to Wayne for pointing this out: it works beautifully. Maybe it
would be relatively easy to implement "Virtual Image" functionality but I
am more than happy using the VS routines.

  -- Mark

  Mark J. Chopping, Ph.D.
  Associate Professor, Earth & Environmental Studies
  Montclair State University, Montclair, NJ 07043
  NASA EOS/MISR ST/LCLUC ST/North American Carbon Program
  Tel: [phone]  Fax: [phone]
  -------------------------------------------------------
  http://csam.montclair.edu/~chopping/wood

[ctrueden]

Hi,

Another way to conserve memory is to use the Bio-Formats Importer plugin to
crop images on initial import. If you check the "Crop on import" box, the
importer will read only those portions of the image within the specified
range, to conserve memory. The importer only allows you to specify a single
region, but you could script it in a macro to open up multiple pieces of the
image into tiles or some such.

-Curtis

On Feb 1, 2008 2:11 PM, Mark J. Chopping <[hidden email]>
wrote:

> Hi Christian,
>
> If you do not need to access the entire image, I would advise looking at
> the Virtual Stack functionality in 1.39. I use this to access a large
> image (much larger than memory) and extract manageable slices to work on.
> Many thanks to Wayne for pointing this out: it works beautifully. Maybe it
> would be relatively easy to implement "Virtual Image" functionality but I
> am more than happy using the VS routines.
>
>  -- Mark
>
>  Mark J. Chopping, Ph.D.
>  Associate Professor, Earth & Environmental Studies
>  Montclair State University, Montclair, NJ 07043
>  NASA EOS/MISR ST/LCLUC ST/North American Carbon Program
>  Tel: [phone]  Fax: [phone]
>  -------------------------------------------------------
>  http://csam.montclair.edu/~chopping/wood<http://csam.montclair.edu/%7Echopping/wood>
>