OutOfMemoryError caused by Analyze Particles plugin

[lakshmi]

Hi Admin,

I have a macro that sequentially calls a set of 9 plugins and
processes more than 3000 images.
I am using a 64 bit windows OS with 8GB RAM. The memory limit for Fiji
by default was about 6095 MB(75% of RAM).
The macro that I have written works fine for approximately 300 images
and then gives an error:- java.lang.OutOfMemoryError: Java heap space
I did a unit testing by running individual plugins separately and also
by combining the first 8 plugins together. None of these plugins when
run separately/together gave the 'outofmemory' error.
But when I included the "Analyze Particles" plugin the Fiji threw an
error immediately after 300 images. (6Gb was not sufficient for >300
images). Increasing/Decreasing the memory used by Fiji did not help in
fixing this.

I am trying to detect ellipses whose area falls within a range in the
"Analyze Particles" plugins. The output is saved to a csv file. Can
you please let me know if I need to do anything to fix this issue.

Thanks,
Lakshmi

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

[Peter Haub]

Hi Lakshmi,

do you have / do the Particle Analyser creates a lot of ROIs (thousends
of ROIs)?
I run into this kind of problem once.

Peter

On 23.08.2013 23:10, lakshmi narjala wrote:

> Hi Admin,
>
> I have a macro that sequentially calls a set of 9 plugins and
> processes more than 3000 images.
> I am using a 64 bit windows OS with 8GB RAM. The memory limit for Fiji
> by default was about 6095 MB(75% of RAM).
> The macro that I have written works fine for approximately 300 images
> and then gives an error:- java.lang.OutOfMemoryError: Java heap space
> I did a unit testing by running individual plugins separately and also
> by combining the first 8 plugins together. None of these plugins when
> run separately/together gave the 'outofmemory' error.
> But when I included the "Analyze Particles" plugin the Fiji threw an
> error immediately after 300 images. (6Gb was not sufficient for >300
> images). Increasing/Decreasing the memory used by Fiji did not help in
> fixing this.
>
> I am trying to detect ellipses whose area falls within a range in the
> "Analyze Particles" plugins. The output is saved to a csv file. Can
> you please let me know if I need to do anything to fix this issue.
>
> Thanks,
> Lakshmi
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Rasband, Wayne (NIH/NIMH) [E]]

On Aug 23, 2013, at 5:10 PM, lakshmi narjala wrote:

> Hi Admin,
>
> I have a macro that sequentially calls a set of 9 plugins and
> processes more than 3000 images.
> I am using a 64 bit windows OS with 8GB RAM. The memory limit for Fiji
> by default was about 6095 MB(75% of RAM).
> The macro that I have written works fine for approximately 300 images
> and then gives an error:- java.lang.OutOfMemoryError: Java heap space

Are all images closed after each image is processed? You can verify this by adding

   print(nImages);

to the end of the processing loop. It will display 0 if all images are closed. You can insure that all images are closed by adding

    run("Close All");

to the end of the processing loop.

-wayne

> I did a unit testing by running individual plugins separately and also
> by combining the first 8 plugins together. None of these plugins when
> run separately/together gave the 'outofmemory' error.
> But when I included the "Analyze Particles" plugin the Fiji threw an
> error immediately after 300 images. (6Gb was not sufficient for >300
> images). Increasing/Decreasing the memory used by Fiji did not help in
> fixing this.
>
> I am trying to detect ellipses whose area falls within a range in the
> "Analyze Particles" plugins. The output is saved to a csv file. Can
> you please let me know if I need to do anything to fix this issue.
>
> Thanks,
> Lakshmi

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

[lakshmi]

Hi Wayne Rasband,

Thank you very much for the reply. The "OutOfMemoryError" memory was solved after I included the command " run("Close All");" and after I updated the imageJ version to the most recent one.

Thanks,
Lakshmi