Memory Limits on Macintosh

[Simon_Carr]

Dear ImageJ,

I have been using FIJI for a while now on a 2.7GHz i5 iMac (with 16Gb RAM), to do image processing and analysis on 3D CT volumes, with no problems.

However, having just recently updated FIJI, I now seem to be hitting lots of memory related problems, and have been unable to increase the memory that FIJI is using beyond 6007Mb. I keep getting an error stating:

"ImageJ is unable to change the memory limit. For more information refer to installation notes at http://imagej.nih.gov/ij/docs/install/     The ImageJ application (ImageJ.app) was not found. Current limit: 6007Mb"

I have searched through the forums and the installation notes, and have checked (and purged) my RAM, but cannot get FIJI to up the memory sufficiently to deal with image stacks that I have previously been able to handle with no problems. Does anyone have any suggestions of the cause of this issue?

Regards,

Simon Carr
Centre for Micromorphology, QMUL, UK

[Simon_Carr]

Just to add some more information, I have downloaded and installed the current version of ImageJ, and have no problems with the memory. The issue seems to arise when using FIJI instead.

[dscho]

Hi Simon,

On Tue, 4 Jun 2013, Simon_Carr wrote:

> Just to add some more information, I have downloaded and installed the
> current version of ImageJ, and have no problems with the memory. The
> issue seems to arise when using FIJI instead.

This was triggered by a change I made recently, trying to reconcile a
couple of unneeded differences between core ImageJ 1.x and Fiji. Turns out
the differences were not *that* unneeded, unfortunately.

Funnily, I encountered that bug yesterday myself, and will try to find
time to fix it this afternoon.

Ciao,
Johannes

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[Simon_Carr]

Many thanks for such a quick response, and I hope you are able to resolve the issue fairly quickly: A volume that normally takes 3-4 hours to fully segment (1024^3 voxels) is 6 hours in, and only about half way!

Regards,

Simon

[Simon_Carr]

Dear Johannes,

Have you had any joy with working out the issue and solution that is hobbling the memory on the Mac FIJI build? I've been updating and updating whenever I open FIJI, but still am restricted to a few Gb of RAM use. I don't like to hassle you, but these problems with FIJI have made me realise just how fundamental the software is to my work!

Regards,

Simon

[dscho]

Hi Simon,

On Thu, 6 Jun 2013, Simon_Carr wrote:

> Have you had any joy with working out the issue and solution that is
> hobbling the memory on the Mac FIJI build? I've been updating and
> updating whenever I open FIJI, but still am restricted to a few Gb of
> RAM use. I don't like to hassle you, but these problems with FIJI have
> made me realise just how fundamental the software is to my work!

Unfortunately, I did not yet have time (all of Wednesday was spent
traveling).

But here is a work-around in the meantime: start Fiji from the
command-line via

        /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --mem=6g

(substitute "6g" by whatever is appropriate). This will override any
automatic memory setting.

Ciao,
Johannes

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

[Simon_Carr]

Dear Johannes,

Have you been able to resolve the memory issue in a new FIJI build as yet? I am using your command line workaround, but it is still not really doing the job properly....

[dscho]

Hi Simon,

On Mon, 17 Jun 2013, Simon_Carr wrote:

> Have you been able to resolve the memory issue in a new FIJI build as
> yet? I am using your command line workaround, but it is still not really
> doing the job properly....

The fix (well, it is more a work-around) is now in place. Sorry for the
long wait!

Ciao,
Johannes

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

[Simon_Carr]

Dear Johannes,

Many thanks for this: very much appreciated! FIJI is working just fine again!

Simon
__________________________________
Dr Simon Carr
School of Geography,
Queen Mary University of London,
Mile End Road, London, E1 4NS, UK.
t: 00 44 20 7882 2780
f: 00 44 20 8981 6276
e: [hidden email]
twitter: @DrSimonCarr







On 6 Jul 2013, at 17:44, Johannes Schindelin <[hidden email]> wrote:

> Hi Simon,
>
> On Mon, 17 Jun 2013, Simon_Carr wrote:
>
>> Have you been able to resolve the memory issue in a new FIJI build as
>> yet? I am using your command line workaround, but it is still not really
>> doing the job properly....
>
> The fix (well, it is more a work-around) is now in place. Sorry for the
> long wait!
>
> Ciao,
> Johannes

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