Memory runs out though plenty available (Mac)

[D.S.Pedersen]

Hi all

I sit and would like to threshold LM images. My routine isn't that complicated:

1) Use colour thresholding (via a MBF-plugin) to threshold picture of GFAP positive neurons
2) The thresholded colour images is converted to 8-bit grey scale
3) Normal thresholding
4) Load my pre-saved ROI on to the images (these are jpg, appr. 12-13 MB compressed and 69 MB in ImageJ)
5) Measure

This routine works well the first (few) time(s), then the Colour Threshold plugin sort of freezes (i.e. sliders can move, numbers don't) and closing and starting that plugin gives the message:

>>>>>>>>>>>>>>>>>>>>>>>>>>>
<Out of memory>
<All available memory (653MB) has been>
<used. Instructions for making more>
<available can be found in the "Memory" >
<sections of the installation notes at>
<http://rsb.info.nih.gov/ij/docs/install/>
>>>>>>>>>>>>>>>>>>>>>>>>>>>

I've tried to tweak the memory already but it won't allow me to have more than 659 MB / 2 threads. This should supposedly be sufficient for the routine, though there seem to be a problem of some kind.

Has anyone else experienced similar memory-related problems, or does anyone have a clever suggestion as to what can be done to avoid this issue?

Thanks in advance!
Dan


Additional info:
Running latest version of ImageJ (v1.41k)
Mac OS X Leopard, 2 GB RAM, w/ only Preview and Safari running
Macbook, 1. gen., 2 GHz CoreDuo, +30 GB available on disk.

[D.S.Pedersen]

New about the problem: I just found out, that if one forgets to return the colour thresholded picture to 'Original' before closing it, it locks up the 'Threshold Colour' plugin, which upon restart sets of the memory warning, as described in my above post. I.e. before I close the normally thresholded 8-bit image, I press 'Original' to be sure that this memory "deadlock" is avoided.

[Gabriel Landini]

On Monday 15 September 2008 14:29:41 D.S.Pedersen wrote:
> New about the problem: I just found out, that if one forgets to return the
> colour thresholded picture to 'Original' before closing it, it locks up the
> 'Threshold Colour' plugin, which upon restart sets of the memory warning,
> as described in my above post. I.e. before I close the normally thresholded
> 8-bit image, I press 'Original' to be sure that this memory "deadlock" is
> avoided.

Have you run the plugin with the memory monitor? If so, is the memory released
after finishing the plugin?

Not sure what version of theplugin you are using, but try 1.9 from here:

http://www.dentistry.bham.ac.uk/landinig/software/software.html

Bob Dougherty found a fix earlier this year to a thread  being  kept running
after closing the plugin. Maybe memory was not being released after closing
it. Please report if if that version resolves the problem.

Regards

G.

[Asad Moten]

Quoting Gabriel Landini <[hidden email]>:

> On Monday 15 September 2008 14:29:41 D.S.Pedersen wrote:
>> New about the problem: I just found out, that if one forgets to return the
>> colour thresholded picture to 'Original' before closing it, it locks up the
>> 'Threshold Colour' plugin, which upon restart sets of the memory warning,
>> as described in my above post. I.e. before I close the normally thresholded
>> 8-bit image, I press 'Original' to be sure that this memory "deadlock" is
>> avoided.
>
> Have you run the plugin with the memory monitor? If so, is the memory
> released
> after finishing the plugin?
>
> Not sure what version of theplugin you are using, but try 1.9 from here:
>
> http://www.dentistry.bham.ac.uk/landinig/software/software.html
>
> Bob Dougherty found a fix earlier this year to a thread  being  kept running
> after closing the plugin. Maybe memory was not being released after closing
> it. Please report if if that version resolves the problem.
>
> Regards
>
> G.
>

[Robert Dougherty]

Dan,

The value 653 MB seems awfully familiar.  See the thread "unexplainable
memory limit in ImageJ64" in the archives last week.

Bob

> <Out of memory>
> <All available memory (653MB) has been>
> <used. Instructions for making more>
> Mac OS X Leopard, 2 GB RAM, w/ only Preview and Safari running
> Macbook, 1. gen., 2 GHz CoreDuo, +30 GB available on disk.

[jmutterer]

Instructions to join or leave the list and about how to modify your
subscription are available at:

http://rsb.info.nih.gov/ij/list.html

jerome

[Daniel James White]

Dan,

In summary,
you need to check what intel chip you have.
Core duo is 32 bit (like in my revA/early macbook pro)
and coreduo2 is 64 bit (newer mac book pros and mac books)

you cant run the 64 bit java (1.6) or 64 bit imageJ unless you have a  
64 bit processor.

Dan

On Sep 16, 2008, at 6:00 AM, IMAGEJ automatic digest system wrote:

> Date:    Mon, 15 Sep 2008 06:29:41 -0700
> From:    "D.S.Pedersen" <[hidden email]>
> Subject: Re: Memory runs out though plenty available (Mac)
>
> New about the problem: I just found out, that if one forgets to  
> return the
> colour thresholded picture to 'Original' before closing it, it locks  
> up the
> 'Threshold Colour' plugin, which upon restart sets of the memory  
> warning, as
> described in my above post. I.e. before I close the normally  
> thresholded
> 8-bit image, I press 'Original' to be sure that this memory  
> "deadlock" is
> avoided.
>
> -----
> Dan S. Pedersen
> MSc Biology, PhD-student
> Section of Neuroprotection
> University of Copenhagen, Denmark

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


New Mobile Number!!!

[phone] (German Mobile)
+49  (0)351 210 2627 (Work phone at MPI-CBG)
+49  (0)351 210 1078 (Fax MPI-CBG LMF)

http://www.bioimagexd.net
http://www.chalkie.org.uk
[hidden email]
( [hidden email] )

[D.S.Pedersen]

Hi again, ImageJ-users

I'm quite sure that I had an older version of Threshold Colour (as last modified in 2005 - info) so I downloaded version 1.9 to be sure to have the most recent version.

Also, I found out that my Intel Core Duo processor is not 64-bit compliant, and as I somewhere in the past trashed the 32-bit version of ImageJ, I downloaded the full ImageJ package and installed and updated both the 32 and 64 bit version, though both should work independently of each other.

So far everything seems to work fine. I've been able to change the values of 'Memory & Threads' to 1000 MB / two threads, and it seems to be working just fine.

The only thing I miss now, is the possibility of saving/loading values in Threshold Colour pane, but that's something quite else.

All your advices have really been appreciated, thanks a lot!

/Dan

_____________________________________________________________________

Bugzilla from [e-mail] wrote

On Monday 15 September 2008 14:29:41 D.S.Pedersen wrote:
> New about the problem: I just found out, that if one forgets to return the
> colour thresholded picture to 'Original' before closing it, it locks up the
> 'Threshold Colour' plugin, which upon restart sets of the memory warning,
> as described in my above post. I.e. before I close the normally thresholded
> 8-bit image, I press 'Original' to be sure that this memory "deadlock" is
> avoided.

Have you run the plugin with the memory monitor? If so, is the memory released
after finishing the plugin?

Not sure what version of theplugin you are using, but try 1.9 from here:

http://www.dentistry.bham.ac.uk/landinig/software/software.html

Bob Dougherty found a fix earlier this year to a thread  being  kept running
after closing the plugin. Maybe memory was not being released after closing
it. Please report if if that version resolves the problem.

Regards

G.

[Gabriel Landini]

On Tuesday 16 September 2008 10:44:25 D.S.Pedersen wrote:
> The only thing I miss now, is the possibility of saving/loading values in
> Threshold Colour pane, but that's something quite else.

If you need to just apply the same settings to other images, just open the
macro recorder, and when you are ready with the colour threshold press
the "Macro" button in the plugin dialog. This will record a macro that
thresholds any other image with the same values without having to run the
plugin and set the sliders again.

I hope this helps.
Cheers

G.

[D.S.Pedersen]

I haven't worked with macros before. I've recorded the macro using the 'Macro' button in the Thresholding colour window, and saved it in the Macro-folder; however, I can find it anywhere in the menues. However, I can run the macro by opening it manually and it starts a long row of windows, spliting to H, S and B respectively. I think I'd rather adjust the sliders once and then keep the Thresholding pane open for the entire session of pictures undergoing thresholding.

But thanks. I will, however, se how I can utilize the macro function in the near future.

/Dan

Bugzilla from [e-mail] wrote

On Tuesday 16 September 2008 10:44:25 D.S.Pedersen wrote:
> The only thing I miss now, is the possibility of saving/loading values in
> Threshold Colour pane, but that's something quite else.

If you need to just apply the same settings to other images, just open the
macro recorder, and when you are ready with the colour threshold press
the "Macro" button in the plugin dialog. This will record a macro that
thresholds any other image with the same values without having to run the
plugin and set the sliders again.

I hope this helps.
Cheers

G.