FIJI related memory issue

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FIJI related memory issue

fabrice senger-2
Hi there,

I'm probably not the only one experiencing problems with memory wich
doesn't get released. Even no single image is open, and after hiting the
garbage collector.

Is there something new about that issue.

It seems it has been related at some point to the hyperstack opener of LOCI
...

In the meantime the only workarouns is to close FIJI and restart

Thank you all for your help,

Fabrice.

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Re: FIJI related memory issue

ctrueden
Hi Fabrice,

> experiencing problems with memory wich doesn't get released. Even no
> single image is open, and after hiting the garbage collector.

I am unable to duplicate this problem. I tried opening the Mitosis sample,
repeatedly duplicating it, closing all images, and clicking the status bar.

Can you please describe a precise sequence of operations that, if executed
repeatedly on your system, results in memory consumption increasing?

> It seems it has been related at some point to the hyperstack opener of
> LOCI

Why do you think that? Do you mean the old Data Browser plugin [1]? Are you
using it? That plugin is not actively supported or maintained.

Thanks,
Curtis

[1] https://loci.wisc.edu/software/data-browser

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Thu, Feb 8, 2018 at 11:18 AM, Fabrice Senger <[hidden email]>
wrote:

> Hi there,
>
> I'm probably not the only one experiencing problems with memory wich
> doesn't get released. Even no single image is open, and after hiting the
> garbage collector.
>
> Is there something new about that issue.
>
> It seems it has been related at some point to the hyperstack opener of LOCI
> ...
>
> In the meantime the only workarouns is to close FIJI and restart
>
> Thank you all for your help,
>
> Fabrice.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
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Re: FIJI related memory issue

fabrice senger-2
Hi there,

I'm using FIJI ImageJ 2.0.0-rc-64/1.51s;Java 1.8.0_66(64-bit) with 3 GB
allocated memory on a MacBookAir OS 10.10.4.

I really noticed the problem while opening Metamorph files. I usually open
them with BioFormats. All works fine but after a while I get a message
telling me that the selections I made would take too much memory. When I
check, by clicking on the status bar, while having no image open, it
happens that 30% of memory are used ...by what ?

Clicking on the garbage collector doesn't help, so I have to restart FIJI.

I think this thread is discussed for a while now on the forum but I have
the feeling there's no explanation on how and why this happens.

If you need further details or want me to perform some test ...

Best,

Fabrice.

2018-02-08 19:39 GMT+01:00 Curtis Rueden <[hidden email]>:

> Hi Fabrice,
>
> > experiencing problems with memory wich doesn't get released. Even no
> > single image is open, and after hiting the garbage collector.
>
> I am unable to duplicate this problem. I tried opening the Mitosis sample,
> repeatedly duplicating it, closing all images, and clicking the status bar.
>
> Can you please describe a precise sequence of operations that, if executed
> repeatedly on your system, results in memory consumption increasing?
>
> > It seems it has been related at some point to the hyperstack opener of
> > LOCI
>
> Why do you think that? Do you mean the old Data Browser plugin [1]? Are you
> using it? That plugin is not actively supported or maintained.
>
> Thanks,
> Curtis
>
> [1] https://loci.wisc.edu/software/data-browser
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Thu, Feb 8, 2018 at 11:18 AM, Fabrice Senger <[hidden email]>
> wrote:
>
> > Hi there,
> >
> > I'm probably not the only one experiencing problems with memory wich
> > doesn't get released. Even no single image is open, and after hiting the
> > garbage collector.
> >
> > Is there something new about that issue.
> >
> > It seems it has been related at some point to the hyperstack opener of
> LOCI
> > ...
> >
> > In the meantime the only workarouns is to close FIJI and restart
> >
> > Thank you all for your help,
> >
> > Fabrice.
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
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Re: FIJI related memory issue

ctrueden
Hi Fabrice,

Would you be able to post a sample Metamorph file that suffers from this
issue? It may be a format-specific bug in Bio-Formats—these have arisen in
the past.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Fri, Feb 9, 2018 at 9:09 AM, Fabrice Senger <[hidden email]>
wrote:

> Hi there,
>
> I'm using FIJI ImageJ 2.0.0-rc-64/1.51s;Java 1.8.0_66(64-bit) with 3 GB
> allocated memory on a MacBookAir OS 10.10.4.
>
> I really noticed the problem while opening Metamorph files. I usually open
> them with BioFormats. All works fine but after a while I get a message
> telling me that the selections I made would take too much memory. When I
> check, by clicking on the status bar, while having no image open, it
> happens that 30% of memory are used ...by what ?
>
> Clicking on the garbage collector doesn't help, so I have to restart FIJI.
>
> I think this thread is discussed for a while now on the forum but I have
> the feeling there's no explanation on how and why this happens.
>
> If you need further details or want me to perform some test ...
>
> Best,
>
> Fabrice.
>
> 2018-02-08 19:39 GMT+01:00 Curtis Rueden <[hidden email]>:
>
> > Hi Fabrice,
> >
> > > experiencing problems with memory wich doesn't get released. Even no
> > > single image is open, and after hiting the garbage collector.
> >
> > I am unable to duplicate this problem. I tried opening the Mitosis
> sample,
> > repeatedly duplicating it, closing all images, and clicking the status
> bar.
> >
> > Can you please describe a precise sequence of operations that, if
> executed
> > repeatedly on your system, results in memory consumption increasing?
> >
> > > It seems it has been related at some point to the hyperstack opener of
> > > LOCI
> >
> > Why do you think that? Do you mean the old Data Browser plugin [1]? Are
> you
> > using it? That plugin is not actively supported or maintained.
> >
> > Thanks,
> > Curtis
> >
> > [1] https://loci.wisc.edu/software/data-browser
> >
> > Regards,
> > Curtis
> >
> > --
> > Curtis Rueden
> > LOCI software architect - https://loci.wisc.edu/software
> > ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> > Did you know ImageJ has a forum? http://forum.imagej.net/
> >
> >
> > On Thu, Feb 8, 2018 at 11:18 AM, Fabrice Senger <
> [hidden email]>
> > wrote:
> >
> > > Hi there,
> > >
> > > I'm probably not the only one experiencing problems with memory wich
> > > doesn't get released. Even no single image is open, and after hiting
> the
> > > garbage collector.
> > >
> > > Is there something new about that issue.
> > >
> > > It seems it has been related at some point to the hyperstack opener of
> > LOCI
> > > ...
> > >
> > > In the meantime the only workarouns is to close FIJI and restart
> > >
> > > Thank you all for your help,
> > >
> > > Fabrice.
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
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Re: FIJI related memory issue

fabrice senger-2
Dear Curtis,

following several discussion onthat memmory issue ( Ithink the thread is
"mmemmory not released") I tried to open my stack with the option "split
channels" in that case I can open close and re-open files as long as I want.

Maybe this helps,

Fabrice.

2018-02-10 20:20 GMT+01:00 Curtis Rueden <[hidden email]>:

> Hi Fabrice,
>
> Would you be able to post a sample Metamorph file that suffers from this
> issue? It may be a format-specific bug in Bio-Formats—these have arisen in
> the past.
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Fri, Feb 9, 2018 at 9:09 AM, Fabrice Senger <[hidden email]>
> wrote:
>
> > Hi there,
> >
> > I'm using FIJI ImageJ 2.0.0-rc-64/1.51s;Java 1.8.0_66(64-bit) with 3 GB
> > allocated memory on a MacBookAir OS 10.10.4.
> >
> > I really noticed the problem while opening Metamorph files. I usually
> open
> > them with BioFormats. All works fine but after a while I get a message
> > telling me that the selections I made would take too much memory. When I
> > check, by clicking on the status bar, while having no image open, it
> > happens that 30% of memory are used ...by what ?
> >
> > Clicking on the garbage collector doesn't help, so I have to restart
> FIJI.
> >
> > I think this thread is discussed for a while now on the forum but I have
> > the feeling there's no explanation on how and why this happens.
> >
> > If you need further details or want me to perform some test ...
> >
> > Best,
> >
> > Fabrice.
> >
> > 2018-02-08 19:39 GMT+01:00 Curtis Rueden <[hidden email]>:
> >
> > > Hi Fabrice,
> > >
> > > > experiencing problems with memory wich doesn't get released. Even no
> > > > single image is open, and after hiting the garbage collector.
> > >
> > > I am unable to duplicate this problem. I tried opening the Mitosis
> > sample,
> > > repeatedly duplicating it, closing all images, and clicking the status
> > bar.
> > >
> > > Can you please describe a precise sequence of operations that, if
> > executed
> > > repeatedly on your system, results in memory consumption increasing?
> > >
> > > > It seems it has been related at some point to the hyperstack opener
> of
> > > > LOCI
> > >
> > > Why do you think that? Do you mean the old Data Browser plugin [1]? Are
> > you
> > > using it? That plugin is not actively supported or maintained.
> > >
> > > Thanks,
> > > Curtis
> > >
> > > [1] https://loci.wisc.edu/software/data-browser
> > >
> > > Regards,
> > > Curtis
> > >
> > > --
> > > Curtis Rueden
> > > LOCI software architect - https://loci.wisc.edu/software
> > > ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> > > Did you know ImageJ has a forum? http://forum.imagej.net/
> > >
> > >
> > > On Thu, Feb 8, 2018 at 11:18 AM, Fabrice Senger <
> > [hidden email]>
> > > wrote:
> > >
> > > > Hi there,
> > > >
> > > > I'm probably not the only one experiencing problems with memory wich
> > > > doesn't get released. Even no single image is open, and after hiting
> > the
> > > > garbage collector.
> > > >
> > > > Is there something new about that issue.
> > > >
> > > > It seems it has been related at some point to the hyperstack opener
> of
> > > LOCI
> > > > ...
> > > >
> > > > In the meantime the only workarouns is to close FIJI and restart
> > > >
> > > > Thank you all for your help,
> > > >
> > > > Fabrice.
> > > >
> > > > --
> > > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > > >
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
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Re: FIJI related memory issue

Robert Smith
To all with the memory issues.

Have you gone to edit>options>memory & threads an re-allocated more memory space?

I am running windows 10 with FIJI and allocated 8000 in memory. I process up to 1000 or more images without problem.

 I hope this helps.



Bob


________________________________
From: Fabrice Senger <[hidden email]>
Sent: Friday, March 2, 2018 11:33 AM
To: [hidden email]
Subject: Re: FIJI related memory issue

Dear Curtis,

following several discussion onthat memmory issue ( Ithink the thread is
"mmemmory not released") I tried to open my stack with the option "split
channels" in that case I can open close and re-open files as long as I want.

Maybe this helps,

Fabrice.

2018-02-10 20:20 GMT+01:00 Curtis Rueden <[hidden email]>:

> Hi Fabrice,
>
> Would you be able to post a sample Metamorph file that suffers from this
> issue? It may be a format-specific bug in Bio-Formats—these have arisen in
> the past.
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
[https://gravatar.com/avatar/63df759e2779af56fd050a968ff98d09]<https://imagej.net/User:Rueden>

User:Rueden - ImageJ<https://imagej.net/User:Rueden>
imagej.net
Curtis Rueden directs the software development efforts of LOCI. He is the principal architect of ImageJ2, and the current maintainer of the Fiji distribution of ImageJ.



> Did you know ImageJ has a forum? http://forum.imagej.net/
[http://forum.imagej.net/uploads/default/original/1X/d2fe983e291b72beb863ed580e265423374deee9.png]<http://forum.imagej.net/>

ImageJ Forum<http://forum.imagej.net/>
forum.imagej.net
A discussion forum for ImageJ users and developers!



>
>
> On Fri, Feb 9, 2018 at 9:09 AM, Fabrice Senger <[hidden email]>
> wrote:
>
> > Hi there,
> >
> > I'm using FIJI ImageJ 2.0.0-rc-64/1.51s;Java 1.8.0_66(64-bit) with 3 GB
> > allocated memory on a MacBookAir OS 10.10.4.
> >
> > I really noticed the problem while opening Metamorph files. I usually
> open
> > them with BioFormats. All works fine but after a while I get a message
> > telling me that the selections I made would take too much memory. When I
> > check, by clicking on the status bar, while having no image open, it
> > happens that 30% of memory are used ...by what ?
> >
> > Clicking on the garbage collector doesn't help, so I have to restart
> FIJI.
> >
> > I think this thread is discussed for a while now on the forum but I have
> > the feeling there's no explanation on how and why this happens.
> >
> > If you need further details or want me to perform some test ...
> >
> > Best,
> >
> > Fabrice.
> >
> > 2018-02-08 19:39 GMT+01:00 Curtis Rueden <[hidden email]>:
> >
> > > Hi Fabrice,
> > >
> > > > experiencing problems with memory wich doesn't get released. Even no
> > > > single image is open, and after hiting the garbage collector.
> > >
> > > I am unable to duplicate this problem. I tried opening the Mitosis
> > sample,
> > > repeatedly duplicating it, closing all images, and clicking the status
> > bar.
> > >
> > > Can you please describe a precise sequence of operations that, if
> > executed
> > > repeatedly on your system, results in memory consumption increasing?
> > >
> > > > It seems it has been related at some point to the hyperstack opener
> of
> > > > LOCI
> > >
> > > Why do you think that? Do you mean the old Data Browser plugin [1]? Are
> > you
> > > using it? That plugin is not actively supported or maintained.
> > >
> > > Thanks,
> > > Curtis
> > >
> > > [1] https://loci.wisc.edu/software/data-browser
Data Browser | LOCI<https://loci.wisc.edu/software/data-browser>
loci.wisc.edu
The Data Browser is an ImageJ plugin that facilitates quick browsing of multichannel, multi-focal plane time course datasets. It is integrated with the Bio-Formats ...



> > >
> > > Regards,
> > > Curtis
> > >
> > > --
> > > Curtis Rueden
> > > LOCI software architect - https://loci.wisc.edu/software
> > > ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
[https://gravatar.com/avatar/63df759e2779af56fd050a968ff98d09]<https://imagej.net/User:Rueden>

User:Rueden - ImageJ<https://imagej.net/User:Rueden>
imagej.net
Curtis Rueden directs the software development efforts of LOCI. He is the principal architect of ImageJ2, and the current maintainer of the Fiji distribution of ImageJ.



> > > Did you know ImageJ has a forum? http://forum.imagej.net/
[http://forum.imagej.net/uploads/default/original/1X/d2fe983e291b72beb863ed580e265423374deee9.png]<http://forum.imagej.net/>

ImageJ Forum<http://forum.imagej.net/>
forum.imagej.net
A discussion forum for ImageJ users and developers!



> > >
> > >
> > > On Thu, Feb 8, 2018 at 11:18 AM, Fabrice Senger <
> > [hidden email]>
> > > wrote:
> > >
> > > > Hi there,
> > > >
> > > > I'm probably not the only one experiencing problems with memory wich
> > > > doesn't get released. Even no single image is open, and after hiting
> > the
> > > > garbage collector.
> > > >
> > > > Is there something new about that issue.
> > > >
> > > > It seems it has been related at some point to the hyperstack opener
> of
> > > LOCI
> > > > ...
> > > >
> > > > In the meantime the only workarouns is to close FIJI and restart
> > > >
> > > > Thank you all for your help,
> > > >
> > > > Fabrice.
> > > >
> > > > --
> > > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
ImageJ Mailing List<http://imagej.nih.gov/ij/list.html>
imagej.nih.gov
home | news | docs | download | plugins | resources | list | links. ImageJ Mailing List The ImageJ mailing list is a discussion group for ImageJ users and developers.



> > > >
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
ImageJ Mailing List<http://imagej.nih.gov/ij/list.html>
imagej.nih.gov
home | news | docs | download | plugins | resources | list | links. ImageJ Mailing List The ImageJ mailing list is a discussion group for ImageJ users and developers.



> > >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
ImageJ Mailing List<http://imagej.nih.gov/ij/list.html>
imagej.nih.gov
home | news | docs | download | plugins | resources | list | links. ImageJ Mailing List The ImageJ mailing list is a discussion group for ImageJ users and developers.



> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
ImageJ Mailing List<http://imagej.nih.gov/ij/list.html>
imagej.nih.gov
home | news | docs | download | plugins | resources | list | links. ImageJ Mailing List The ImageJ mailing list is a discussion group for ImageJ users and developers.



>

--
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imagej.nih.gov
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