Out of memory issue

[Pang, Zhengyu (GE Global Research)]

Dear folks,

I recently have an issue with "Out of memory" when I batch processed
40-100 images (each has a size of  10M). My computer has  2 G memory. Do
you know what is the cause and how to fix it?

Thanks,

Zhengyu
> g Global Research Center
>
> ______________________________________________________________________
>
>           Zhengyu Pang, Ph.D.
                        Bioanalytics and Protein Science Laboratory
                        Biosciences Global Technology Organization
> One Research Circle, K1 5B37A
> Niskayuna, NY12309
> * [hidden email]
> *[phone]
>
>

[Pang, Zhengyu (GE Global Research)]

Wayne,

I checked my current setting (only 334 M was assigned to ImageJ), and I
did not close the image after I opened it. Thanks for your advice.

Zhengyu

-----Original Message-----
From: Wayne Rasband [mailto:[hidden email]]
Sent: Monday, May 05, 2008 2:43 PM
To: Pang, Zhengyu (GE, Research)
Subject: Re: Out of memory issue

> Dear folks,
>
> I recently have an issue with "Out of memory" when I batch processed
> 40-100 images (each has a size of  10M). My computer has  2 G memory.
> Do
> you know what is the cause and how to fix it?

Zhengyu,

How much memory have you assigned to ImageJ in the Edit>Options>Memory &
Threads dialog? Does you macro close each image after it has finished
processing it? You can monitor the number of open images as the macro is
running by adding a "print(nImages);" statement.

-wayne

[Pang, Zhengyu (GE Global Research)]

 Wayne and other experts,

For the current version of ImageJ at NIH site (1.40), I found that it
can automatically open ZVI file and separate them into different
windows. After I learnt the concept of the stack, I would rather to use
stack. I downloaded the Bio-Format Plugin, but it does not seem to be
necessary.

I uninstalled 1.40 ImageJ and installed my previous ImageJ (1.38) and
put Bio-Format plugin into plugin folder. Then everything seems to go
back to normal.

For the Bio-Format import window, there is quite some options to select
and I always just select "Autoscale the image". When I try to make a
macro to batch processing on ZVI files. This window becomes a little bit
annoying, because I have to click "OK" for each file. Is there anyway
for me to bypass this. I have tried to record the macro to see what I
could get. However, using the recorded macro is not working.

Thanks for your help!

Zhengyu

-----Original Message-----
From: Wayne Rasband [mailto:[hidden email]]
Sent: Tuesday, May 06, 2008 6:26 PM
To: Pang, Zhengyu (GE, Research)
Subject: Re: Duplication


On May 6, 2008, at 3:47 PM, Pang, Zhengyu (GE, Research) wrote:

> Wayne,
>
> Thanks for your help. It works.
>
> I recently downloaded a version 1.40 from NIH website, as I suspected
> that my version might have been disrupted. When I open ZVI file, it
> automatically opened it in individual window instead of a stack. How
> could I get around with that?
>
> Do I have to download BioFormat plugin?

To use it, you have to download it. Give it a try; it may work better.

-wayne

[ctrueden]

Hi Zhengyu,

First of all, I am not sure why ZVI files would work out of the box with
version 1.40... as far as I know you need the Bio-Formats plugin for ZVI
regardless of which version of ImageJ you use. I also do not understand your
rationale for switching back to 1.38 -- is there something you do not like
about 1.40?

Regarding the Bio-Formats importer, the dialog should not appear if you call
it from a macro. Try using the macro recorder and then executing the result.
If the importer dialog appears, it is a bug that we (the LOCI team) needs to
fix.

-Curtis

On Wed, May 7, 2008 at 10:41 AM, Pang, Zhengyu (GE, Research) <
[hidden email]> wrote:

>  Wayne and other experts,
>
> For the current version of ImageJ at NIH site (1.40), I found that it
> can automatically open ZVI file and separate them into different
> windows. After I learnt the concept of the stack, I would rather to use
> stack. I downloaded the Bio-Format Plugin, but it does not seem to be
> necessary.
>
> I uninstalled 1.40 ImageJ and installed my previous ImageJ (1.38) and
> put Bio-Format plugin into plugin folder. Then everything seems to go
> back to normal.
>
> For the Bio-Format import window, there is quite some options to select
> and I always just select "Autoscale the image". When I try to make a
> macro to batch processing on ZVI files. This window becomes a little bit
> annoying, because I have to click "OK" for each file. Is there anyway
> for me to bypass this. I have tried to record the macro to see what I
> could get. However, using the recorded macro is not working.
>
> Thanks for your help!
>
> Zhengyu
>
> -----Original Message-----
> From: Wayne Rasband [mailto:[hidden email]]
> Sent: Tuesday, May 06, 2008 6:26 PM
> To: Pang, Zhengyu (GE, Research)
> Subject: Re: Duplication
>
>
> On May 6, 2008, at 3:47 PM, Pang, Zhengyu (GE, Research) wrote:
>
> > Wayne,
> >
> > Thanks for your help. It works.
> >
> > I recently downloaded a version 1.40 from NIH website, as I suspected
> > that my version might have been disrupted. When I open ZVI file, it
> > automatically opened it in individual window instead of a stack. How
> > could I get around with that?
> >
> > Do I have to download BioFormat plugin?
>
> To use it, you have to download it. Give it a try; it may work better.
>
> -wayne
>

[Pang, Zhengyu (GE Global Research)]

Hi, Curtis,

I re-installed version 1.40 and found that I  can still open ZVI file in
different windows. If you suspected that ImageJ itself could not open
it, then I believe that some other software installed on my computer
might be the blame. I have quite lots of imaging softwares installed
such as AxioVision, GIMP, Matlab IPT, Cell profiler, etc. The old vesion
definitely need Bio-Format plugin to open it.

After I used Wayne's macro, I had no problem with skipping the
Bio-Format window. Thanks!

Zhengyu

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Curtis Rueden
Sent: Wednesday, May 07, 2008 12:06 PM
To: [hidden email]
Subject: Re: Different versions of ImageJ

Hi Zhengyu,

First of all, I am not sure why ZVI files would work out of the box with
version 1.40... as far as I know you need the Bio-Formats plugin for ZVI
regardless of which version of ImageJ you use. I also do not understand
your rationale for switching back to 1.38 -- is there something you do
not like about 1.40?

Regarding the Bio-Formats importer, the dialog should not appear if you
call it from a macro. Try using the macro recorder and then executing
the result.
If the importer dialog appears, it is a bug that we (the LOCI team)
needs to fix.

-Curtis

On Wed, May 7, 2008 at 10:41 AM, Pang, Zhengyu (GE, Research) <
[hidden email]> wrote:

>  Wayne and other experts,
>
> For the current version of ImageJ at NIH site (1.40), I found that it
> can automatically open ZVI file and separate them into different
> windows. After I learnt the concept of the stack, I would rather to
> use stack. I downloaded the Bio-Format Plugin, but it does not seem to

> be necessary.
>
> I uninstalled 1.40 ImageJ and installed my previous ImageJ (1.38) and
> put Bio-Format plugin into plugin folder. Then everything seems to go
> back to normal.
>
> For the Bio-Format import window, there is quite some options to
> select and I always just select "Autoscale the image". When I try to
> make a macro to batch processing on ZVI files. This window becomes a
> little bit annoying, because I have to click "OK" for each file. Is
> there anyway for me to bypass this. I have tried to record the macro
> to see what I could get. However, using the recorded macro is not

working.

>
> Thanks for your help!
>
> Zhengyu
>
> -----Original Message-----
> From: Wayne Rasband [mailto:[hidden email]]
> Sent: Tuesday, May 06, 2008 6:26 PM
> To: Pang, Zhengyu (GE, Research)
> Subject: Re: Duplication
>
>
> On May 6, 2008, at 3:47 PM, Pang, Zhengyu (GE, Research) wrote:
>
> > Wayne,
> >
> > Thanks for your help. It works.
> >
> > I recently downloaded a version 1.40 from NIH website, as I
> > suspected that my version might have been disrupted. When I open ZVI

> > file, it automatically opened it in individual window instead of a
> > stack. How could I get around with that?
> >
> > Do I have to download BioFormat plugin?
>
> To use it, you have to download it. Give it a try; it may work better.
>
> -wayne
>