Zeiss Zen 2008 w/ LSM 710 crashing issue

[Matiar Jafari]

Dear Confocal List Serv Users,

I was wondering if you guys could help me with an issue I've ran into
now TWICE.  When I shoot a 6 micron z stack with pixel settings of
.029x.029x.086(.09) with averaging of 8 lines at a speed of 8
2048x2048 16 bit file after the image is done I can see a 3D render
fine etc and i see my image after 59 pain staking minutes of waiting i
go to click save and when i click save the entire program crashes and
i get the error windows you see attached in this email and uploaded in
the link below.  Any advice and help would be GREATLY appreciated.

one of the errors is: "Not enough storage is available to process this command."

http://img38.imageshack.us/img38/8689/50043540.jpg

Thank You
--
Matiar Jafari

[Matiar Jafari]

Dear Confocal Microscopy Users,

I forgot to include the specs on the computer.  It has 3 GB of RAM 500
GB of free space.  Another thing that may have affected this is that i
was saving on a network drive.  I only did that once the second time i
tried saving to the hardrive and i got the sam error.


On Thu, May 28, 2009 at 3:34 AM, Matiar Jafari <[hidden email]> wrote:

> Dear Confocal List Serv Users,
>
> I was wondering if you guys could help me with an issue I've ran into
> now TWICE.  When I shoot a 6 micron z stack with pixel settings of
> .029x.029x.086(.09) with averaging of 8 lines at a speed of 8
> 2048x2048 16 bit file after the image is done I can see a 3D render
> fine etc and i see my image after 59 pain staking minutes of waiting i
> go to click save and when i click save the entire program crashes and
> i get the error windows you see attached in this email and uploaded in
> the link below.  Any advice and help would be GREATLY appreciated.
>
> one of the errors is: "Not enough storage is available to process this command."
>
> http://img38.imageshack.us/img38/8689/50043540.jpg
>
> Thank You
> --
> Matiar Jafari
>

--
Matiar Jafari

[Guy Cox]

By my rough calculation your stack will be ~600MB, so you would seem to have enough RAM to hold the image and a same-size buffer with plenty to spare.   So it looks like a software issue - maybe the program has allocated 1GB, which will not hold your stack twice over, so when it moves it from work-space to buffer there isn't enough room.  The 710 is a fairly new system so I guess there will be fairly frequent software upgrades, and your best bet would be to make sure Zeiss are aware of the issue.  Meanwhile, try other stack sizes till you find out the limit.  

                                       Guy



Optical Imaging Techniques in Cell Biology
by Guy Cox    CRC Press / Taylor & Francis
    http://www.guycox.com/optical.htm
______________________________________________
Associate Professor Guy Cox, MA, DPhil(Oxon)
Electron Microscope Unit, Madsen Building F09,
University of Sydney, NSW 2006
______________________________________________
Phone [phone]     Fax [phone]
Mobile [phone]
______________________________________________
     http://www.guycox.net
-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Matiar Jafari
Sent: Thursday, 28 May 2009 8:35 PM
To: [hidden email]
Subject: Zeiss Zen 2008 w/ LSM 710 crashing issue

Dear Confocal List Serv Users,

I was wondering if you guys could help me with an issue I've ran into now TWICE.  When I shoot a 6 micron z stack with pixel settings of
.029x.029x.086(.09) with averaging of 8 lines at a speed of 8
2048x2048 16 bit file after the image is done I can see a 3D render fine etc and i see my image after 59 pain staking minutes of waiting i go to click save and when i click save the entire program crashes and i get the error windows you see attached in this email and uploaded in the link below.  Any advice and help would be GREATLY appreciated.

one of the errors is: "Not enough storage is available to process this command."

http://img38.imageshack.us/img38/8689/50043540.jpg

Thank You
--
Matiar Jafari

Internal Virus Database is out-of-date.
Checked by AVG.
Version: 7.5.560 / Virus Database: 270.12.26/2116 - Release Date: 15/05/2009 6:16 AM
 

Internal Virus Database is out-of-date.
Checked by AVG.
Version: 7.5.560 / Virus Database: 270.12.26/2116 - Release Date: 15/05/2009 6:16 AM
 

[Prashanth Ravindran]

Dear Matiar,

This application appears to be written in Java, in which case this appears to be an issue related to the amount of memory that is available to the java virtual machine. I suspect that the default memory that is allocated is not sufficient to handle the images of the size that you are creating.

Also there is a known limitation when it comes to Java with 32 bit machines. i.e the JVM is unable to use more than 1.6 Gigabytes of memory even if more is available. Is the typical image size for the settings you mentioned greater (or very close to) this number ? Also does your computer have a 32 bit processor? In that case you appear to be out of luck.

If the above worst case scenario is not true, you can try to increase the amount of memory available to jvm. If as a previous poster has pointed out, the size of your stack is ~600MB, it may be possible for you to do that.

You can do this by issuing a command like the following

.\jre\bin\javaw.exe -Xmx1500m -cp <Name of Zeiss App>

You will have to figure out how the app is invoked.

--Prashanth

P.S: All of the above rests on multiple layers of assumptions i.e that its a Java app and that memory is the problem, so please take it with a grain of salt. As the previous poster said, you are probably better off just talking to the zeiss folks and letting them know that this happens. I have nothing to do with zeiss or the app

---

From: Matiar Jafari <[hidden email]>
To: [hidden email]
Sent: Thursday, May 28, 2009 4:10:59 PM
Subject: Re: Zeiss Zen 2008 w/ LSM 710 crashing issue

Dear Confocal Microscopy Users,

I forgot to include the specs on the computer.  It has 3 GB of RAM 500
GB of free space.  Another thing that may have affected this is that i
was saving on a network drive.  I only did that once the second time i
tried saving to the hardrive and i got the sam error.


On Thu, May 28, 2009 at 3:34 AM, Matiar Jafari <[hidden email]> wrote:

> Dear Confocal List Serv Users,
>
> I was wondering if you guys could help me with an issue I've ran into
> now TWICE.  When I shoot a 6 micron z stack with pixel settings of
> .029x.029x.086(.09) with averaging of 8 lines at a speed of 8
> 2048x2048 16 bit file after the image is done I can see a 3D render
> fine etc and i see my image after 59 pain staking minutes of waiting i
> go to click save and when i click save the entire program crashes and
> i get the error windows you see attached in this email and uploaded in
> the link below.  Any advice and help would be GREATLY appreciated.
>
> one of the errors is: "Not enough storage is available to process this command."
>
> http://img38.imageshack.us/img38/8689/50043540.jpg
>
> Thank You
> --
> Matiar Jafari
>

--
Matiar Jafari

[Matiar Jafari]

Dear Prashanth,

Yes the computer has a 32 bit processor.  Its a microscope in the core so probably going to have to wait and talk to the people at Zeiss.  But regarding the command you typed what does it do does it just increase the amount of ram available to the JVM? or does this not apply to me because im on the 32 bit computer.

Thank You

--

Matiar Jafari

On May 28, 2009, at 4:25 AM, Prashanth Ravindran wrote:

Dear Matiar,

This application appears to be written in Java, in which case this appears to be an issue related to the amount of memory that is available to the java virtual machine. I suspect that the default memory that is allocated is not sufficient to handle the images of the size that you are creating. 

Also there is a known limitation when it comes to Java with 32 bit machines. i.e the JVM is unable to use more than 1.6 Gigabytes of memory even if more is available. Is the typical image size for the settings you mentioned greater (or very close to) this number ? Also does your computer have a 32 bit processor? In that case you appear to be out of luck.

If the above worst case scenario is not true, you can try to increase the amount of memory available to jvm. If as a previous poster has pointed out, the size of your stack is ~600MB, it may be possible for you to do that.

You can do this by issuing a command like the following 

.\jre\bin\javaw.exe -Xmx1500m -cp <Name of Zeiss App>

You will have to figure out how the app is invoked.

--Prashanth

P.S: All of the above rests on multiple layers of assumptions i.e that its a Java app and that memory is the problem, so please take it with a grain of salt. As the previous poster said, you are probably better off just talking to the zeiss folks and letting them know that this happens. I have nothing to do with zeiss or the app

---

From: Matiar Jafari <[hidden email]>
To: [hidden email]
Sent: Thursday, May 28, 2009 4:10:59 PM
Subject: Re: Zeiss Zen 2008 w/ LSM 710 crashing issue

Dear Confocal Microscopy Users,

I forgot to include the specs on the computer.  It has 3 GB of RAM 500
GB of free space.  Another thing that may have affected this is that i
was saving on a network drive.  I only did that once the second time i
tried saving to the hardrive and i got the sam error.


On Thu, May 28, 2009 at 3:34 AM, Matiar Jafari <[hidden email]> wrote:

> Dear Confocal List Serv Users,
>
> I was wondering if you guys could help me with an issue I've ran into
> now TWICE.  When I shoot a 6 micron z stack with pixel settings of
> .029x.029x.086(.09) with averaging of 8 lines at a speed of 8
> 2048x2048 16 bit file after the image is done I can see a 3D render
> fine etc and i see my image after 59 pain staking minutes of waiting i
> go to click save and when i click save the entire program crashes and
> i get the error windows you see attached in this email and uploaded in
> the link below.  Any advice and help would be GREATLY appreciated.
>
> one of the errors is: "Not enough storage is available to process this command."
>
> http://img38.imageshack.us/img38/8689/50043540.jpg
>
> Thank You
> --
> Matiar Jafari
>

-- 
Matiar Jafari

Thank You

-----

Matiar Jafari

[Prashanth Ravindran]

Dear Matiar-

It does apply to you. you can try this if a condition is satisfied. The condition being

If you right click on the zeiss zen icon and select properties, Go to the 'shortcut' tab there should be a field called target. If the target is pointing to <some file name>.exe, then you are out of luck. There is no way of knowing exactly which file is invoked.

If not the command will be of the form that was described, and you can just change the number to something bigger.

Needless to say, try all this only if you are in a major hurry  :)

--Prashanth

---

From: Matiar Jafari <[hidden email]>
To: [hidden email]
Sent: Thursday, May 28, 2009 5:10:17 PM
Subject: Re: Zeiss Zen 2008 w/ LSM 710 crashing issue

Dear Prashanth,

Yes the computer has a 32 bit processor.  Its a microscope in the core so probably going to have to wait and talk to the people at Zeiss.  But regarding the command you typed what does it do does it just increase the amount of ram available to the JVM? or does this not apply to me because im on the 32 bit computer.

Thank You

--

Matiar Jafari

On May 28, 2009, at 4:25 AM, Prashanth Ravindran wrote:

Dear Matiar,

This application appears to be written in Java, in which case this appears to be an issue related to the amount of memory that is available to the java virtual machine. I suspect that the default memory that is allocated is not sufficient to handle the images of the size that you are creating. 

Also there is a known limitation when it comes to Java with 32 bit machines. i.e the JVM is unable to use more than 1.6 Gigabytes of memory even if more is available. Is the typical image size for the settings you mentioned greater (or very close to) this number ? Also does your computer have a 32 bit processor? In that case you appear to be out of luck.

If the above worst case scenario is not true, you can try to increase the amount of memory available to jvm. If as a previous poster has pointed out, the size of your stack is ~600MB, it may be possible for you to do that.

You can do this by issuing a command like the following 

.\jre\bin\javaw.exe -Xmx1500m -cp <Name of Zeiss App>

You will have to figure out how the app is invoked.

--Prashanth

P.S: All of the above rests on multiple layers of assumptions i.e that its a Java app and that memory is the problem, so please take it with a grain of salt. As the previous poster said, you are probably better off just talking to the zeiss folks and letting them know that this happens. I have nothing to do with zeiss or the app

---

From: Matiar Jafari <[hidden email]>
To: [hidden email]
Sent: Thursday, May 28, 2009 4:10:59 PM
Subject: Re: Zeiss Zen 2008 w/ LSM 710 crashing issue

Dear Confocal Microscopy Users,

I forgot to include the specs on the computer.  It has 3 GB of RAM 500
GB of free space.  Another thing that may have affected this is that i
was saving on a network drive.  I only did that once the second time i
tried saving to the hardrive and i got the sam error.


On Thu, May 28, 2009 at 3:34 AM, Matiar Jafari <[hidden email]> wrote:

> Dear Confocal List Serv Users,
>
> I was wondering if you guys could help me with an issue I've ran into
> now TWICE.  When I shoot a 6 micron z stack with pixel settings of
> .029x.029x.086(.09) with averaging of 8 lines at a speed of 8
> 2048x2048 16 bit file after the image is done I can see a 3D render
> fine etc and i see my image after 59 pain staking minutes of waiting i
> go to click save and when i click save the entire program crashes and
> i get the error windows you see attached in this email and uploaded in
> the link below.  Any advice and help would be GREATLY appreciated.
>
> one of the errors is: "Not enough storage is available to process this command."
>
> http://img38.imageshack.us/img38/8689/50043540.jpg
>
> Thank You
> --
> Matiar Jafari
>

-- 
Matiar Jafari

Thank You

-----

Matiar Jafari

[Emmanuel Gustin]

Hi Prashanth,

 

Although there is some similarity in syntax, from the error message this is a C# application, not java. System.Windows.Media is part of the Microsoft Windows Presentation Foundation.

 

Googling for the HRESULT error value delivers that this is an error occurring in a number of different applications, so blame Microsoft rather than Zeiss :-) There are hints that this may be related to hardware acceleration on specific  graphics drivers, not necessarily a memory issue. (http://social.msdn.microsoft.com/Forums/en-US/wpf/thread/b2aa4601-3f66-4dd6-8a20-0744265c5f1c)  Error handlers sometimes (well, often) produce misleading interpretations of the problem. In that case, you might try switching off hardware acceleration (I know, horrible thing to do on an imaging station.)

 

Best Regards,

 

Emmanuel

 

--
 Emmanuel Gustin,    Tel. [phone],    e-mail: [hidden email]

 

From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Prashanth Ravindran
Sent: Thursday, May 28, 2009 13:25
To: [hidden email]
Subject: Re: Zeiss Zen 2008 w/ LSM 710 crashing issue

 

Dear Matiar,

This application appears to be written in Java, in which case this appears to be an issue related to the amount of memory that is available to the java virtual machine. I suspect that the default memory that is allocated is not sufficient to handle the images of the size that you are creating.

Also there is a known limitation when it comes to Java with 32 bit machines. i.e the JVM is unable to use more than 1.6 Gigabytes of memory even if more is available. Is the typical image size for the settings you mentioned greater (or very close to) this number ? Also does your computer have a 32 bit processor? In that case you appear to be out of luck.

If the above worst case scenario is not true, you can try to increase the amount of memory available to jvm. If as a previous poster has pointed out, the size of your stack is ~600MB, it may be possible for you to do that.

You can do this by issuing a command like the following

.\jre\bin\javaw.exe -Xmx1500m -cp <Name of Zeiss App>

You will have to figure out how the app is invoked.

--Prashanth

P.S: All of the above rests on multiple layers of assumptions i.e that its a Java app and that memory is the problem, so please take it with a grain of salt. As the previous poster said, you are probably better off just talking to the zeiss folks and letting them know that this happens. I have nothing to do with zeiss or the app

 

---

From: Matiar Jafari <[hidden email]>
To: [hidden email]
Sent: Thursday, May 28, 2009 4:10:59 PM
Subject: Re: Zeiss Zen 2008 w/ LSM 710 crashing issue

Dear Confocal Microscopy Users,

I forgot to include the specs on the computer.  It has 3 GB of RAM 500
GB of free space.  Another thing that may have affected this is that i
was saving on a network drive.  I only did that once the second time i
tried saving to the hardrive and i got the sam error.


On Thu, May 28, 2009 at 3:34 AM, Matiar Jafari <[hidden email]> wrote:
> Dear Confocal List Serv Users,
>
> I was wondering if you guys could help me with an issue I've ran into
> now TWICE.  When I shoot a 6 micron z stack with pixel settings of
> .029x.029x.086(.09) with averaging of 8 lines at a speed of 8
> 2048x2048 16 bit file after the image is done I can see a 3D render
> fine etc and i see my image after 59 pain staking minutes of waiting i
> go to click save and when i click save the entire program crashes and
> i get the error windows you see attached in this email and uploaded in
> the link below.  Any advice and help would be GREATLY appreciated.
>
> one of the errors is: "Not enough storage is available to process this command."
>
> http://img38.imageshack.us/img38/8689/50043540.jpg
>
> Thank You
> --
> Matiar Jafari
>



--
Matiar Jafari

[Matiar Jafari]

Dear Emmanuel,

Thanks ill ask to see if i can try that. Ill keep you posted

Thank You

--

Matiar Jafari

On May 28, 2009, at 5:29 AM, Gustin, Emmanuel [TIBBE] wrote:

Hi Prashanth,

 

Although there is some similarity in syntax, from the error message this is a C# application, not java. System.Windows.Media is part of the Microsoft Windows Presentation Foundation.

 

Googling for the HRESULT error value delivers that this is an error occurring in a number of different applications, so blame Microsoft rather than Zeiss :-) There are hints that this may be related to hardware acceleration on specific  graphics drivers, not necessarily a memory issue. (http://social.msdn.microsoft.com/Forums/en-US/wpf/thread/b2aa4601-3f66-4dd6-8a20-0744265c5f1c)  Error handlers sometimes (well, often) produce misleading interpretations of the problem. In that case, you might try switching off hardware acceleration (I know, horrible thing to do on an imaging station.)

 

Best Regards,

 

Emmanuel

 

--
 Emmanuel Gustin,    Tel. [phone],    e-mail: [hidden email]

 

From: Confocal Microscopy List [[hidden email]] On Behalf Of Prashanth Ravindran
Sent: Thursday, May 28, 2009 13:25
To: [hidden email]
Subject: Re: Zeiss Zen 2008 w/ LSM 710 crashing issue

 

Dear Matiar,

This application appears to be written in Java, in which case this appears to be an issue related to the amount of memory that is available to the java virtual machine. I suspect that the default memory that is allocated is not sufficient to handle the images of the size that you are creating. 

Also there is a known limitation when it comes to Java with 32 bit machines. i.e the JVM is unable to use more than 1.6 Gigabytes of memory even if more is available. Is the typical image size for the settings you mentioned greater (or very close to) this number ? Also does your computer have a 32 bit processor? In that case you appear to be out of luck.

If the above worst case scenario is not true, you can try to increase the amount of memory available to jvm. If as a previous poster has pointed out, the size of your stack is ~600MB, it may be possible for you to do that.

You can do this by issuing a command like the following

.\jre\bin\javaw.exe -Xmx1500m -cp <Name of Zeiss App>

You will have to figure out how the app is invoked.

--Prashanth

P.S: All of the above rests on multiple layers of assumptions i.e that its a Java app and that memory is the problem, so please take it with a grain of salt. As the previous poster said, you are probably better off just talking to the zeiss folks and letting them know that this happens. I have nothing to do with zeiss or the app

 

---

From: Matiar Jafari <[hidden email]>
To: [hidden email]
Sent: Thursday, May 28, 2009 4:10:59 PM
Subject: Re: Zeiss Zen 2008 w/ LSM 710 crashing issue

Dear Confocal Microscopy Users,

I forgot to include the specs on the computer.  It has 3 GB of RAM 500
GB of free space.  Another thing that may have affected this is that i
was saving on a network drive.  I only did that once the second time i
tried saving to the hardrive and i got the sam error.


On Thu, May 28, 2009 at 3:34 AM, Matiar Jafari <[hidden email]> wrote:

> Dear Confocal List Serv Users,
>
> I was wondering if you guys could help me with an issue I've ran into
> now TWICE.  When I shoot a 6 micron z stack with pixel settings of
> .029x.029x.086(.09) with averaging of 8 lines at a speed of 8
> 2048x2048 16 bit file after the image is done I can see a 3D render
> fine etc and i see my image after 59 pain staking minutes of waiting i
> go to click save and when i click save the entire program crashes and
> i get the error windows you see attached in this email and uploaded in
> the link below.  Any advice and help would be GREATLY appreciated.
>
> one of the errors is: "Not enough storage is available to process this command."
>
> http://img38.imageshack.us/img38/8689/50043540.jpg
>
> Thank You
> --
> Matiar Jafari
>

-- 
Matiar Jafari

Thank You

-----

Matiar Jafari

[Prashanth Ravindran]

 

>Although there is some similarity in syntax, from the error message this is a C# application, not java. >System.Windows.Media is part of the Microsoft Windows Presentation Foundation.

Oops..My bad.. good luck Matiar

--Prashanth

---

From: Matiar Jafari <[hidden email]>
To: [hidden email]
Sent: Thursday, May 28, 2009 6:03:44 PM
Subject: Re: Zeiss Zen 2008 w/ LSM 710 crashing issue

Dear Emmanuel,

Thanks ill ask to see if i can try that. Ill keep you posted

Thank You

--

Matiar Jafari

On May 28, 2009, at 5:29 AM, Gustin, Emmanuel [TIBBE] wrote:

Hi Prashanth,

 

Although there is some similarity in syntax, from the error message this is a C# application, not java. System.Windows.Media is part of the Microsoft Windows Presentation Foundation.

 

Googling for the HRESULT error value delivers that this is an error occurring in a number of different applications, so blame Microsoft rather than Zeiss :-) There are hints that this may be related to hardware acceleration on specific  graphics drivers, not necessarily a memory issue. (http://social.msdn.microsoft.com/Forums/en-US/wpf/thread/b2aa4601-3f66-4dd6-8a20-0744265c5f1c)  Error handlers sometimes (well, often) produce misleading interpretations of the problem. In that case, you might try switching off hardware acceleration (I know, horrible thing to do on an imaging station.)

 

Best Regards,

 

Emmanuel

 

--
 Emmanuel Gustin,    Tel. [phone],    e-mail: [hidden email]

 

From: Confocal Microscopy List [[hidden email]] On Behalf Of Prashanth Ravindran
Sent: Thursday, May 28, 2009 13:25
To: [hidden email]
Subject: Re: Zeiss Zen 2008 w/ LSM 710 crashing issue

 

Dear Matiar,

This application appears to be written in Java, in which case this appears to be an issue related to the amount of memory that is available to the java virtual machine. I suspect that the default memory that is allocated is not sufficient to handle the images of the size that you are creating. 

Also there is a known limitation when it comes to Java with 32 bit machines. i.e the JVM is unable to use more than 1.6 Gigabytes of memory even if more is available. Is the typical image size for the settings you mentioned greater (or very close to) this number ? Also does your computer have a 32 bit processor? In that case you appear to be out of luck.

If the above worst case scenario is not true, you can try to increase the amount of memory available to jvm. If as a previous poster has pointed out, the size of your stack is ~600MB, it may be possible for you to do that.

You can do this by issuing a command like the following

.\jre\bin\javaw.exe -Xmx1500m -cp <Name of Zeiss App>

You will have to figure out how the app is invoked.

--Prashanth

P.S: All of the above rests on multiple layers of assumptions i.e that its a Java app and that memory is the problem, so please take it with a grain of salt. As the previous poster said, you are probably better off just talking to the zeiss folks and letting them know that this happens. I have nothing to do with zeiss or the app

 

---

From: Matiar Jafari <[hidden email]>
To: [hidden email]
Sent: Thursday, May 28, 2009 4:10:59 PM
Subject: Re: Zeiss Zen 2008 w/ LSM 710 crashing issue

Dear Confocal Microscopy Users,

I forgot to include the specs on the computer.  It has 3 GB of RAM 500
GB of free space.  Another thing that may have affected this is that i
was saving on a network drive.  I only did that once the second time i
tried saving to the hardrive and i got the sam error.


On Thu, May 28, 2009 at 3:34 AM, Matiar Jafari <[hidden email]> wrote:

> Dear Confocal List Serv Users,
>
> I was wondering if you guys could help me with an issue I've ran into
> now TWICE.  When I shoot a 6 micron z stack with pixel settings of
> .029x.029x.086(.09) with averaging of 8 lines at a speed of 8
> 2048x2048 16 bit file after the image is done I can see a 3D render
> fine etc and i see my image after 59 pain staking minutes of waiting i
> go to click save and when i click save the entire program crashes and
> i get the error windows you see attached in this email and uploaded in
> the link below.  Any advice and help would be GREATLY appreciated.
>
> one of the errors is: "Not enough storage is available to process this command."
>
> http://img38.imageshack.us/img38/8689/50043540.jpg
>
> Thank You
> --
> Matiar Jafari
>

-- 
Matiar Jafari

Thank You

-----

Matiar Jafari

[Michael Weber-4]

Dear Matiar,

every 710 is still under warranty, so did you talk to Zeiss about this
issue? Even if it, in case of a software issue, will take some time to
fix, it's still the best way. Only with the user feedback the company can
improve the product.

Now as a suggestion, there should be an option in ZEN which allows you to
temporally store the acquired data on the hard disc, and not in the RAM.
This frees up main memory and might allow you to acquire your stacks
without problems. Ask your local Zeiss application specialist about this
option. It's useful for big datasets like stacks and/or time-series.
However, too much data should not cause the whole program to crash, it
should give you a useful hint. This leads back to my first paragraph :).

Michael

> Dear Confocal List Serv Users,
>
> I was wondering if you guys could help me with an issue I've ran into
> now TWICE.  When I shoot a 6 micron z stack with pixel settings of
> .029x.029x.086(.09) with averaging of 8 lines at a speed of 8
> 2048x2048 16 bit file after the image is done I can see a 3D render
> fine etc and i see my image after 59 pain staking minutes of waiting i
> go to click save and when i click save the entire program crashes and
> i get the error windows you see attached in this email and uploaded in
> the link below.  Any advice and help would be GREATLY appreciated.
>
> one of the errors is: "Not enough storage is available to process this
> command."
>
> http://img38.imageshack.us/img38/8689/50043540.jpg
>
> Thank You
> --
> Matiar Jafari

[Steve Baxter-2]

Hi,

My guess is that this is to do with the availability of contiguous  
address space rather than RAM. A 32-bit Windows computer makes 2 GB of  
address space available to applications, this can be increased to 3 GB  
with a switch in the boot.ini file. It doesn't matter how much RAM you  
have (or don't have) in your computer, these are hard per-process  
limits that date from when 2 GB of storage was an unimaginably large  
amount that nobody would ever fill.

Unfortunately, the story gets even worse. The 2 (or 3) GB of address  
space is not empty - Windows may load libraries at various points in  
that address space, fragmenting it into smaller contiguous blocks. If  
you perform operations that allocate and free memory, this may cause  
further fragmentation. The upshot of this is that your process might  
have 1.9 GB of free address space, but no blocks big enough to work  
with your 600 MB dataset.

There are some strategies that you might try to get around this - I  
would definitely check with Zeiss first though as they may not be  
compatible with Zen!

* Increase the address space available to applications by using the /
3GB switch and by making sure the page file is big enough. There are  
some instructions on our website that describe how to do this - they  
apply to Volocity but should apply equally to Zen:

http://www.improvision.com/support/tech_notes/detail.php?id=356

* Restart the application just before starting the acquisition and  
save immediately afterwards. This helps to ensure that address space  
fragmentation is minimised.

Please note - I *really* would talk to Zeiss before changing the /3GB  
switch. Increasing the address space for applications decreases the  
space available for drivers. I would make sure that there will be no  
driver issues on your system as a result of making this change and  
that they have tested against this configuration.

In the end, the best solution for working with large datasets is a 64-
bit application running on a 64-bit operating system such as Windows  
XP x64 or Vista x64. With 64-bit systems the address space available  
to applications is generally limited only by available disk space and  
this problem will go away. The challenge with 64-bit is that the OS,  
application and all the drivers have to be 64-bit for everything to  
work!

There's some more information on 64-bit here (the second link is  
commercial interest!):

http://www.microsoft.com/windows/windows-vista/compare-editions/64-bit.aspx
http://www.improvision.com/support/simon_vipoir/tips/detail.php?id=57

Cheers,

Steve

On 28 May 2009, at 12:12, Guy Cox wrote:

> By my rough calculation your stack will be ~600MB, so you would seem  
> to have enough RAM to hold the image and a same-size buffer with  
> plenty to spare.   So it looks like a software issue - maybe the  
> program has allocated 1GB, which will not hold your stack twice  
> over, so when it moves it from work-space to buffer there isn't  
> enough room.  The 710 is a fairly new system so I guess there will  
> be fairly frequent software upgrades, and your best bet would be to  
> make sure Zeiss are aware of the issue.  Meanwhile, try other stack  
> sizes till you find out the limit.
>
>                                       Guy
>
>
>
> Optical Imaging Techniques in Cell Biology
> by Guy Cox    CRC Press / Taylor & Francis
>    http://www.guycox.com/optical.htm
> ______________________________________________
> Associate Professor Guy Cox, MA, DPhil(Oxon)
> Electron Microscope Unit, Madsen Building F09,
> University of Sydney, NSW 2006
> ______________________________________________
> Phone [phone]     Fax [phone]
> Mobile [phone]
> ______________________________________________
>     http://www.guycox.net
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]
> ] On Behalf Of Matiar Jafari
> Sent: Thursday, 28 May 2009 8:35 PM
> To: [hidden email]
> Subject: Zeiss Zen 2008 w/ LSM 710 crashing issue
>
> Dear Confocal List Serv Users,
>
> I was wondering if you guys could help me with an issue I've ran  
> into now TWICE.  When I shoot a 6 micron z stack with pixel settings  
> of
> .029x.029x.086(.09) with averaging of 8 lines at a speed of 8
> 2048x2048 16 bit file after the image is done I can see a 3D render  
> fine etc and i see my image after 59 pain staking minutes of waiting  
> i go to click save and when i click save the entire program crashes  
> and i get the error windows you see attached in this email and  
> uploaded in the link below.  Any advice and help would be GREATLY  
> appreciated.
>
> one of the errors is: "Not enough storage is available to process  
> this command."
>
> http://img38.imageshack.us/img38/8689/50043540.jpg
>
> Thank You
> --
> Matiar Jafari
>
> Internal Virus Database is out-of-date.
> Checked by AVG.
> Version: 7.5.560 / Virus Database: 270.12.26/2116 - Release Date:  
> 15/05/2009 6:16 AM
>
>
> Internal Virus Database is out-of-date.
> Checked by AVG.
> Version: 7.5.560 / Virus Database: 270.12.26/2116 - Release Date:  
> 15/05/2009 6:16 AM
>

Steve Baxter
R&D CoE Leader
Improvision, a PerkinElmer Company
[hidden email]
[phone]

Image Processing and Vision Company Limited (trading as Improvision)  
is a company registered in England and Wales with company number  
2505778.  VAT number GB536188722.

[Mark Cannell]

You should look up Nyquist sampling in Pawley's book and set your pixel
spacing to more sensible numbers. That way your stack will be MUCH
smaller and you won't run out of memory.

This should help, but there does seem to be a memeory leak problem
somwhere... Vista is pretty awful too.


Mark Cannell

Matiar Jafari wrote:

> Dear Confocal List Serv Users,
>
> I was wondering if you guys could help me with an issue I've ran into
> now TWICE.  When I shoot a 6 micron z stack with pixel settings of
> .029x.029x.086(.09) with averaging of 8 lines at a speed of 8
> 2048x2048 16 bit file after the image is done I can see a 3D render
> fine etc and i see my image after 59 pain staking minutes of waiting i
> go to click save and when i click save the entire program crashes and
> i get the error windows you see attached in this email and uploaded in
> the link below.  Any advice and help would be GREATLY appreciated.
>
> one of the errors is: "Not enough storage is available to process this command."
>
> http://img38.imageshack.us/img38/8689/50043540.jpg
>
> Thank You
> --
> Matiar Jafari
>  

[Jacqueline Ross]

Hi Matiar,

Have you installed the ZEN service pack(s)? We also had a lot of
problems with memory, which were improved quite a lot after we loaded
the service pack. You can see them here:
http://www.zeiss.com/c12567be0045acf1/Contents-Frame/b955891346fee6f8c12
56a87004abdf9 Check first with your Zeiss support person before you load
them however.

I recommend that you are very careful with regard to loading/upgrading
drivers, etc. on your computer yourself if you are under warranty or
service contract. We have been advised not to do anything on our
computer without checking with the Zeiss engineer. This includes any
updates of Vista, etc.

Kind regards,

Jacqui

Jacqueline Ross

Biomedical Imaging Microscopist
Biomedical Imaging Research Unit
School of Medical Sciences
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland, NEW ZEALAND

Tel: [phone] Ext 87438
Fax: [phone]

http://www.fmhs.auckland.ac.nz/sms/biru/


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]]
On Behalf Of Matiar Jafari
Sent: Thursday, 28 May 2009 10:35 p.m.
To: [hidden email]
Subject: Zeiss Zen 2008 w/ LSM 710 crashing issue

Dear Confocal List Serv Users,

I was wondering if you guys could help me with an issue I've ran into
now TWICE.  When I shoot a 6 micron z stack with pixel settings of
.029x.029x.086(.09) with averaging of 8 lines at a speed of 8
2048x2048 16 bit file after the image is done I can see a 3D render
fine etc and i see my image after 59 pain staking minutes of waiting i
go to click save and when i click save the entire program crashes and
i get the error windows you see attached in this email and uploaded in
the link below.  Any advice and help would be GREATLY appreciated.

one of the errors is: "Not enough storage is available to process this
command."

http://img38.imageshack.us/img38/8689/50043540.jpg

Thank You
--
Matiar Jafari

[Williams, Geoffrey]

Have you tried just collecting in 12 bit?  File size is the same but
processing 4096 levels vs 65,000 is not to be overlooked.  Sure the
hardware is 16bit native, but, do you really have 65,000+ discrete
photon intensities in your 2kx2k image?  Probably not.  I'm sure it can
be argued that you don't even see 12 bits of intensity variation.

Also, 8 lines at speed of 8?  Why not go with 2 or 4 line average and a
speed of 6?  It is a routine demonstration that I do when training new
users on the 710 (ZEN 2008) or the 510Meta here.  *Generally* slowing
the rate down and cutting the line average down gets you the same or
better quality image.  As a rule I never average more than 4 lines.

So try collecting a 12 bit stack under the same conditions, you may find
it works.  

Geoff Williams
Leduc Bioimaging Facility Manager
Brown University
 
http://www.brown.edu/Facilities/Leduc_Bioimaging_Facility/

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]]
On Behalf Of Matiar Jafari
Sent: Thursday, May 28, 2009 6:35 AM
To: [hidden email]
Subject: Zeiss Zen 2008 w/ LSM 710 crashing issue

Dear Confocal List Serv Users,

I was wondering if you guys could help me with an issue I've ran into
now TWICE.  When I shoot a 6 micron z stack with pixel settings of
.029x.029x.086(.09) with averaging of 8 lines at a speed of 8
2048x2048 16 bit file after the image is done I can see a 3D render
fine etc and i see my image after 59 pain staking minutes of waiting i
go to click save and when i click save the entire program crashes and
i get the error windows you see attached in this email and uploaded in
the link below.  Any advice and help would be GREATLY appreciated.

one of the errors is: "Not enough storage is available to process this
command."

http://img38.imageshack.us/img38/8689/50043540.jpg

Thank You
--
Matiar Jafari