ZEN 2012 crashing in a Windows7 computer with 8GB of RAM

[Zervantonakis, Ioannis]

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Hello,

Using our LSM700 and the Zen Black 2012 software we are running a long-term timelapse, multi-point, multi-titles, multi-Z using Zen Black 2012. The projected file-size for this experiment was 26gb. The computer is old, it is from 2012 and has 8GB of ram.

Windows 7 give us "Low system memory error" and Microsoft.NET framework after acquiring 4 time-points and saving 8gb of data (we use auto-save).

Has anyone else experienced this issue?  We think it may be due to the fact that only 8GB of virtual memory was allocated in Windows.

Has anyone upgraded the original computer that came with LSM7 to a newer computer with Windows 10 and multi-core ? We are waiting to get a quote for Zeiss for upgrading the computer and it would be great to hear if anyone has experience with this.

Thank you!
Yannis


______________________

Ioannis K. Zervantonakis

Assistant Professor

Dept. of Bioengineering

U. Pittsburgh Swanson School of Engineering

UPMC Hillman Cancer Center

(e) [hidden email]<mailto:[hidden email]>

(w) www.zervalab.com<http://www.zervalab.com/>

(p) 4126484442

[Arcroyal Systems]

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Loannis,

            We offer computer upgrades to Window 10 64 bit for all Zeiss systems, from the LSM 510 on forward including LSM 700,710,780,

Thank you,

www.Arcroyal.com<http://www.Arcroyal.com>

Arcroyal Systems







From: Confocal Microscopy List <[hidden email]>
Date: Saturday, December 12, 2020 at 11:01 AM
To: [hidden email] <[hidden email]>
Subject: ZEN 2012 crashing in a Windows7 computer with 8GB of RAM
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Hello,

Using our LSM700 and the Zen Black 2012 software we are running a long-term timelapse, multi-point, multi-titles, multi-Z using Zen Black 2012. The projected file-size for this experiment was 26gb. The computer is old, it is from 2012 and has 8GB of ram.

Windows 7 give us "Low system memory error" and Microsoft.NET framework after acquiring 4 time-points and saving 8gb of data (we use auto-save).

Has anyone else experienced this issue?  We think it may be due to the fact that only 8GB of virtual memory was allocated in Windows.

Has anyone upgraded the original computer that came with LSM7 to a newer computer with Windows 10 and multi-core ? We are waiting to get a quote for Zeiss for upgrading the computer and it would be great to hear if anyone has experience with this.

Thank you!
Yannis


______________________

Ioannis K. Zervantonakis

Assistant Professor

Dept. of Bioengineering

U. Pittsburgh Swanson School of Engineering

UPMC Hillman Cancer Center

(e) [hidden email]<mailto:[hidden email]>

(w) www.zervalab.com<http://www.zervalab.com/>

(p) 4126484442

[Arvydas Matiukas]

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Hi Ioannis,

We have been experiencing low memory warning and even freezing of ZEN 2012 software on 780 system with 16GB RAM computer. This may happen even acquiring tiled z-stack image of 1GB. I noticed that restarting Windows 7 and/or closing all extra image windows in Zen (i.e. freeing as much memory as possible) often helps to avoid the problem.

As a cheap alternative I would try to upgrade RAM to the max supported (it may be 16-32GB) and upgrade/clone your hard drive to a fast SSD drive. Your IMT would be able to make the upgrade and also increase virtual Windows memory. Modern SSDs are fast enough to save images during acquisition.

Best,
Arvydas



Arvydas Matiukas, Ph.D.

Director of  Neuroscience  Microscopy Core

Manager of NRB Shared Research Equipment

SUNY Upstate Medical University
Neuroscience & Physiology Dept


________________________________
From: Confocal Microscopy List <[hidden email]> on behalf of Arcroyal Systems <[hidden email]>
Sent: Saturday, December 12, 2020 1:35 PM
To: [hidden email] <[hidden email]>
Subject: [EXTERNAL] Re: ZEN 2012 crashing in a Windows7 computer with 8GB of RAM

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Loannis,

            We offer computer upgrades to Window 10 64 bit for all Zeiss systems, from the LSM 510 on forward including LSM 700,710,780,

Thank you,

https://urldefense.com/v3/__http://www.Arcroyal.com__;!!GobTDDpD7A!d1zzY2tRiIq10BBUOhBxEsbyDNKnvtIN227Ie5yafM6xoudHbzEYNoKJQQZNQn6EtQ$ <https://urldefense.com/v3/__http://www.Arcroyal.com__;!!GobTDDpD7A!d1zzY2tRiIq10BBUOhBxEsbyDNKnvtIN227Ie5yafM6xoudHbzEYNoKJQQZNQn6EtQ$ >

Arcroyal Systems







From: Confocal Microscopy List <[hidden email]>
Date: Saturday, December 12, 2020 at 11:01 AM
To: [hidden email] <[hidden email]>
Subject: ZEN 2012 crashing in a Windows7 computer with 8GB of RAM
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Hello,

Using our LSM700 and the Zen Black 2012 software we are running a long-term timelapse, multi-point, multi-titles, multi-Z using Zen Black 2012. The projected file-size for this experiment was 26gb. The computer is old, it is from 2012 and has 8GB of ram.

Windows 7 give us "Low system memory error" and Microsoft.NET framework after acquiring 4 time-points and saving 8gb of data (we use auto-save).

Has anyone else experienced this issue?  We think it may be due to the fact that only 8GB of virtual memory was allocated in Windows.

Has anyone upgraded the original computer that came with LSM7 to a newer computer with Windows 10 and multi-core ? We are waiting to get a quote for Zeiss for upgrading the computer and it would be great to hear if anyone has experience with this.

Thank you!
Yannis


______________________

Ioannis K. Zervantonakis

Assistant Professor

Dept. of Bioengineering

U. Pittsburgh Swanson School of Engineering

UPMC Hillman Cancer Center

(e) [hidden email]<mailto:[hidden email]>

(w) https://urldefense.com/v3/__http://www.zervalab.com__;!!GobTDDpD7A!d1zzY2tRiIq10BBUOhBxEsbyDNKnvtIN227Ie5yafM6xoudHbzEYNoKJQQbsWyPLnQ$ <https://urldefense.com/v3/__http://www.zervalab.com/__;!!GobTDDpD7A!d1zzY2tRiIq10BBUOhBxEsbyDNKnvtIN227Ie5yafM6xoudHbzEYNoKJQQYEVXrA9g$ >

(p) 4126484442

[Zdenek Svindrych-2]

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I've yet to see a microscopy software that's happier (i.e. more stable,
more responsive) under windows 10 than 7.
So far, with NIS, ZEN, LAS X, I choose Win 7 if I can ...
zdenek

On Sat, Dec 12, 2020 at 1:36 PM Arcroyal Systems <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Loannis,
>
>             We offer computer upgrades to Window 10 64 bit for all Zeiss
> systems, from the LSM 510 on forward including LSM 700,710,780,
>
> Thank you,
>
> www.Arcroyal.com<http://www.Arcroyal.com>
>
> Arcroyal Systems
>
>
>
>
>
>
>
> From: Confocal Microscopy List <[hidden email]>
> Date: Saturday, December 12, 2020 at 11:01 AM
> To: [hidden email] <[hidden email]>
> Subject: ZEN 2012 crashing in a Windows7 computer with 8GB of RAM
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hello,
>
> Using our LSM700 and the Zen Black 2012 software we are running a
> long-term timelapse, multi-point, multi-titles, multi-Z using Zen Black
> 2012. The projected file-size for this experiment was 26gb. The computer is
> old, it is from 2012 and has 8GB of ram.
>
> Windows 7 give us "Low system memory error" and Microsoft.NET framework
> after acquiring 4 time-points and saving 8gb of data (we use auto-save).
>
> Has anyone else experienced this issue?  We think it may be due to the
> fact that only 8GB of virtual memory was allocated in Windows.
>
> Has anyone upgraded the original computer that came with LSM7 to a newer
> computer with Windows 10 and multi-core ? We are waiting to get a quote for
> Zeiss for upgrading the computer and it would be great to hear if anyone
> has experience with this.
>
> Thank you!
> Yannis
>
>
> ______________________
>
> Ioannis K. Zervantonakis
>
> Assistant Professor
>
> Dept. of Bioengineering
>
> U. Pittsburgh Swanson School of Engineering
>
> UPMC Hillman Cancer Center
>
> (e) [hidden email]<mailto:[hidden email]>
>
> (w) www.zervalab.com<http://www.zervalab.com/>
>
> (p) 4126484442
>

--
--
Zdenek Svindrych, Ph.D.
Research Scientist - Microscopy Imaging Specialist
Department of Biochemistry and Cell Biology
Geisel School of Medicine at Dartmouth

[Zdenek Svindrych-2]

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Hi Yannis,

I think we don't go below 64 GB RAM with ZEN; well, I'll check the oldest
workstation (LSM 510) for specs...

Win 10 ain't not gonna help you with old software, I'd stick with Win 7
(well, you know, that's me...).

If you want to upgrade, I'd suggest to clone the main HDD to a new disk
(SSD preferably), and plug this to a not-so-old workstation (HP Z 800 might
be a good starting point) and see if it boots to Windows. If it does,
you're 99% there! You just need to move all the pci(e) card(s) and
dongle(s) (if your ZEN copy is not protected by a dongle, you need to clone
a particular network interface with the right MAC address), and you should
be good to go!

Fingers crossed!

Note, server workstations often use serial RAM (called ECC), which is very
different (and incompatible with) traditional parallel (non-ECC) RAM!

2nd note, if you're able to upgrade to a more modern PC, like HP Z 860, you
could benefit from NVMe storage, which is much faster than SATA SSDs. Ask
your local IT nerd!

Best, zdenek


On Sat, Dec 12, 2020 at 12:01 PM Zervantonakis, Ioannis <[hidden email]>
wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hello,
>
> Using our LSM700 and the Zen Black 2012 software we are running a
> long-term timelapse, multi-point, multi-titles, multi-Z using Zen Black
> 2012. The projected file-size for this experiment was 26gb. The computer is
> old, it is from 2012 and has 8GB of ram.
>
> Windows 7 give us "Low system memory error" and Microsoft.NET framework
> after acquiring 4 time-points and saving 8gb of data (we use auto-save).
>
> Has anyone else experienced this issue?  We think it may be due to the
> fact that only 8GB of virtual memory was allocated in Windows.
>
> Has anyone upgraded the original computer that came with LSM7 to a newer
> computer with Windows 10 and multi-core ? We are waiting to get a quote for
> Zeiss for upgrading the computer and it would be great to hear if anyone
> has experience with this.
>
> Thank you!
> Yannis
>
>
> ______________________
>
> Ioannis K. Zervantonakis
>
> Assistant Professor
>
> Dept. of Bioengineering
>
> U. Pittsburgh Swanson School of Engineering
>
> UPMC Hillman Cancer Center
>
> (e) [hidden email]<mailto:[hidden email]>
>
> (w) www.zervalab.com<http://www.zervalab.com/>
>
> (p) 4126484442
>

--
--
Zdenek Svindrych, Ph.D.
Research Scientist - Microscopy Imaging Specialist
Department of Biochemistry and Cell Biology
Geisel School of Medicine at Dartmouth

[Jason M. Kirk]

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Hi Yannis,

There are two things that we do to reduce memory usage for such long time lapse experiments.  The first is in Auto-save try to use the bare minimum of separate files for the acquisition.  I try to limit my separate files to one - typically position.  This will reduce the volume of saving functions executed during your experiment.  

The second is to make sure that in Maintain > System Options you have your temporary files directory pointed to a drive that does not contain the OS.

Good luck!

-Jason

-------------------------------------------------------------------
Jason M. Kirk
Technical Director, Optical Imaging & Vital Microscopy Core (OiVM)
Baylor College of Medicine
Ph: 713.798.6486
Email: [hidden email]
http://www.bcm.edu/oivm

[Armstrong, Brian]

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Hi Jason, can you clarify/provide explanation for "limit separate files to one"?

Thank you!

Brian Armstrong PhD
Associate Research Professor
Developmental and Stem Cell Biology
Diabetes and Metabolic Diseases
Director, Light Microscopy Core
Beckman Research Institute, City of Hope


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Jason M. Kirk
Sent: Monday, December 14, 2020 6:37 AM
To: [hidden email]
Subject: Re: ZEN 2012 crashing in a Windows7 computer with 8GB of RAM

[Attention: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.]

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Hi Yannis,

There are two things that we do to reduce memory usage for such long time lapse experiments.  The first is in Auto-save try to use the bare minimum of separate files for the acquisition.  I try to limit my separate files to one - typically position.  This will reduce the volume of saving functions executed during your experiment.  

The second is to make sure that in Maintain > System Options you have your temporary files directory pointed to a drive that does not contain the OS.

Good luck!

-Jason

-------------------------------------------------------------------
Jason M. Kirk
Technical Director, Optical Imaging & Vital Microscopy Core (OiVM) Baylor College of Medicine
Ph: 713.798.6486
Email: [hidden email]
https://urldefense.com/v3/__http://www.bcm.edu/oivm__;!!Fou38LsQmgU!8xLpzGPyvfAYG0Oaelytw0Va7xY8e963FvPR5tJLA3e6mxbSJILOOR63XePYduw$ 

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[Jason M. Kirk]

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Hi Brian,

Using Yannis' example - an experiment with four possible file separations - tile, z, position, time - I would only select position to be saved as separate files.  The more separate files that ZEN is concurrently writing to will increase memory usage.

-Jason

-------------------------------------------------------------------
Jason M. Kirk
Technical Director, Optical Imaging & Vital Microscopy Core (OiVM)
Baylor College of Medicine
Ph: 713.798.6486
Email: [hidden email]
http://www.bcm.edu/oivm

-----Original Message-----
From: Confocal Microscopy List <[hidden email]> On Behalf Of Brian Armstrong
Sent: Monday, December 14, 2020 10:25 AM
To: [hidden email]
Subject: Re: ZEN 2012 crashing in a Windows7 computer with 8GB of RAM

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Hi Jason, can you clarify/provide explanation for "limit separate files to one"?

Thank you!

Brian Armstrong PhD
Associate Research Professor
Developmental and Stem Cell Biology
Diabetes and Metabolic Diseases
Director, Light Microscopy Core
Beckman Research Institute, City of Hope


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Jason M. Kirk
Sent: Monday, December 14, 2020 6:37 AM
To: [hidden email]
Subject: Re: ZEN 2012 crashing in a Windows7 computer with 8GB of RAM

[Attention: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.]

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Post images on https://urldefense.com/v3/__http://www.imgur.com__;!!Fou38LsQmgU!8xLpzGPyvfAYG0Oaelytw0Va7xY8e963FvPR5tJLA3e6mxbSJILOOR63iSf3eUo$  and include the link in your posting.
*****

Hi Yannis,

There are two things that we do to reduce memory usage for such long time lapse experiments.  The first is in Auto-save try to use the bare minimum of separate files for the acquisition.  I try to limit my separate files to one - typically position.  This will reduce the volume of saving functions executed during your experiment.  

The second is to make sure that in Maintain > System Options you have your temporary files directory pointed to a drive that does not contain the OS.

Good luck!

-Jason

-------------------------------------------------------------------
Jason M. Kirk
Technical Director, Optical Imaging & Vital Microscopy Core (OiVM) Baylor College of Medicine
Ph: 713.798.6486
Email: [hidden email]
https://urldefense.com/v3/__http://www.bcm.edu/oivm__;!!Fou38LsQmgU!8xLpzGPyvfAYG0Oaelytw0Va7xY8e963FvPR5tJLA3e6mxbSJILOOR63XePYduw$ 

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