Analyze 3D skeleton of stacks

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Analyze 3D skeleton of stacks

Munarin, Fabiola
Hi! I am a Postdoc at the Coulombe lab, Brown University. I am working with
the Analyze skeleton Plugin and I am trying to process a stack of 1500
images. However, the software is always crashing when I use stacks composed
of more than 550 images (even when I work with high-performance computing
resources). Do you have any idea how to overcome this problem?

Thanks,
Fabiola


--
*Fabiola Munarin*
Post Doc Research Associate
Coulombe Lab
Brown University
School of Engineering
184 Hope St, Providence, RI 02912
Office: Bert 312
401-863-5846
[hidden email]

*A good head and a good heart are always a formidable combination.*
*(Nelson Mandela)*

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Re: Analyze 3D skeleton of stacks

Ignacio Arganda-Carreras-2
Dear Fabiola,

Could you please specify the error message you get, the image size and
type, and your computer specifications (operative system, RAM, etc)?

thanks!

On Thu, Jan 11, 2018 at 5:58 PM, Munarin, Fabiola <[hidden email]
> wrote:

> Hi! I am a Postdoc at the Coulombe lab, Brown University. I am working with
> the Analyze skeleton Plugin and I am trying to process a stack of 1500
> images. However, the software is always crashing when I use stacks composed
> of more than 550 images (even when I work with high-performance computing
> resources). Do you have any idea how to overcome this problem?
>
> Thanks,
> Fabiola
>
>
> --
> *Fabiola Munarin*
> Post Doc Research Associate
> Coulombe Lab
> Brown University
> School of Engineering
> 184 Hope St, Providence, RI 02912
> Office: Bert 312
> 401-863-5846
> [hidden email]
>
> *A good head and a good heart are always a formidable combination.*
> *(Nelson Mandela)*
>
> <http://www.avg.com/email-signature?utm_medium=email&
> utm_source=link&utm_campaign=sig-email&utm_content=webmail>
> Virus-free.
> www.avg.com
> <http://www.avg.com/email-signature?utm_medium=email&
> utm_source=link&utm_campaign=sig-email&utm_content=webmail>
> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>



--
Ignacio Arganda-Carreras, Ph.D.
Ikerbasque Research Fellow
Departamento de Ciencia de la Computacion e Inteligencia Artificial
Facultad de Informatica, Universidad del Pais Vasco
Paseo de Manuel Lardizabal, 1
20018 Donostia-San Sebastian
Guipuzcoa, Spain

Phone : +34 943 01 73 25
Website: http://sites.google.com/site/iargandacarreras/

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Re: Analyze 3D skeleton of stacks

Munarin, Fabiola
Hi Ignacio,
I don't get any error, Fiji just closes a few seconds after I click on
Analyze Skeleton. I am trying to analyze a stack of 1500 b/w skeleton
images, their size is 2-4 GB. I can analyze stacks up to 500 images, that
is, their size is around 1GB.
My operative system is Windows 7 Enterprise 64-bit, 8GB RAM, and I have
also tried to work with high performance resources, setting 30GB as maximum
memory in Memory and Threads under the Edit menu, but I get the same issue.
Thanks!
Fabiola


<http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>
Virus-free.
www.avg.com
<http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>
<#m_-3415130188116227884_m_-8334184731403329370_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

On Fri, Jan 12, 2018 at 4:41 AM, Ignacio Arganda-Carreras <
[hidden email]> wrote:

> Dear Fabiola,
>
> Could you please specify the error message you get, the image size and
> type, and your computer specifications (operative system, RAM, etc)?
>
> thanks!
>
> On Thu, Jan 11, 2018 at 5:58 PM, Munarin, Fabiola <
> [hidden email]
> > wrote:
>
> > Hi! I am a Postdoc at the Coulombe lab, Brown University. I am working
> with
> > the Analyze skeleton Plugin and I am trying to process a stack of 1500
> > images. However, the software is always crashing when I use stacks
> composed
> > of more than 550 images (even when I work with high-performance computing
> > resources). Do you have any idea how to overcome this problem?
> >
> > Thanks,
> > Fabiola
> >
> >
> > --
> > *Fabiola Munarin*
> > Post Doc Research Associate
> > Coulombe Lab
> > Brown University
> > School of Engineering
> > 184 Hope St, Providence, RI 02912
> > Office: Bert 312
> > 401-863-5846
> > [hidden email]
> >
> > *A good head and a good heart are always a formidable combination.*
> > *(Nelson Mandela)*
> >
> > <http://www.avg.com/email-signature?utm_medium=email&
> > utm_source=link&utm_campaign=sig-email&utm_content=webmail>
> > Virus-free.
> > www.avg.com
> > <http://www.avg.com/email-signature?utm_medium=email&
> > utm_source=link&utm_campaign=sig-email&utm_content=webmail>
> > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
>
>
> --
> Ignacio Arganda-Carreras, Ph.D.
> Ikerbasque Research Fellow
> Departamento de Ciencia de la Computacion e Inteligencia Artificial
> Facultad de Informatica, Universidad del Pais Vasco
> Paseo de Manuel Lardizabal, 1
> 20018 Donostia-San Sebastian
> Guipuzcoa, Spain
>
> Phone : +34 943 01 73 25
> Website: http://sites.google.com/site/iargandacarreras/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>



--
*Fabiola Munarin*
Post Doc Research Associate
Coulombe Lab
Brown University
School of Engineering
184 Hope St, Providence, RI 02912
Office: Bert 312
401-863-5846
[hidden email]

*A good head and a good heart are always a formidable combination.*
*(Nelson Mandela)*

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: Analyze 3D skeleton of stacks

Ignacio Arganda-Carreras-2
It definitely looks like a memory issue. The AnalyzeSkeleton plugin is not
optimized for very large skeletons. I will try to work on it, but the
fastest solution right now is to use more RAM.

ignacio

On Fri, Jan 12, 2018 at 4:35 PM, Munarin, Fabiola <[hidden email]
> wrote:

> Hi Ignacio,
> I don't get any error, Fiji just closes a few seconds after I click on
> Analyze Skeleton. I am trying to analyze a stack of 1500 b/w skeleton
> images, their size is 2-4 GB. I can analyze stacks up to 500 images, that
> is, their size is around 1GB.
> My operative system is Windows 7 Enterprise 64-bit, 8GB RAM, and I have
> also tried to work with high performance resources, setting 30GB as maximum
> memory in Memory and Threads under the Edit menu, but I get the same issue.
> Thanks!
> Fabiola
>
>
> <http://www.avg.com/email-signature?utm_medium=email&
> utm_source=link&utm_campaign=sig-email&utm_content=webmail>
> Virus-free.
> www.avg.com
> <http://www.avg.com/email-signature?utm_medium=email&
> utm_source=link&utm_campaign=sig-email&utm_content=webmail>
> <#m_-3415130188116227884_m_-8334184731403329370_DAB4FAD8-
> 2DD7-40BB-A1B8-4E2AA1F9FDF2>
>
> On Fri, Jan 12, 2018 at 4:41 AM, Ignacio Arganda-Carreras <
> [hidden email]> wrote:
>
> > Dear Fabiola,
> >
> > Could you please specify the error message you get, the image size and
> > type, and your computer specifications (operative system, RAM, etc)?
> >
> > thanks!
> >
> > On Thu, Jan 11, 2018 at 5:58 PM, Munarin, Fabiola <
> > [hidden email]
> > > wrote:
> >
> > > Hi! I am a Postdoc at the Coulombe lab, Brown University. I am working
> > with
> > > the Analyze skeleton Plugin and I am trying to process a stack of 1500
> > > images. However, the software is always crashing when I use stacks
> > composed
> > > of more than 550 images (even when I work with high-performance
> computing
> > > resources). Do you have any idea how to overcome this problem?
> > >
> > > Thanks,
> > > Fabiola
> > >
> > >
> > > --
> > > *Fabiola Munarin*
> > > Post Doc Research Associate
> > > Coulombe Lab
> > > Brown University
> > > School of Engineering
> > > 184 Hope St, Providence, RI 02912
> > > Office: Bert 312
> > > 401-863-5846
> > > [hidden email]
> > >
> > > *A good head and a good heart are always a formidable combination.*
> > > *(Nelson Mandela)*
> > >
> > > <http://www.avg.com/email-signature?utm_medium=email&
> > > utm_source=link&utm_campaign=sig-email&utm_content=webmail>
> > > Virus-free.
> > > www.avg.com
> > > <http://www.avg.com/email-signature?utm_medium=email&
> > > utm_source=link&utm_campaign=sig-email&utm_content=webmail>
> > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> >
> >
> >
> > --
> > Ignacio Arganda-Carreras, Ph.D.
> > Ikerbasque Research Fellow
> > Departamento de Ciencia de la Computacion e Inteligencia Artificial
> > Facultad de Informatica, Universidad del Pais Vasco
> > Paseo de Manuel Lardizabal, 1
> > 20018 Donostia-San Sebastian
> > Guipuzcoa, Spain
> >
> > Phone : +34 943 01 73 25
> > Website: http://sites.google.com/site/iargandacarreras/
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
>
>
> --
> *Fabiola Munarin*
> Post Doc Research Associate
> Coulombe Lab
> Brown University
> School of Engineering
> 184 Hope St, Providence, RI 02912
> Office: Bert 312
> 401-863-5846
> [hidden email]
>
> *A good head and a good heart are always a formidable combination.*
> *(Nelson Mandela)*
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>



--
Ignacio Arganda-Carreras, Ph.D.
Ikerbasque Research Fellow
Departamento de Ciencia de la Computacion e Inteligencia Artificial
Facultad de Informatica, Universidad del Pais Vasco
Paseo de Manuel Lardizabal, 1
20018 Donostia-San Sebastian
Guipuzcoa, Spain

Phone : +34 943 01 73 25
Website: http://sites.google.com/site/iargandacarreras/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: Analyze 3D skeleton of stacks

Munarin, Fabiola
Ok thank you!

On Sun, Jan 14, 2018 at 11:41 AM, Ignacio Arganda-Carreras <
[hidden email]> wrote:

> It definitely looks like a memory issue. The AnalyzeSkeleton plugin is not
> optimized for very large skeletons. I will try to work on it, but the
> fastest solution right now is to use more RAM.
>
> ignacio
>
> On Fri, Jan 12, 2018 at 4:35 PM, Munarin, Fabiola <
> [hidden email]
> > wrote:
>
> > Hi Ignacio,
> > I don't get any error, Fiji just closes a few seconds after I click on
> > Analyze Skeleton. I am trying to analyze a stack of 1500 b/w skeleton
> > images, their size is 2-4 GB. I can analyze stacks up to 500 images, that
> > is, their size is around 1GB.
> > My operative system is Windows 7 Enterprise 64-bit, 8GB RAM, and I have
> > also tried to work with high performance resources, setting 30GB as
> maximum
> > memory in Memory and Threads under the Edit menu, but I get the same
> issue.
> > Thanks!
> > Fabiola
> >
> >
> > <http://www.avg.com/email-signature?utm_medium=email&
> > utm_source=link&utm_campaign=sig-email&utm_content=webmail>
> > Virus-free.
> > www.avg.com
> > <http://www.avg.com/email-signature?utm_medium=email&
> > utm_source=link&utm_campaign=sig-email&utm_content=webmail>
> > <#m_-3415130188116227884_m_-8334184731403329370_DAB4FAD8-
> > 2DD7-40BB-A1B8-4E2AA1F9FDF2>
> >
> > On Fri, Jan 12, 2018 at 4:41 AM, Ignacio Arganda-Carreras <
> > [hidden email]> wrote:
> >
> > > Dear Fabiola,
> > >
> > > Could you please specify the error message you get, the image size and
> > > type, and your computer specifications (operative system, RAM, etc)?
> > >
> > > thanks!
> > >
> > > On Thu, Jan 11, 2018 at 5:58 PM, Munarin, Fabiola <
> > > [hidden email]
> > > > wrote:
> > >
> > > > Hi! I am a Postdoc at the Coulombe lab, Brown University. I am
> working
> > > with
> > > > the Analyze skeleton Plugin and I am trying to process a stack of
> 1500
> > > > images. However, the software is always crashing when I use stacks
> > > composed
> > > > of more than 550 images (even when I work with high-performance
> > computing
> > > > resources). Do you have any idea how to overcome this problem?
> > > >
> > > > Thanks,
> > > > Fabiola
> > > >
> > > >
> > > > --
> > > > *Fabiola Munarin*
> > > > Post Doc Research Associate
> > > > Coulombe Lab
> > > > Brown University
> > > > School of Engineering
> > > > 184 Hope St, Providence, RI 02912
> > > > Office: Bert 312
> > > > 401-863-5846
> > > > [hidden email]
> > > >
> > > > *A good head and a good heart are always a formidable combination.*
> > > > *(Nelson Mandela)*
> > > >
> > > > <http://www.avg.com/email-signature?utm_medium=email&
> > > > utm_source=link&utm_campaign=sig-email&utm_content=webmail>
> > > > Virus-free.
> > > > www.avg.com
> > > > <http://www.avg.com/email-signature?utm_medium=email&
> > > > utm_source=link&utm_campaign=sig-email&utm_content=webmail>
> > > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> > > >
> > > > --
> > > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > > >
> > >
> > >
> > >
> > > --
> > > Ignacio Arganda-Carreras, Ph.D.
> > > Ikerbasque Research Fellow
> > > Departamento de Ciencia de la Computacion e Inteligencia Artificial
> > > Facultad de Informatica, Universidad del Pais Vasco
> > > Paseo de Manuel Lardizabal, 1
> > > 20018 Donostia-San Sebastian
> > > Guipuzcoa, Spain
> > >
> > > Phone : +34 943 01 73 25
> > > Website: http://sites.google.com/site/iargandacarreras/
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> >
> >
> >
> > --
> > *Fabiola Munarin*
> > Post Doc Research Associate
> > Coulombe Lab
> > Brown University
> > School of Engineering
> > 184 Hope St, Providence, RI 02912
> > Office: Bert 312
> > 401-863-5846
> > [hidden email]
> >
> > *A good head and a good heart are always a formidable combination.*
> > *(Nelson Mandela)*
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
>
>

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