measuring totuosity with imagej

Hi all,

I am wanting to measure the toruosity of blood vessels ater binary
segmentation of the vessels from a 2D picture.  I am not computer savy
enough to write a program, but am looking for a imagej plugin. I have read
that Vesgen 2D is a good imagej plugin to do this and other analyses.  Does
anyone know if this is a free imagej plugin and where I find it.  There is
also a plugin called image skeleton.  I would also want to measure the
number of vessels seen end on - ie as dots in the picture.  any other
suggestions re appropriate plugins.

Thanks,

Matt

[Ignacio Arganda-Carreras]

Hey Matt,

You can use the Skeletonization and AnalzyeSkeleton plugins:

http://pacific.mpi-cbg.de/wiki/index.php/Skeletonize3D

<http://pacific.mpi-cbg.de/wiki/index.php/Skeletonize3D>
http://pacific.mpi-cbg.de/wiki/index.php/AnalyzeSkeleton

<http://pacific.mpi-cbg.de/wiki/index.php/AnalyzeSkeleton>AnalyzeSkeleton
provides you with the regular and Euclidean distance of the branches, what
you can use to calculate the tortuosity.

Both plugins are included in BoneJ: http://bonej.org/


ignacio


On Wed, May 18, 2011 at 6:17 PM, Matthew Salamonsen <
[hidden email]> wrote:

> Hi all,
>
> I am wanting to measure the toruosity of blood vessels ater binary
> segmentation of the vessels from a 2D picture.  I am not computer savy
> enough to write a program, but am looking for a imagej plugin. I have read
> that Vesgen 2D is a good imagej plugin to do this and other analyses.  Does
> anyone know if this is a free imagej plugin and where I find it.  There is
> also a plugin called image skeleton.  I would also want to measure the
> number of vessels seen end on - ie as dots in the picture.  any other
> suggestions re appropriate plugins.
>
> Thanks,
>
> Matt
>

--
Ignacio Arganda-Carreras, Ph.D.
Seung's lab, 46-5065
Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St.
Cambridge, MA 02139
USA

Phone: [phone]
Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html

Thanks Ignacio,

I'll give it a go.

Matt

Sent from my iPhone

On 25/05/2011, at 5:30 AM, Ignacio Arganda-Carreras <[hidden email]> wrote:

> Hey Matt,
>
> You can use the Skeletonization and AnalzyeSkeleton plugins:
>
> http://pacific.mpi-cbg.de/wiki/index.php/Skeletonize3D
>
> <http://pacific.mpi-cbg.de/wiki/index.php/Skeletonize3D>
> http://pacific.mpi-cbg.de/wiki/index.php/AnalyzeSkeleton
>
> <http://pacific.mpi-cbg.de/wiki/index.php/AnalyzeSkeleton>AnalyzeSkeleton
> provides you with the regular and Euclidean distance of the branches, what
> you can use to calculate the tortuosity.
>
> Both plugins are included in BoneJ: http://bonej.org/
>
>
> ignacio
>
>
> On Wed, May 18, 2011 at 6:17 PM, Matthew Salamonsen <
> [hidden email]> wrote:
>
>> Hi all,
>>
>> I am wanting to measure the toruosity of blood vessels ater binary
>> segmentation of the vessels from a 2D picture.  I am not computer savy
>> enough to write a program, but am looking for a imagej plugin. I have read
>> that Vesgen 2D is a good imagej plugin to do this and other analyses.  Does
>> anyone know if this is a free imagej plugin and where I find it.  There is
>> also a plugin called image skeleton.  I would also want to measure the
>> number of vessels seen end on - ie as dots in the picture.  any other
>> suggestions re appropriate plugins.
>>
>> Thanks,
>>
>> Matt
>>
>
>
>
> --
> Ignacio Arganda-Carreras, Ph.D.
> Seung's lab, 46-5065
> Department of Brain and Cognitive Sciences
> Massachusetts Institute of Technology
> 43 Vassar St.
> Cambridge, MA 02139
> USA
>
> Phone: [phone]
> Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html

[ckhripin]

Matt and Ignacio,

I am trying to calculate the tortuosity of carbon nanotubes in an image. Unfortunately, the perimeter length/max separation definition (which is used in Skeletonize) does not work for me because it does not distinguish between kinked and curved nanotubes. I need tortuosity based on one of the new definitions that are curvature-based. Any ideas?

Constantine

[Ignacio Arganda-Carreras]

Which definition do you want to use?

ignacio

On Thu, Mar 29, 2012 at 3:13 PM, ckhripin <[hidden email]>wrote:

> Matt and Ignacio,
>
> I am trying to calculate the tortuosity of carbon nanotubes in an image.
> Unfortunately, the perimeter length/max separation definition (which is
> used
> in Skeletonize) does not work for me because it does not distinguish
> between
> kinked and curved nanotubes. I need tortuosity based on one of the new
> definitions that are curvature-based. Any ideas?
>
> Constantine
>
> --
> View this message in context:
> http://imagej.1557.n6.nabble.com/measuring-totuosity-with-imagej-tp3684451p4668849.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>

--
Ignacio Arganda-Carreras, Ph.D.
Seung's lab, 46-5065
Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St.
Cambridge, MA 02139
USA

Phone: [phone]
Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html