From 3D Projection back to stack

[Romina Plitman]

Hi all,

I am relatively new to Imagej and I am trying to find the skeleton of a
complex microvasculature.

I manage to find the Skeleton and reduce noise using the features
'skeletonize' and 'Analize skeleton'. However, there is still some noise
that I have to clean manually. To do so, I do a 3D projection of my
skeleton (is easier to see the noise), manually select the noise and export
their XY coordinates. I wrote a simple code in matlab that removes those
pixels and I finally obtain my clean skeleton. The problem is that now I
have a clean 3D projection, and to analyze the branches and junctions I
need to go back to the 'normal' stack (the one before the 3D projection).
Basically, I need to do the 3D projection in the opposite way.

Is there something to do it in ImageJ? If not, can someone advice on how to
achieve this?

Many thanks!
Romina

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[Ignacio Arganda-Carreras-2]

Hello Romina,

there is no such a thing, but you could save the XY coordinates of the
voxels to be removed and try to match them in 3D by finding their
correspondences in the volume.

What kind of noise are we talking about?

Maybe you can post an example in the ImageJ Forum <http://forum.imagej.net/>
to get more opinions?

ignacio

On Thu, Aug 4, 2016 at 11:23 AM, Romina Plitman <[hidden email]> wrote:

> Hi all,
>
> I am relatively new to Imagej and I am trying to find the skeleton of a
> complex microvasculature.
>
> I manage to find the Skeleton and reduce noise using the features
> 'skeletonize' and 'Analize skeleton'. However, there is still some noise
> that I have to clean manually. To do so, I do a 3D projection of my
> skeleton (is easier to see the noise), manually select the noise and export
> their XY coordinates. I wrote a simple code in matlab that removes those
> pixels and I finally obtain my clean skeleton. The problem is that now I
> have a clean 3D projection, and to analyze the branches and junctions I
> need to go back to the 'normal' stack (the one before the 3D projection).
> Basically, I need to do the 3D projection in the opposite way.
>
> Is there something to do it in ImageJ? If not, can someone advice on how to
> achieve this?
>
> Many thanks!
> Romina
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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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 : [phone]
Website: http://sites.google.com/site/iargandacarreras/
<http://biocomp.cnb.csic.es/~iarganda/index_EN.html>

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