Convex Hull in 3D - Open and Closed Porosity

[Sidnei Paciornik]

Dear All

Is there any plugin in ImageJ or FIJI to obtain the 3D Convex Hull of a 3D
object?

I am actually trying to discriminate open (connected) and closed
(unconnected) pores.

So my rationale was:
1) Segment the object and fill the pores.These would be the closed pores.
2) Obtain the 3D hull and fill the pores. Now the open pores would be
closed by the convex hull and would also be filled, along with the previous
closed pore.
3) Subtract to obtain just the open pores.

Of course, when I mention "fill holes" above I have to consider 2D or 3D
filling, which brings me to the other question:
Is there a 3D fill holes operator in ImageJ/FIJI?

Several 3D programs (e.g. CTan, Avizo, ORS) have some form to discriminate
open and closed porosity.

Any suggestions?

Thank you !

Prof. Sidnei Paciornik
Grupo de Análise de Imagens e Microscopia Digital
DEQM - Departamento de Engenharia de Química e de Materiais
PUC-Rio <http://www.puc-rio.br/>
Rua Marquês de São Vicente 225
Prédio Leme, Sala 501L
Gávea - Rio de Janeiro - RJ
22451-900 - Brasil
tel: [phone]

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[Michael Doube-4]

Hi Sidnei,

By open and closed porosity, do you mean cavities vs holes in the
topological sense? Cavities are isolated from the outside while holes
are loops through the opposite phase.

You might consider a connected components labeller like BoneJ's particle
analyser, which can additionally tell you the Euler characteristic of
each pore - maybe that will help you discriminate open / closed porosity?

http://bonej.org/particles

Michael

On 25/05/15 22:26, Sidnei Paciornik wrote:

> Dear All
>
> Is there any plugin in ImageJ or FIJI to obtain the 3D Convex Hull of a 3D
> object?
>
> I am actually trying to discriminate open (connected) and closed
> (unconnected) pores.
>
> So my rationale was:
> 1) Segment the object and fill the pores.These would be the closed pores.
> 2) Obtain the 3D hull and fill the pores. Now the open pores would be
> closed by the convex hull and would also be filled, along with the previous
> closed pore.
> 3) Subtract to obtain just the open pores.
>
> Of course, when I mention "fill holes" above I have to consider 2D or 3D
> filling, which brings me to the other question:
> Is there a 3D fill holes operator in ImageJ/FIJI?
>
> Several 3D programs (e.g. CTan, Avizo, ORS) have some form to discriminate
> open and closed porosity.
>
> Any suggestions?
>
> Thank you !
>
> Prof. Sidnei Paciornik
> Grupo de Análise de Imagens e Microscopia Digital
> DEQM - Departamento de Engenharia de Química e de Materiais
> PUC-Rio <http://www.puc-rio.br/>
> Rua Marquês de São Vicente 225
> Prédio Leme, Sala 501L
> Gávea - Rio de Janeiro - RJ
> 22451-900 - Brasil
> tel: [phone]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Michael Doube
BPhil BVSc PGCert(Vet Ed) PhD FHEA MRCVS
Lecturer, Comparative Biomedical Sciences
The Royal Veterinary College, University of London
London NW1 0TU
United Kingdom

[phone] (Internal: 5503)
@mdoube
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