Is it possible to refine a segmentation?

[cromatina]

Hi ImageJ people!

I'm trying to segment some structures from a 3D recostructions of
cryo-tomography experiments. I've used the segmentation editor. At this
moment, I have been able to segment a structure, but since there are some
slices that have a few pixels corresponding to the structure, when I look
at the labels in 3D Viewer, it looks ugly, with some single pixels floating
in the edges of the segmented structure.

I want to know if there is some plugin or something to smooth/refine the
segmented structure to make it look better.

Best regards,

Andrea

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Ignacio Arganda-Carreras-2]

Dear Andrea,

One way to do it would be to apply a set of morphological filters (erosion,
dilation, etc) to your label image. You can find these filters in
MorphoLibJ (https://github.com/ijpb/MorphoLibJ)

Another option would be to save the reconstruction from the 3D viewer and
load it in a computer graphics software like Blender (
https://www.blender.org/) to smooth directly the 3D surfaces.

I hope this helps!

ignacio



On Thu, Jun 25, 2015 at 9:03 AM, Andrea Chicano <[hidden email]>
wrote:

> Hi ImageJ people!
>
> I'm trying to segment some structures from a 3D recostructions of
> cryo-tomography experiments. I've used the segmentation editor. At this
> moment, I have been able to segment a structure, but since there are some
> slices that have a few pixels corresponding to the structure, when I look
> at the labels in 3D Viewer, it looks ugly, with some single pixels floating
> in the edges of the segmented structure.
>
> I want to know if there is some plugin or something to smooth/refine the
> segmented structure to make it look better.
>
> Best regards,
>
> Andrea
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Ignacio Arganda-Carreras, Ph.D.
Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech
Bâtiment 2
INRA Centre de Versailles-Grignon
Route de St-Cyr (RD10)
78026 Versailles Cedex France

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

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[cromatina]

Dear Ignacio,

morphological filters work! Thanks a lot! I was loosing my mind trying all
the options available!

Best,

Andrea

2015-06-25 10:59 GMT+02:00 Ignacio Arganda-Carreras <
[hidden email]>:

> Dear Andrea,
>
> One way to do it would be to apply a set of morphological filters (erosion,
> dilation, etc) to your label image. You can find these filters in
> MorphoLibJ (https://github.com/ijpb/MorphoLibJ)
>
> Another option would be to save the reconstruction from the 3D viewer and
> load it in a computer graphics software like Blender (
> https://www.blender.org/) to smooth directly the 3D surfaces.
>
> I hope this helps!
>
> ignacio
>
>
>
> On Thu, Jun 25, 2015 at 9:03 AM, Andrea Chicano <[hidden email]>
> wrote:
>
> > Hi ImageJ people!
> >
> > I'm trying to segment some structures from a 3D recostructions of
> > cryo-tomography experiments. I've used the segmentation editor. At this
> > moment, I have been able to segment a structure, but since there are some
> > slices that have a few pixels corresponding to the structure, when I look
> > at the labels in 3D Viewer, it looks ugly, with some single pixels
> floating
> > in the edges of the segmented structure.
> >
> > I want to know if there is some plugin or something to smooth/refine the
> > segmented structure to make it look better.
> >
> > Best regards,
> >
> > Andrea
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
>
>
> --
> Ignacio Arganda-Carreras, Ph.D.
> Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech
> Bâtiment 2
> INRA Centre de Versailles-Grignon
> Route de St-Cyr (RD10)
> 78026 Versailles Cedex France
>
> Tel : [phone] - fax : [phone]
> Website: http://sites.google.com/site/iargandacarreras/
> <http://biocomp.cnb.csic.es/~iarganda/index_EN.html>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html