Filtering particles by other parameters

[Sidnei Paciornik]

Dear colleagues,

In analyze particles one can filter particles by area and circularity. Is
there any easy way to filter particles by other measurement parameters?

For instance, I would like to filter particles by Feret and/or Roundness.

Thank you!

Prof. Sidnei Paciornik
Grupo de Análise de Imagens e Microscopia Digital
DEMa <http://www.dema.puc-rio.br/> - Departamento de Engenharia 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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[G. Esteban Fernandez]

Look at Jan Brocher's (BioVoxxel) toolbox at
http://fiji.sc/List_of_update_sites

-Esteban
On Jun 5, 2013 12:08 PM, "Sidnei Paciornik" <[hidden email]> wrote:

> Dear colleagues,
>
> In analyze particles one can filter particles by area and circularity. Is
> there any easy way to filter particles by other measurement parameters?
>
> For instance, I would like to filter particles by Feret and/or Roundness.
>
> Thank you!
>
> Prof. Sidnei Paciornik
> Grupo de Análise de Imagens e Microscopia Digital
> DEMa <http://www.dema.puc-rio.br/> - Departamento de Engenharia 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
>

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

[Gabriel Landini]

On Wednesday 05 Jun 2013 19:52:41 Sidnei Paciornik wrote:
> In analyze particles one can filter particles by area and circularity. Is
> there any easy way to filter particles by other measurement parameters?
>
> For instance, I would like to filter particles by Feret and/or Roundness.

Once you have the descriptors in the results table, you can do this by writing
a small macro or using this plugin which is in the morphology plugins
collection:

http://www.dentistry.bham.ac.uk/landinig/software/classify/classify.html

Cheers

Gabriel

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[Sidnei Paciornik]

Just perfect!

Thank you Esteban and Gabriel.




On Wed, Jun 5, 2013 at 6:23 PM, G. Esteban Fernandez <
[hidden email]> wrote:

> Look at Jan Brocher's (BioVoxxel) toolbox at
> http://fiji.sc/List_of_update_sites
>
> -Esteban
> On Jun 5, 2013 12:08 PM, "Sidnei Paciornik" <[hidden email]> wrote:
>
> > Dear colleagues,
> >
> > In analyze particles one can filter particles by area and circularity. Is
> > there any easy way to filter particles by other measurement parameters?
> >
> > For instance, I would like to filter particles by Feret and/or Roundness.
> >
> > Thank you!
> >
> > Prof. Sidnei Paciornik
> > Grupo de Análise de Imagens e Microscopia Digital
> > DEMa <http://www.dema.puc-rio.br/> - Departamento de Engenharia 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
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[gankaku]

Hi Sidnei,

As you might have tried already, besides the analysis according to a specific shape descriptor in the "Advanced Particle Analyzer" in the Toolbox as Esteban mentioned, you can also use the "Shape Descriptor Maps" if you don't really know which parameters might be the correct ones to limit such an analysis. This map gives you all standard IJ shape descriptors in a color coded stack. Thus, you might be able to identify features by there shape without previous experimenting to find the necessary upper and lower limits. Furthermore you could use these color coded stacks also to apply a color threshold for extraction of the respective features as a binary images.

Kind regards,
Jan

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

[jumpfunky]

Dear Sidnei,

please take a look on a plugin I have developed: Shape Filter
https://code.google.com/p/ijblob/

--
Kind regards

Thorsten Wagner, M.Sc.
Biomedical Imaging Group
University of Applied Sciences and Arts Dortmund




Am Mittwoch, den 05.06.2013, 15:52 -0300 schrieb Sidnei Paciornik:

> Dear colleagues,
>
> In analyze particles one can filter particles by area and circularity. Is
> there any easy way to filter particles by other measurement parameters?
>
> For instance, I would like to filter particles by Feret and/or Roundness.
>
> Thank you!
>
> Prof. Sidnei Paciornik
> Grupo de Análise de Imagens e Microscopia Digital
> DEMa <http://www.dema.puc-rio.br/> - Departamento de Engenharia 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

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