Pattern Spectrum Algorithm

[rmakanza]

Dear everyone
I am looking for a algorithm that fill gaps (not holes). I have tried to use the close algorithm from the mathematical morphology methods:http://imagej.net/MorphoLibJ and this is not producing good results. However when I did a further search I came across the following ppt:http://www.intelligence.tuc.gr/~petrakis/courses/computervision/binary.pdf, and the gap filling I would to perfom is illustrated on page 29-30. Is there an algorithm that does this in image j.

Thank you

Best Regards

Richard

[Krs5]

Dear Richard,

You might be looking for the plugin Morphological Operators (http://svg.dmi.unict.it/iplab/imagej/Plugins/Morphological%20Operators/Morphological%20Operators/MorphologicalOperatorsPlugin.htm) or Fast Morphology (http://imagejdocu.tudor.lu/doku.php?id=plugin:morphology:fast_morphological_filters:start)

Best wishes

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of rmakanza
Sent: 18 July 2016 13:48
To: [hidden email]
Subject: Pattern Spectrum Algorithm

Dear everyone
I am looking for a algorithm that fill gaps (not holes). I have tried to use the close algorithm from the mathematical morphology methods:http://imagej.net/MorphoLibJ and this is not producing good results.
However when I did a further search I came across the following ppt:http://www.intelligence.tuc.gr/~petrakis/courses/computervision/binary.pdf,
and the gap filling I would to perfom is illustrated on page 29-30. Is there an algorithm that does this in image j.

Thank you

Best Regards

Richard



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[rmakanza]

Dear Kees.
Thank you very much for a quick help. I have managed to try the Mophology algorithm:(http://svg.dmi.unict.it/iplab/imagej/Plugins/Morphological%20Operators/Morphological%20Operators/MorphologicalOperatorsPlugin.htm), but the second link is not openning.

I liked it because it enables me to create my own Structure Element (SE) to fill the gaps. However I am not able to maintain the distances between individual objects after applying it. Objects are getting connected even after using the close method, affecting my segmentation. In this link:http://www.intelligence.tuc.gr/~petrakis/courses/computervision/binary.pdf,  on page 30, it looks like its possible to maintain these distances and the formular to do so is given. Any clue or code to achieve this?

[Ignacio Arganda-Carreras-2]

You might want to give a try to the morphological operators available in
MorphoLibJ <http://imagej.net/MorphoLibJ>.

If you post an image, I can try to find the beset solution among the
existing tools.

On Mon, Aug 1, 2016 at 11:42 AM, rmakanza <[hidden email]> wrote:

> Dear Kees.
> Thank you very much for a quick help. I have managed to try the Mophology
> algorithm:(
> http://svg.dmi.unict.it/iplab/imagej/Plugins/Morphological%20Operators/Morphological%20Operators/MorphologicalOperatorsPlugin.htm
> ),
> but the second link is not openning.
>
> I liked it because it enables me to create my own Structure Element (SE) to
> fill the gaps. However I am not able to maintain the distances between
> individual objects after applying it. Objects are getting connected even
> after using the close method, affecting my segmentation. In this
> link:
> http://www.intelligence.tuc.gr/~petrakis/courses/computervision/binary.pdf
> ,
> on page 30, it looks like its possible to maintain these distances and the
> formular to do so is given. Any clue or code to achieve this?
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Pattern-Spectrum-Algorithm-tp5016904p5016961.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
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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