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Re: Weka Trainable Segmentation alternative

Posted by Ignacio Arganda-Carreras-2 on Jan 06, 2018; 9:55pm
URL: http://imagej.273.s1.nabble.com/Weka-Trainable-Segmentation-alternative-tp5019833p5019837.html

Dear Adrián,

Can you please manually annotate one of your images with the result you
expect so we better understand what you are trying to achieve?

Best regards,

ignacio

On Sat, Jan 6, 2018 at 6:51 PM, Adrián Villalba <[hidden email]> wrote:

> ​
>  wEKA_INSULITIS0004.tif
> <https://drive.google.com/file/d/1cAtH2qKeDXdE9uEAg1lC9V2EP98JP
> bUD/view?usp=drive_web>
> ​​
>  wEKA_INSULITIS0005.tif
> <https://drive.google.com/file/d/15yHjug2I4gu8rXbRIcEEBGKRrOcgA
> O51/view?usp=drive_web>
> ​​
>  wEKA_INSULITIS0006.tif
> <https://drive.google.com/file/d/1VK5YmHAfTHMZwTW7XFnFXMPjkyeiU
> F72/view?usp=drive_web>
> ​​
>  wEKA_INSULITIS0007.tif
> <https://drive.google.com/file/d/1Bojzu-_vz8Nut13-
> zaGCw5CN5wyn1H1i/view?usp=drive_web>
> ​​
>  wEKA_INSULITIS0008.tif
> <https://drive.google.com/file/d/1uPdOlprtusdaXbsjdGj-
> 6QK-0T6f9ctS/view?usp=drive_web>
> ​Dear all,
>
> Sorry for the example JPG-compressed file. Here I attach some examples of
> tiff acquired images. Weka Trainable Segmentation plufin is not very
> sensitive in order to split the islet (round shaped) versus the rest of
> exocrine tissue. Indeed, every islet is scored different in base of the
> surrounding cell layer. Do you know how can i approach this problem?
>
> Thank you in advance,
>
> 2018-01-06 0:39 GMT+01:00 Adrián Villalba <[hidden email]>:
>
> > Dear all,
> >
> > I am trying to use the Weka Trainable Segmentation plugin in order to
> > classify islets of Langerhans in Hematoxilin/Eosin tissues. There are
> four
> > different types of islets depending on insulitis (immune cell
> infiltration
> > within the islet) as i show you in an attached JPG-picture (just to show
> > you the expected result, not to manipulate).
> >
> > My goal is to do it automatically in imageJ, rather tan manual scoring of
> > pictures. So i thought it would be a good idea to use the Trainable Weka
> > Segmentation plugin just to train the algorithm to do it automatically
> but
> > it fails. (I cannot attach the classifier.model archive because it is
> > rejected by the mailing list conditions).
> >
> > I think that maybe it is not a proble for the Weka, instead being a
> > conceptual problem and that maybe you could know another imageJ tool to
> > pursuit that goal.
> >
> > Thank you very much in advance!
> >
> > --
> >
> >    - Adrián Villalba Felipe.
> >    https://es.linkedin.com/in/adrianvillalba
> >
> >
>
>
> --
>
>    - Adrián Villalba Felipe.
>    https://es.linkedin.com/in/adrianvillalba
>
> --
> 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 : +34 943 01 73 25
Website: http://sites.google.com/site/iargandacarreras/

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