Segmentation of adjoining cells that are irregularly shaped

[kirbyfloss]

Hi -

I'm struggling with properly segmenting irregularly shaped cells that are close together. I have experimented with the Biovoxxel irregular watershed tool and the Process>Binary>Watershed tool after eroding/dilating without much success.

Is there any way to separate cells that are connected at thin junctures? Or are there any suggestions? I've attached some sample images that have been binarized, as well as a sample image of a raw image (H&E stained muscle cells). We are interested in calculating the cross-sectional area of the dark pink cells with purple nuclei on the interior.

Thanks!

[Ignacio Arganda-Carreras-2]

You can also give a try to the Trainable Weka Segmentation:

http://fiji.sc/Trainable_Weka_Segmentation

This is what I got with that plugin:

[image: Inline image 1]

On Sat, Oct 24, 2015 at 12:33 AM, kirbyfloss <[hidden email]>
wrote:

> Hi -
>
> I'm struggling with properly segmenting irregularly shaped cells that are
> close together. I have experimented with the Biovoxxel irregular watershed
> tool and the Process>Binary>Watershed tool after eroding/dilating without
> much success.
>
> Is there any way to separate cells that are connected at thin junctures? Or
> are there any suggestions? I've attached some sample images that have been
> binarized, as well as a sample image of a raw image (H&E stained muscle
> cells). We are interested in calculating the cross-sectional area of the
> dark pink cells with purple nuclei on the interior.
>
> Thanks!
> <http://imagej.1557.x6.nabble.com/file/n5014752/Screen_Shot.png>
> <http://imagej.1557.x6.nabble.com/file/n5014752/Screen_Shot2.png>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Segmentation-of-adjoining-cells-that-are-irregularly-shaped-tp5014752.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 Ciencias 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>

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