Re: Morphological Segmentation of Distinct Parts of Corn Kernels

Posted by Ignacio Arganda-Carreras-2 on Jun 26, 2015; 5:09pm
URL: http://imagej.273.s1.nabble.com/Morphological-Segmentation-of-Distinct-Parts-of-Corn-Kernels-tp5013319p5013322.html

Hello Caleb,

In general, the default features of Trainable Weka Segmentation are mostly
border detectors. You might want to try (as Curtis suggested) other
features that act like texture descriptors (minimum, maximum, median,
variance, etc). In principle, the default classifier (a random forest)
should be able to use the best (most informative) of all the features you
create.

Best,

ignacio

On Fri, Jun 26, 2015 at 6:53 PM, Curtis Rueden <[hidden email]> wrote:

> Hi Caleb,
>
> > I'm having difficulty when I try to separate parts of the kernels
> > themselves (the Embryo, the tip, and the rest of the kernel) from each
> > other.
>
> Did you enable the additional training features in the TWS's Settings
> dialog?
>
> If so, and that still didn't help: you could post an example image
> somewhere for others to try their hand.
>
> Note also that in the future, TWS will support custom features (as a type
> of ImageJ2 plugin), but this work is not yet complete. That sort of thing
> will eventually help solve use cases like yours though.
>
> Regards,
> Curtis
>
> On Fri, Jun 26, 2015 at 10:50 AM, Cmhulbert <[hidden email]> wrote:
>
> > Hi all,
> >
> > I have been playing around with ImageJ for a few weeks now, and have
> tried
> > various segmentation methods, with the goal in mind of eventually
> measuring
> > color values from kernels of corn. I have the kernels scanned in on a
> > regular house scanner, at 300dpi. I can easily segment the from each
> other,
> > and the background, with Weka Segmentation training, but I'm having
> > difficulty when I try to separate parts of the kernels themselves (the
> > Embryo, the tip, and the rest of the kernel) from each other. It seems
> like
> > the Weka Segmentation gives too much weight to the color
> > diferences/similarities, rather than the morphological differences  (such
> > as
> > the grainy tips, or the raised "crater-like" appeareance around the
> > embryo).
> > Does anyone have suggestions as to what settings in Weka I should use to
> > train for this? Or whether there is a better way to do this?
> >
> > Thanks,
> > Caleb
> >
> >
> >
> > --
> > View this message in context:
> >
> http://imagej.1557.x6.nabble.com/Morphological-Segmentation-of-Distinct-Parts-of-Corn-Kernels-tp5013319.html
> > Sent from the ImageJ mailing list archive at Nabble.com.
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
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>

--
Ignacio Arganda-Carreras, Ph.D.
Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech
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