http://imagej.273.s1.nabble.com/Getting-stats-from-Trainable-Weka-Segmentation-plugin-tp5004723p5004916.html
I'd be interested in possibly having up to 10 classes, between 8-10 would be great.
As it is now, the plugin GUI only accepts 5 classes. If more people are
interested, I can change that value. The only reason I set it to 5 is not
to have a huge interface with too many buttons. How many classes would you
> Thanks for that, it worked perfectly!
> Would there be any way to increase the amount of classes allowed within
> one classifier set?
> Or do I just need to make several classifier sets to run on the same image?
>
> Cheers,
> Patrick
> ________________________________________
> From: ImageJ Interest Group [
[hidden email]] on behalf of Ignacio
> Arganda-Carreras [
[hidden email]]
> Sent: 11 September 2013 05:43 PM
> To:
[hidden email]
> Subject: Re: Getting stats from Trainable Weka Segmentation plugin?
>
> My bad, the macro assumes you have clicked on "Create result" and therefore
> the "Classified image" window is there. I should have told you.
>
> ignacio
>
>
> On Tue, Sep 10, 2013 at 11:49 PM, Mr Patrick Fortuna <
>
[hidden email]> wrote:
>
> > Hi Ignacio,
> >
> > Thanks for the reply!
> > I tried running the macro, but it comes back with this message:
> > 'No window with the title "Classified image" found'.
> > Followed by giving the same area measurement for the image 5 times.
> > I tried changing the "selectwindow" to Trainable Weka Segmentation
> > thinking that this might locate the image, but no luck with that on
> getting
> > different area measurements as the output.
> > Any ideas on how to fix this?
> >
> > Thanks and regards,
> > Patrick
> > ________________________________________
> > From: ImageJ Interest Group [
[hidden email]] on behalf of Ignacio
> > Arganda-Carreras [
[hidden email]]
> > Sent: 09 September 2013 07:30 PM
> > To:
[hidden email]
> > Subject: Re: Getting stats from Trainable Weka Segmentation plugin?
> >
> > Dear Patrick,
> >
> > Here you are a macro that does (I believe) what you want. Let me know if
> > you have questions.
> >
> > (i copy/paste it here because the server doesn't seem to like me
> attaching
> > it)
> >
> > <code>
> >
> >
> > // id values of each class in the classified image
> > classLabels = newArray( 0, 64, 128, 191, 255 );
> >
> > setBatchMode( true );
> > run("Set Measurements...", "area_fraction redirect=None decimal=3");
> >
> > for( i=0; i<classLabels.length; i ++ )
> > {
> > minTh = classLabels[ i ];
> > maxTh = classLabels[ i ];
> > if( i < classLabels.length - 1 )
> > maxTh = classLabels[ i+1 ] -1;
> > else // last value is assumed to be 255
> > {
> > minTh = classLabels[ i-1 ] +1;
> > maxTh = classLabels[ i ];
> > }
> > selectWindow("Classified image");
> > run("Duplicate...", "title=[to-be-thresholded]");
> > selectWindow("to-be-thresholded");
> > setThreshold( minTh, maxTh );
> > run("Convert to Mask");
> > run("Measure");
> > close();
> > }
> >
> >
> >
> >
> > </code>
> >
> >
> >
> > Cheers!
> >
> > ignacio
> >
> >
> >
> > On Mon, Sep 9, 2013 at 7:47 AM, Mr Patrick Fortuna <
> >
[hidden email]> wrote:
> >
> > > Hi ImageJ users/developers,
> > >
> > > I'm quite new with using ImageJ (Fiji) and was wondering if anyone
> could
> > > help out with getting some stats?
> > > I'm using the Trainable Weka Segmentation plugin through Fiji to train
> > and
> > > segment an H/E stained section of a teratoma (benign tumor formed from
> > > undifferentiated stem cells).
> > > Once I've trained the classifiers for the various classes I'm
> interested
> > > in, I'd be really interested in getting stats on what percentage of
> each
> > > classifier is present within the image I'm working with.
> > > I've tried using the Measurement of Percent Area (as described here:
> > >
http://www.nist.gov/lispix/imlab/measure/pctarea.html) although I
> > > couldn't seem to set the threshold cause I have more than one color in
> > the
> > > segmented image (due to 5 classifiers being run at the same time).
> > > Could anyone recommend how to get the stats of my interested classes?
> > > Any help would be much appreciated!
> > >
> > > Thanks and regards,
> > > Patrick
> > >
> > > --
> > > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> > >
> >
> >
> >
> > --
> > Ignacio Arganda-Carreras, Ph.D.
> > Seung's lab, 46-5065
> > Department of Brain and Cognitive Sciences
> > Massachusetts Institute of Technology
> > 43 Vassar St.
> > Cambridge, MA 02139
> > USA
> >
> > Phone: (001) 617-324-3747
> > Website:
http://bioweb.cnb.csic.es/~iarganda/index_EN.html> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >
> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >
>
>
>
> --
> Ignacio Arganda-Carreras, Ph.D.
> Seung's lab, 46-5065
> Department of Brain and Cognitive Sciences
> Massachusetts Institute of Technology
> 43 Vassar St.
> Cambridge, MA 02139
> USA
>
> Phone: (001) 617-324-3747
> Website:
http://bioweb.cnb.csic.es/~iarganda/index_EN.html>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>