Re: how to load label data in trainable weka segmentation GUI?

Posted by Ignacio Arganda-Carreras on May 29, 2013; 7:18am
URL: http://imagej.273.s1.nabble.com/Re-how-to-load-label-data-in-trainable-weka-segmentation-GUI-tp5003142.html

Dear Shahab,

Thanks for your interest in the plugin. Let me answer you with copy to
the ImageJ list, so anybody else with the same question can find the
answer here.

> I am using the weka segmentation GUI in Fiji.
> would you please let me know how I can add my labels file (which is a binary image of my 2 class labels) in the software?
> now I can just add labels manually using the 'add to' button. I have found out that in the java we can add it but it is not provided in the GUI if I am not wrong.

There is no option to add directly the labels from the binary image
because the GUI is designed for interactive learning. However, there's
a workaround you can use:

1) click on your binary image and then on Edit > Selection > Create Selection.
2) click on the Trainable Weka Segmentation GUI and then on Edit >
Selection > Restore Selection.
3) add that ROI to one of the classes.
4) click on your binary image and then on Edit > Selection > Make Inverse.
5) click on the Trainable Weka Segmentation GUI and then on Edit >
Selection > Restore Selection.
6) add that ROI to the other class

Then you'll be ready to train.

Just a warning: adding the ROIs like may make things slow at the
beginning of the training, since the program needs to check for every
pixel if it's inside or outside the ROI.

Let me know what you think.

Best,

ignacio

--
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: [phone]
Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html

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