Weka Segmentation: Generating ROI from semantic segmentation and cropping

[Mohaja14]

Hello I am Samuel,

I am trying to study fuel cells for my graduate degree, where I have to
study many images. I am trying to build a macro that will generate a ROI
around the top most layer and crop it. As you can see in the picture below,
the top most layer is called the CL layer.
<http://imagej.1557.x6.nabble.com/file/t382438/Fig-SEM-Micrograph-of-Cross-section-of-SOFC-Single-Cell.png>
I would like this macro to run on a batch of images, but not every image is
the same. Sometimes the contact layer can be higher/lower, or
thinner/thicker. So I cannot simply hard code specific retangular ROI
dimensions, because it may capture not enough of the CL layer, or it may
capture some of the layer below it.
I am trying to use the Trainable Weka Segmentation, because it seemed best
suited for this task. Where I can train it to select only the CL layer.
<http://imagej.1557.x6.nabble.com/file/t382438/trained.jpg>  
In the image above I have cropped the CL layer and the layer below it, the
CFL layer. I then trained my classifier to segment the image into 3 parts,
the CL layer, the CFL layer, and the background. Now my real question is: In
a macro, how can I generate a ROI around the area with the most red traces,
and then crop it so it only contains the CL layer with a batch of images?

Thank you,
Samuel Sayed



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[Krs5]

Dear Samuel,

On the image you provided the code below seems not too bad. Not sure how it
will work on other images. I used the mean intensity on a line measurement
in the green channel to select the ROI and arbitrary I have set the
threshold for the selected ROI below 100. You could play around with this
(or use another parameter than mean).

title = getTitle();
run("Duplicate...", "title=test");
run("Split Channels");
selectWindow("test (green)");
getDimensions(width, height, channels, slices, frames);
mean=1000;
for (i=10; mean>100;i++){
        makeLine(0, height-i, width, height-i);
        getRawStatistics(nPixels, mean, min, max, std, histogram);
}
selectWindow(title);
makeRectangle(0, 0, width, height-i);
run("Crop");

Best wishes

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
www.le.ac.uk/advanced-imaging-facility
<https://www.le.ac.uk/advanced-imaging-facility>  





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