Posted by
Krs5 on
Oct 02, 2019; 8:32am
URL: http://imagej.273.s1.nabble.com/Weka-Segmentation-Generating-ROI-from-semantic-segmentation-and-cropping-tp5022476p5022479.html
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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