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How to better segment out and label brown-colored lymphatic vessels on a histology image?

asked 2017-02-15 06:27:05 -0600

mat29 gravatar image

updated 2017-02-15 07:15:48 -0600

Eduardo gravatar image

How to better segment out and label brown-colored lymphatic vessels on a histology image?

Need to choose a proper conversion, segmentation, labelling methods and respective image processing libraries.

image description

I have tried Java Open CV code:

    package javaopencvapp;
    import org.opencv.core.Core;
    import org.opencv.core.Mat;
    import org.opencv.core.CvType; 
    import org.opencv.core.Scalar;
    import javaopencvapp.ImageViewer;
    import org.opencv.core.Mat;
    import org.opencv.imgcodecs.Imgcodecs;
    import org.opencv.imgproc.Imgproc;

    public class JavaOpenCVapp {

    static{ System.loadLibrary(Core.NATIVE_LIBRARY_NAME); }
    public static void main(String[] args) throws Exception {
    String filePath = "src/images/imth2.tif";
    Mat newImage = Imgcodecs.imread(filePath);

            Imgproc.threshold(newImage, newImage, 172, 179.0, Imgproc.THRESH_BINARY);
           //* Imgproc.threshold(newImage, newImage, 0, 125, Imgproc.THRESH_BINARY + Imgproc.THRESH_OTSU);
           //*  Imgproc.adaptiveThreshold(newImage, newImage, 255, Imgproc.ADAPTIVE_THRESH_GAUSSIAN_C, Imgproc.THRESH_BINARY, 11, 2); 
      //* Imgproc.adaptiveThreshold(newImage,newImage, 255, Imgproc.ADAPTIVE_THRESH_MEAN_C,Imgproc. THRESH_BINARY, 15, 40);

    if(newImage.dataAddr()==0){
        System.out.println("Couldn't open file " + filePath);
    }else{
        ImageViewer imageViewer;
                    imageViewer = new ImageViewer();
        imageViewer.show(newImage, "Loaded image");
    }
}
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ImageJ / Fiji are more appropriate tools for image analysis in my opinion. For example, you can test the different auto threshold methods directly in the application.

Eduardo gravatar imageEduardo ( 2017-02-15 07:13:11 -0600 )edit

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answered 2017-02-15 07:19:51 -0600

mat29 gravatar image

updated 2017-02-15 07:20:04 -0600

Thx, however, I need to write a code for my custom software, need to choose functions from Java or Python OpenCV

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Asked: 2017-02-15 06:27:05 -0600

Seen: 171 times

Last updated: Feb 15 '17