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Watershed not segmenting correctly

asked 2016-05-23 15:16:54 -0500

Guyygarty gravatar image

updated 2016-05-25 11:36:57 -0500


I am trying to implement a watershed segmentation to separate touching blobs. I want to separate the blobs from each other but I am getting a separation of the blobs from each other and from the background. In my final segmented image, each blob has a halo like this, instead of just being an isolated blob:

Original Image:

image description

Segmented image:

image description

What am I doing wrong?

Here is the code I am using:

    System::Void Watershed(Mat DAPI, Mat DAPIBin, int Param)
    imwrite("Bin.tif", DAPIBin);
    Mat dist_8u;
    Mat dist(DAPIBin.size(), CV_32F);
    if (Param > 0)
        distanceTransform(DAPIBin, dist, CV_DIST_L2, CV_DIST_MASK_PRECISE);
        dist_8u = (dist > Param);
    imwrite("dist_8u.tif", dist_8u);
    // Find total markers
        std::vector<std::vector<cv::Point> > contours;
        cv::findContours(dist_8u, contours, CV_RETR_EXTERNAL, CV_CHAIN_APPROX_SIMPLE);
        //Total objects
        int ncomp = (int) contours.size();
        Mat markers = cv::Mat::zeros(dist.size(), CV_32SC1);
        Mat in[] = {dist_8u,dist_8u,dist_8u};
        Mat D3ch;
        cv::merge(in, 3, D3ch);
        for (int i = 0; i < ncomp; i++)
            drawContours(markers, contours, i, cv::Scalar::all(i + 1), -1);

        imwrite("Markers.tif", markers);
        cv::watershed(D3ch, markers);
        Mat Mask=markers>0;
        imwrite("mask.tif", Mask);
        if (ncomp > 0)
        imwrite("Final.tif", DAPIBin);

And the intermediate images:

image description image description image description


Edit: Some more info:

Here is a side by side view of the Markers image before and after the watershed.

image description

After the watershed, the last marker (the one cropped by the top of the image, and which was marker #ncomp) has expanded to fill all area not taken up by other markers. The black outlines in the post-watershed image follow the contours of the pre-watershed markers exactly.


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answered 2016-05-25 11:40:32 -0500

Guyygarty gravatar image

I think I found the problem.

I was passing a binary image instead of a grayscale one to watershed. Fixing this seems to have almost solved my problem. I still get the background merged with one of the blobs, although it's not the last one anymore.


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Asked: 2016-05-23 15:16:54 -0500

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Last updated: May 25 '16