subtract method replace negative values with zeros

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Core.subtract will indeed saturate results for unsigned data types. note, that your allocation here:

   grayImg1=new Mat(300,300,CV_32S);

will get overwritten (it's useless, and you only fool yourself here), and the grayscale result has the same depth as the input (CV_8U);

also note, that opencv uses BGR pixel order, so you have to use COLOR_BGR2GRAY.

to preserve thnegative values, you have to convert the image to some signed (and larger) type, so all in all it should be:

    Mat grayImg1 = new Mat();
    Imgproc.cvtColor(img1, grayImg1, Imgproc.COLOR_BGR2GRAY);

    Mat gray_32 = new Mat();
    grayImg1.convertTo(gray_32, CvType.CV_32S);

    Scalar img1mean = Core.mean(grayImg1);
    Core.subtract(gray_32, img1mean, gray_32);