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I found the solution as following:

• matrix was emtpy because the value of the cols wasn't set
• The transformation of an 16 bit - raw file with 0-65k greyvalues into a 24bit - RGB JPEG works fine

If someone has any idea how I could manage the in-reading of an 16 bit unsigned int into java without using an char-Array, please tell me. The transformation is done with the following code:

img16u.convertTo(imgtmp, CvType.CV_8UC3, (double) 255.0
            / (maxVal - minVal), (double) -minVal * 255.
            / (maxVal - minVal));

Regards, reem