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Here is the helper-method that I wrote to actually perform this task:

private static Mat readInputStreamIntoMat(InputStream inputStream) throws IOException {
    // Read into byte-array
    byte[] temporaryImageInMemory = readStream(inputStream);

    // Decode into mat. Use any IMREAD_ option that describes your image appropriately
    Mat outputImage = Highgui.imdecode(new MatOfByte(temporaryImageInMemory), Highgui.IMREAD_GRAYSCALE);

    return outputImage;
}

private static byte[] readStream(InputStream stream) throws IOException {
    // Copy content of the image to byte-array
    ByteArrayOutputStream buffer = new ByteArrayOutputStream();
    int nRead;
    byte[] data = new byte[16384];

    while ((nRead = stream.read(data, 0, data.length)) != -1) {
        buffer.write(data, 0, nRead);
    }

    buffer.flush();
    byte[] temporaryImageInMemory = buffer.toByteArray();
    buffer.close();
    stream.close();
    return temporaryImageInMemory;
}