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I don't think the way you're converting the RGB values to a Color structure is quite right. Try this instead:
byte [] R = new byte[width, height];//R,G,B arrays not empty it contain data
byte [] G = new byte[width, height];
byte [] B = new byte[width, height];
Bitmap bmp4 = new Bitmap(width, height);
Int32 aa, rr, gg, bb;
for (int x = 0; x < width; x++)
for (int y = 0; y < height; y++)
{
aa = 255; // fully opaque
rr = (int)(0.39 * R[x,y] + 0.5); // add 0.5 so doesn't always round down
gg = (int)(0.59 * G[x,y] + 0.5);
bb = (int)(0.12 * B[x,y] + 0.5);
bmp4.SetPixel(x, y, Color.FromArgb(aa, rr, gg, bb));
}
pictureBox6.Image=bmp4;