I did some research and the value is correct for ImageMagick 6. It seems that the inversion will happen in ImageMagick 7. I will keep it this way for now. You can identify each channel by the Format of the image.
using(PixelCollection pixels = image.GetReadOnlyPixels()) { // RGBA: Pixel pixel = GetPixel(x, y); red = pixel.GetChannel(0); green = pixel.GetChannel(1); blue = pixel.GetChannel(2); alpha = pixel.GetChannel(3); // CMYK: Pixel pixel = GetPixel(x, y); cyan = pixel.GetChannel(0); magenta = pixel.GetChannel(1); yellow = pixel.GetChannel(2); key = pixel.GetChannel(3); // Gray: (uses 4 channels in IM6 this will change in IM7) Pixel pixel = GetPixel(x, y); gray = pixel.GetChannel(0); }