GEM can read in TIFF, JPEG, and SGI images.
These can be in any color format. Gray scale images are loaded in as gray scale (ie, 1 byte per pixel). Everything else is loaded in or converted to an RGBA image (ie, 4 bytes per pixel).
If there is an alpha channel, then it will be respected. Otherwise, the alpha channel will be set to fully opaque (alpha == 255).
GEM can write TIFF and JPEG images. TIFF-images will be full RGBA-images, wheras JPEG-files only support (compressed) RGB.