All the colors used in the output gif are modified by quantizing them into a smaller subset of colors (256 for the algorithm I'm using). This means any color close to black may be assigned to be black in the output gif. Thus, if you check "use black as transparent", those colors would then be made transparent. If the transparent color was changeable, it would still be subject to the above issue as the algorithm controls which colors are combined, but I can put it on my list of things to look into. If you limit yourself to 256 colors (including black), I don't think the algorithm will modify them, but I'm not 100% sure. The max output gif frame size of 1000x1000 is new to me and must be another constraint of the library I'm using to make it all work.