Overlay atoms color optimization.

[huangchieh]

As the scanning region expands, the atoms' colours are lost, leaving only black dots. I believe we are using black to represent the edges of the atoms. I am considering changing the edge color to match the fill color to avoid this issue, or alternatively, reducing the width of the edges.

The above example works fine. However, for the following case when an image is large, all the atoms are black, which is not correct.