As @leedohm mentioned, it looks like subpixel font smoothing, which is particularly noticeable against a dark background. You can disable this globally by unchecking Use LCD font smoothing when available in System Preferences > General. You may need to restart Atom after changing this.
You also can customize this in your Atom stylesheet:
Examples here. Be sure to view in Chrome on a Mac.
P.S. try out System Preferences > Accessibility > Zoom. This lets you instantly zoom in with a trackpad or scroll wheel to get a better look at those pixels.