Print["Processing images..."];
atomImageFile =
  imagesDirectory <> imageTime <> atomImageSuffix <> imageFormat;
noAtomImageFile =
  imagesDirectory <> imageTime <> noAtomImageSuffix <> imageFormat;
backgroundImageFile =
  imagesDirectory <> backgroundImageFileName <> imageFormat;
backgroundImage = Image[Import[backgroundImageFile, "PNG"]];
atomImage = Image[Import[atomImageFile, "PNG"]];
noAtomImage = Image[Import[noAtomImageFile, "PNG"]];
ImageSubtract[atomImage, backgroundImage];

Print["Done."];