Science and Nature are the canonical exaggerators when it comes to headlines. Whole genome, whole mitochondria, complete, total, you name it, there is (nearly?) always an invisible asterisk at the end. When these words are use then Materials and Methods tell you what actually happened.
What's completely crazy in this research is the ability to thin-section fly brains. Thousands and thousands of slices _of a fly brain_, good old physical science at the heart, crowd-sourced to connect the dots (though I'm not positive that's the case in this paper). The open-hardware imaging tools used in some studies like this are also super cool- https://openspim.org/.