As mentioned in the article, single-atom imaging has actually been routine for years. What's new here is the ability to take an X-ray of an atom, which enables scientists to identify the type of atom and its chemical state. Until now, the smallest amount that could be X-rayed was roughly 10,000 atoms.
Warning pedantic comment incoming.
It's not an x-ray, in the sense of "passing x-rays through and measuring how much is absorbed".