In the last 20 years, synchrotron based soft X-ray microscopy has emerged as a powerful technique for chemical microanalysis. By efficiently measuring near-edge X-ray absorption spectroscopy (NEXAFS) at high spatial resolution, it produces information analogous to that delivered by electron energy loss spectroscopy in a transmission electron microscope (TEM-EELS). NEXAFS microscopy has significant advantages for studies of soft matter, which is typically a challenge for TEM-EELS due to radiation damage. It provides unique capabilities for studying wet samples. Here, we describe current state-of-the-art soft X-ray microscopy instrumentation and techniques (including the recently commissioned spectromicroscopy facility at the Canadian Light Source in Saskatoon), provide brief descriptions of a few recent applications, and make explicit comparisons of the strengths and limitations of NEXAFS microscopy - in particular, scanning transmission X-ray microscopy (STXM) - relative to TEM-EELS for spatially resolved materials analysis by inner shell spectroscopy.