Soft X ray spectroscopy can be used to provide information on the concentration of various organic functional groups. By taking a series of images over a closely-spaced range of photon energies around an x-ray absorption edge, one obtains spectrum-per-pixel data much as is done in spectrum imaging in electron energy loss spectroscopy. At Stony Brook, we have developed a series of scanning transmission x-ray microscope systems which operate in the 280-800 eV energy range at the National Synchrotron Light Source. These microscopes use Fresnel zone plates as focusing optics; recent optics have 30 nm finest zone width and 160 micron diameter for good working distance when used for studies at the carbon edge (290 eV). When using this system for studies in biological and environmental science specimens, one obtains very rich but complex data which are not possible to analyze by traditional approaches (exhaustive electronic state modeling and spectrum fitting) used for studies of single molecular types. Instead, we have developed pattern recognition approaches which allow one to analyze the data in terms of the predominant spectroscopic themes. Recent applications in biological and environmental science will be described.