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The high brightness and coherence of X-ray synchrotron sources and steady development in X-ray optics are critical ingredients in novel imaging techniques for a variety of domains. We employed several different approaches and a wide energy spectrum of radiation to demonstrate the applicability of synchrotron X-ray imaging in soft granular matter and life science. We applied refraction-enhanced contrast tomography to the Distinct Element Method (DEM) to predict instant granular jamming in an hourglass. The validation of numerical simulations as a DEM is mostly confined to global properties. We present a stringent microscopic test in the case of instant flow jamming in hourglasses: synchrotron X-ray microtomography coupled to advanced image analysis. The results show that DEM is amazingly successful in predicting the actual microscopic position of individual particles from given initial conditions through to the end of the instant jamming process. We further report refraction-enhanced radiology employed in the study of Drosophila Melanogaster wing development. The objective of the study was to reveal the morphological difference between two different phenotypes of fruit flies. Refraction-enhanced radiology is highly sensitive to morphological information, whereas fluorescent X-ray microanalysis techniques can reveal the distribution of heavy elements containing molecules. Here we report the design of a fast fluorescence detection system coupled to an existing radiology setup at the B01A beamline, NSRRC, Taiwan and the successful test on cartilage samples. Since its invention in 1930, Zernike phase contrast has been a pillar in visible microscopy – and more recently in X-ray microscopy – of low-absorption-contrast objects such as biological specimens. We experimentally demonstrated hard-X-ray Zernike microscopy with lateral resolution beyond 30 nm, opening up many new research opportunities in biomedicine and materials science. In the soft X-ray regime we show that synchrotron X-ray fluorescence microscopy can map molecules with fluorine-containing labels and quantitatively measure the fluorine concentration with micrometer spatial resolution. This is an important result for life science since fluorine is a very widely used molecule label for a variety of investigations such as metabolic processes or therapeutic agents. Our results specifically concern Fluorodeoxyglucose and are therefore directly relevant to the crucial neurobiology issue of glucose metabolism.