STXMPy: a new software package for automated region of interest selection and statistical analysis of XANES data

We have implemented a set of functions and scripts in Python to provide a semiautomatic treatment of data obtained using scanning transmission X-ray microscopy. The toolkit includes a novel line-by-line absorption conversion and data filtering automatically identifying image components with significant absorption. Results are provided to the user by direct graphical output to the screen and by output images and data files, including the average and standard deviation of the X-ray absorption spectrum. Using isolated mouse melanosomes as a sample biological tissue, application of STXMPy in analysis of biological tissues is illustrated.The STXMPy package allows both interactive and automated batch processing of scanning transmission X-ray microscopic data. It is open source, cross platform, and offers rapid script development using the interpreted Python language.Scanning transmission X-ray microscopy (STXM) is a synchrotron based technique for the investigation of sample structure and composition with nanoscale (c. a. 30 - 50 nm) resolution [1,2]. High resolution X-ray microscopy is based on X-ray absorption spectroscopy and X-ray absorption near-edge structure analysis (XANES) which provides the chemical information about the specimen.Compared to electrons soft X-rays have excellent tissue penetrating capability. Using photon energies in the so called "water window" between the carbon and oxygen K-shell absorption edges, STXM allows imaging of naturally occurring absorption contrast differences within biological samples. The spectral information of soft X-ray XANES combined with the high spatial resolution of STXM near the carbon or the oxygen K-shell energy (about 284 eV or about 533 eV) holds promise for discovering and studying chemical changes underlying a wide-range of biological phenomenon and disease states.One challenge in the biological application of these techniques pertains to sample variability within and between individual preparations. Biological sampl