SI2-SSI Integration of Synchrotron X-Ray Analysis Software Methods into the Larch Framework

University Of Chicago, Chicago IL

Investigators

Abstract

The solutions to many of the outstanding problems in geology, environmental science, material science, and biology require understanding the chemical state and detailed atomic structure of the molecules and solids that make up our world. Such problems range from understanding the molecular forms of arsenic in rice, determining the chemical composition of the earths interior, and improving the performance and reducing the environmental impact of batteries that are in our laptops, cellphones, and cars. The nation's synchrotron facilities provide powerful X-ray facilities that allow researchers to study these questions by investigating the chemical makeup and crystal structure of complex, real-world materials such as plant seeds, contaminated soils, human and animal tissue, minerals and meteorites, and working batteries and catalysts. Synchrotron measurement techniques have developed very rapidly over the past few decades, and are being used by many more researchers. The ability to handle and interpret the large and complex datasets now being routinely generated at these facilities is often a significant challenge, even for experts. The work here will develop the Larch X-ray analysis framework to provide open-source software that is easy to use and specific enough to correctly interpret several categories of synchrotron X-ray data. The approach will provide tools that are flexible enough to enable researchers to explore and interpret new combinations of data easily enough to make new connections and discoveries in a wide variety of scientific areas. This project will integrate visualization and analysis software for multiple synchrotron X-ray techniques into the open source and extensible Larch X-ray Analysis framework. The immediate focus of the work is to support visualization and quantitative analysis of the rich and complex data from X-ray microprobes, including X-ray fluorescence imaging, fluorescence and absorption spectroscopies, and X-ray diffraction. The Larch framework already provides a suite of analysis procedures for X-ray absorption spectroscopy and fluorescence imaging, and has been designed to be readily extensible by adding plug-ins in Python, widely used in scientific computing and being embraced in the synchrotron user communities. Existing state-of-the-art analysis procedures for X-ray fluorescence, X-ray absorption, and X-ray diffraction have been identified to be integrated into the Larch framework, adapting and translating the software as needed to be compatible with the open-source Python framework. With the combination of state-of-the-art analysis methods for multiple data types, Larch will provide a single well-supported and -documented analysis package with robust, easy to use analytic methods for a range of synchrotron X-ray data. By being easily extensible, the Larch package can also accommodate methods for other synchrotron X-ray techniques.