Abstract
BackgroundSoft X-ray spectromicroscopy based absorption near-edge structure analysis, is a spectroscopic technique useful for investigating sample composition at a nanoscale of resolution. While the technique holds great promise for analysis of biological samples, current methodologies are challenged by a lack of automatic analysis software e. g. for selection of regions of interest and statistical comparisons of sample variability.ResultsWe 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.ConclusionThe 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.
Highlights
Soft X-ray spectromicroscopy based absorption near-edge structure analysis, is a spectroscopic technique useful for investigating sample composition at a nanoscale of resolution
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
Analysis of Scanning transmission X-ray microscopy (STXM) data is typically completed using software packages such as the one created by the X-ray physics group of the Stony Brook University or the aXis2000 software provided by the McMaster University
Summary
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
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
