Journal article
STXMPy: a new software package for automated region of interest selection and statistical analysis of XANES data
Chemistry Central journal, Vol.4(1), pp.11-11
12/2010
DOI: 10.1186/1752-153X-4-11
PMCID: PMC2891742
PMID: 20525317
Abstract
Background: Soft 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.
Results: 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.
Conclusion: 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.
Details
- Title: Subtitle
- STXMPy: a new software package for automated region of interest selection and statistical analysis of XANES data
- Creators
- Tamás Haraszti - Biophysical Chemistry, University of Heidelberg, Im Neuenhelmer Feld 253, 69120 Heidelberg, GermanyMichael Grunze - Applied Physical Chemistry, University of Heidelberg, Im Neuenhelmer Feld 253, 69120 Heidelberg, GermanyMichael G Anderson - Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, Iowa 52242, USA
- Resource Type
- Journal article
- Publication Details
- Chemistry Central journal, Vol.4(1), pp.11-11
- DOI
- 10.1186/1752-153X-4-11
- PMID
- 20525317
- PMCID
- PMC2891742
- NLM abbreviation
- Chem Cent J
- ISSN
- 1752-153X
- eISSN
- 1752-153X
- Publisher
- BioMed Central
- Language
- English
- Date published
- 12/2010
- Academic Unit
- Molecular Physiology and Biophysics; Ophthalmology and Visual Sciences
- Record Identifier
- 9984025585102771
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