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Open AccessArticle

OCTAVVS: A Graphical Toolbox for High-Throughput Preprocessing and Analysis of Vibrational Spectroscopy Imaging Data

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Department of Astronomy and Theoretical Physics, Lund University, 223 62 Lund, Sweden
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Department of Biology, Lund University, 223 62 Lund, Sweden
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Centre for Environmental and Climate Research (CEC), Lund University, 223 62 Lund, Sweden
*
Author to whom correspondence should be addressed.
Methods Protoc. 2020, 3(2), 34; https://doi.org/10.3390/mps3020034
Received: 31 March 2020 / Revised: 27 April 2020 / Accepted: 28 April 2020 / Published: 1 May 2020
Modern vibrational spectroscopy techniques enable the rapid collection of thousands of spectra in a single hyperspectral image, allowing researchers to study spatially heterogeneous samples at micrometer resolution. A number of algorithms have been developed to correct for effects such as atmospheric absorption, light scattering by cellular structures and varying baseline levels. After preprocessing, spectra are commonly decomposed and clustered to reveal informative patterns and subtle spectral changes. Several of these steps are slow, labor-intensive and require programming skills to make use of published algorithms and code. We here present a free and platform-independent graphical toolbox that allows rapid preprocessing of large sets of spectroscopic images, including atmospheric correction and a new algorithm for resonant Mie scattering with improved speed. The software also includes modules for decomposition into constituent spectra using the popular Multivariate Curve Resolution–Alternating Least Squares (MCR-ALS) algorithm, augmented by region-of-interest selection, as well as clustering and cluster annotation. View Full-Text
Keywords: infrared spectroscopy; hyperspectral; atmospheric correction; Mie scattering correction; MCR-ALS infrared spectroscopy; hyperspectral; atmospheric correction; Mie scattering correction; MCR-ALS
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Troein, C.; Siregar, S.; Beeck, M.O.D.; Peterson, C.; Tunlid, A.; Persson, P. OCTAVVS: A Graphical Toolbox for High-Throughput Preprocessing and Analysis of Vibrational Spectroscopy Imaging Data. Methods Protoc. 2020, 3, 34.

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