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Photo of Michiel Op de Beeck

Michiel Op de Beeck

Researcher

Photo of Michiel Op de Beeck

OCTAVVS : A graphical toolbox for high-throughput preprocessing and analysis of vibrational spectroscopy imaging data

Author

  • Carl Troein
  • Syahril Siregar
  • Michiel Op De Beeck
  • Carsten Peterson
  • Anders Tunlid
  • Per Persson

Summary, in English

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.

Department/s

  • Computational Biology and Biological Physics - Undergoing reorganization
  • Department of Astronomy and Theoretical Physics - Undergoing reorganization
  • BECC: Biodiversity and Ecosystem services in a Changing Climate
  • MEMEG
  • Molecular Ecology and Evolution Lab
  • Department of Biology
  • Centre for Environmental and Climate Science (CEC)

Publishing year

2020-01-01

Language

English

Pages

1-15

Publication/Series

Methods and Protocols

Volume

3

Issue

2

Document type

Journal article

Publisher

MDPI AG

Topic

  • Biological Sciences
  • Other Physics Topics

Keywords

  • Atmospheric correction
  • Hyperspectral
  • Infrared spectroscopy
  • MCR-ALS
  • Mie scattering correction

Status

Published

Research group

  • Molecular Ecology and Evolution Lab

ISBN/ISSN/Other

  • ISSN: 2409-9279