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

Troein, Carl LU orcid ; Siregar, Syahril LU ; Op De Beeck, Michiel LU orcid ; Peterson, Carsten LU ; Tunlid, Anders LU and Persson, Per LU (2020) In Methods and Protocols 3(2). p.1-15
Abstract

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... (More)

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.

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author
; ; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Atmospheric correction, Hyperspectral, Infrared spectroscopy, MCR-ALS, Mie scattering correction
in
Methods and Protocols
volume
3
issue
2
article number
34
pages
15 pages
publisher
MDPI AG
external identifiers
  • scopus:85089852713
  • pmid:32369914
ISSN
2409-9279
DOI
10.3390/mps3020034
language
English
LU publication?
yes
id
c488309b-0f8f-4235-b508-fb069bcc87ca
date added to LUP
2020-09-07 12:59:23
date last changed
2024-05-01 16:24:08
@article{c488309b-0f8f-4235-b508-fb069bcc87ca,
  abstract     = {{<p>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.</p>}},
  author       = {{Troein, Carl and Siregar, Syahril and Op De Beeck, Michiel and Peterson, Carsten and Tunlid, Anders and Persson, Per}},
  issn         = {{2409-9279}},
  keywords     = {{Atmospheric correction; Hyperspectral; Infrared spectroscopy; MCR-ALS; Mie scattering correction}},
  language     = {{eng}},
  month        = {{01}},
  number       = {{2}},
  pages        = {{1--15}},
  publisher    = {{MDPI AG}},
  series       = {{Methods and Protocols}},
  title        = {{OCTAVVS : A graphical toolbox for high-throughput preprocessing and analysis of vibrational spectroscopy imaging data}},
  url          = {{http://dx.doi.org/10.3390/mps3020034}},
  doi          = {{10.3390/mps3020034}},
  volume       = {{3}},
  year         = {{2020}},
}