OCTAVVS: A Graphical Toolbox for High-Throughput Preprocessing and Analysis of Vibrational Spectroscopy Imaging Data.
Carl TroeinSyahril SiregarMichiel Op De BeeckCarsten PetersonAnders TunlidPer PerssonPublished in: Methods and protocols (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.
Keyphrases
- deep learning
- density functional theory
- high resolution
- machine learning
- high throughput
- single molecule
- single cell
- convolutional neural network
- artificial intelligence
- molecular dynamics
- rna seq
- energy transfer
- big data
- particulate matter
- data analysis
- optical coherence tomography
- escherichia coli
- molecular dynamics simulations
- loop mediated isothermal amplification
- molecular docking
- electronic health record
- air pollution
- genome wide
- klebsiella pneumoniae
- magnetic resonance
- gene expression
- raman spectroscopy
- photodynamic therapy
- sensitive detection