Browsing by Author "Bertinetto, Carlo"

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  • AUTOMATED CHEMOMETRIC PROCEDURE FOR QUANTITATIVE AND QUALITATIVE ANALYSIS OF CONFOCAL RAMAN IMAGES
    (2015) Bertinetto, Carlo; Galvis Rojas, Leonardo; Jokela, Anne; Vuorinen, Tapani; Virkajärvi, Perttu
     Poster
    A chemometric procedure for the analysis of confocal Raman images of biological samples is presented. First, the data matrix undergoes a pre-processing consisting of: removal of cosmic ray peaks, baseline correction [1], wavenumber restriction, noise smoothing, normalization, Principal Component (PC) compression and cluster analysis. The pre-processed data is then unmixed using Band-Target Entropy Minimization (BTEM) [2], a multivariate algorithm for extracting the spectra of pure components within a mixture. It works by seeking the linear combination of PCs that satisfies the following criteria: i) non-negativity of spectral intensities; ii) minimum entropy (which implies maximum simplicity); iii) presence of a certain peak (band-target). BTEM is applied to the whole spectral matrix, as well as to cluster-averaged spectra: the clustering fuzzes some details on major components, but highlights information on other minor ones. All the obtained solutions (one for each band-target) are post-screened to discard replicates and incorrect outcomes. The final set of selected spectra is used to produce images of the relative concentration for each component by a least-squares fit. Several steps of this procedure are automated by in-house written algorithms to minimize user intervention and subjective determination of parameters. This methodology enables the non-invasive mapping of various substances on the same image. In the shown examples taken from various plant tissues, up to seven components were identified, including some with overlapping peaks or small concentration. No a priori chemical knowledge on the sample is needed, although it can be useful for the final post-screening. Because this procedure allows for finding out which compounds are present in a sample (provided that they give a Raman signal), it is also a powerful tool for qualitative analysis. Moreover, it can provide information on certain molecular bonds from relevant peaks in the extracted spectra and on the orientation of ordered structures from their anisotropic response [3] [1] C. G. Bertinetto, and T. Vuorinen, Applied spectroscopy, 68(2):155–164, 2014. [2] E. Widjaja, C. Li, W. Chew, and M. Garland, Analytical chemistry, 75(17):4499–4507, 2003. [3] L. Galvis, C. Bertinetto, U. Holopainen, T. Tamminen, and T. Vuorinen, Journal of Cereal Science. Submitted.
  • AUTOMATIC BASELINE RECOGNITION FOR FAST CORRECTION USING CONTINUOUS WAVELET TRANSFORM
    (2013) Bertinetto, Carlo; Vuorinen, Tapani
     Poster
    A method to perform an automatic and quick recognition of peak and baseline regions in a spectrum is presented. Its characteristics make it especially suitable for the treatment of large amounts of data of similar type, such as those coming from a high-throughput instrument. This algorithm is based on the Continuous Wavelet Transform and is effective on any kind of spectrum in which the baseline is smoother than the rest of the signal. Its parameters are automatically determined using the criteria of Shannon entropy and statistical distribution of noise. If the data are properly grouped into sets of analogous measurements, no user intervention is required. This method was assessed on simulated spectra with different noise levels and baseline amplitudes. It can be combined with various fitting methods for baseline correction. In this study, it was used together with an iterative polynomial fitting to successfully process a real Raman image of 40000 pixels in about 2 1/2 hours.
  • Cellulose elementary fibril orientation in the spruce S1-2 transition layer
    (2019-03-07) Reza, Mehedi; Bertinetto, Carlo; Kesari, Kavindra Kumar; Engelhardt, Peter; Ruokolainen, Janne; Vuorinen, Tapani
     A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
    The tight organization of major wood cell wall polymers limits the swellability, solubility and reactivity of cellulose fibers during the production of regenerated textile fibers, nanocellulose, bioethanol, and many other value-added products. However, the ultrastructural assembly of cellulose elementary fibrils (EF) and matrix materials in one of the outer layers, i.e. S 1-2 transition layer of wood cell wall, is far from being understood. Here, single-axis electron tomography on ultrathin spruce sections was applied to observe the three-dimensional (3D) structure of the S 1-2 layer. The nanoscale geometries of the EFs were further quantitatively modeled through mathematical fitting of the tomographic subvolumes by suitable parametric space curves. The results showed that crisscross, bundled and parallel EF organizations are all present in this layer; the former two exhibit a denser structure. Several quantitative measures such as distances and angles were obtained for the analyzed structures. The result obtained in this study suggests that the S 1-2 transition layer differs in structure than the principal cell wall layers. The structural differences and its possible role in wood cell wall have been discussed. These results will enhance our understanding of the swellability, accessibility and solubility of woody biomass for its conversion into the aforementioned value-added products.
  • Cellulose Elementary Fibrils Assemble into Helical Bundles in S1 Layer of Spruce Tracheid Wall
    (2017-02-13) Reza, Mehedi; Bertinetto, Carlo; Ruokolainen, Janne; Vuorinen, Tapani
     A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
    The ultrastructural organization of cellulose elementary fibrils (EFs) in wood cell wall is considered to be the prime factor regulating the material characteristics of wood in micro to macro levels and the conversion of delignified wood fibers into various products. Specifically, the complex assembly of EFs in wood cell wall limits its swellability, solubility, and reactivity, for example, in dissolution of cellulose for regeneration of textile fibers, fibril separation for the manufacture of nanocellulose, and enzymatic hydrolysis of cellulose into sugars for their subsequent fermentation to various products, like ethanol for future fossil fuels replacement. Here cryo-transmission electron tomography was applied on ultrathin spruce wood sections to reveal the EF assembly in S1 layer of the native cell wall. The resolution of these tomograms was then further enhanced by computational means. For the first time, cellulose in the intact cell wall was visualized to be assembled into helical bundles of several EFs, a structural feature that must have a significant impact on the swelling, accessibility, and solubility of woody biomass for its conversion into the aforementioned value added products.
  • How Does Computational Pre-processing Affect Spectral Analysis? An Investigation on Simulated Spectra
    (2013) Bertinetto, Carlo; Vuorinen, Tapani
     Poster
    The computational recognition and resolution of spectra is usually preceded by Pre-Processing (PP) operations to improve the signal quality and highlight the information of interest. However, little systematic study has been carried out on how the combined use of different PP methods affects the result, often leaving the researcher to rely on common sense when deciding the computational strategy. This work addresses the issue through a simulation experiment. Fictitious spectra of mixtures of five components at varying concentrations and corrupted by different types of noise were processed by various combinations of PP techniques: smoothening, baseline correction, normalization and reduction to Principal Components (PC). The original mixtures were then recognized by k-means Cluster Analysis and the quality of this recognition as a function of the PP procedure and the distance metric was quantified in terms of the Rand and silhouette coefficients. These simulated spectra were designed emulating data commonly encountered in Raman imaging, but these results are applicable to other types of spectroscopy as well. Among the considered PP combinations, the one that yielded the best Rand coefficient employed a polynomial baseline correction method [1], Whittaker smoother, Manhattan normalization, PC transformation explaining 80% of variance and clustering using either Euclidean or city-block distance. A few other combinations had a very similar outcome, whereas certain PP sequences produced a clearly incorrect clustering. The robustness of each PP combination with respect to particular types of noise is also discussed. [1] Carlo G. Bertinetto, Tapani Vuorinen. “Automatic Baseline Recognition for Fast Correction Using Continuous Wavelet Transform (CWT)”. Applied Spectroscopy. Submitted.
  • Kokeellisen datan matemaattista käsittelyä sovelluskohteena infrapuna- ja Raman-spektrit
    (2013-06-04) Solala, Eelis
     Perustieteiden korkeakoulu | Bachelor's thesis
  • Rate-limiting steps in bromide-free TEMPO-mediated oxidation of cellulose-Quantification of the N-Oxoammonium cation by iodometric titration and UV-vis spectroscopy
    (2015) Pääkkönen, Timo; Bertinetto, Carlo; Pönni, Raili; Tummala, Gopi Krishna; Nuopponen, Markus; Vuorinen, Tapani
     A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
    A iodometric titration method was introduced to study the conversion of 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) to the corresponding N-oxoammonium cation (TEMPO+) by hypochlorite in the absence and presence of bromide ion. The validity of the titration was verified with UV-vis spectroscopy combined with a multivariate curve resolution (MCR) algorithm to calculate the concentrations and spectral signatures of the pure components (i.e., TEMPO, Cl(+1) and TEMPO+). The formation of the oxoammonium cation was successfully followed during the activation of TEMPO by HOCl and HOBr. It was found that HOBr is a more effective activator for TEMPO than HOCl is. Moreover, the importance of a separate activation step for TEMPO with bromide-free TEMPO oxidations could be identified with this titration method. The content of TEMPO+ was also monitored during the TEMPO-mediated oxidation of a cellulosic pulp by hypochlorite in the absence and presence of bromide. It was found that the oxidation of the alcoholic groups by TEMPO+ was generally the rate-determining step and much slower than the regeneration of TEMPO+ through oxidation of the hydroxylamine by HOCl and HOBr. However, at high pH the latter reaction became rate-limiting.