Journal Pre-proof

CT-GUI: a graphical user interface to perform calibration transfer for multivariate

calibrations

Puneet Mishra

PII: S0169-7439(21)00106-4
DOI: https://doi.org/10.1016/j.chemolab.2021.104338
Reference: CHEMOM 104338

To appear in: Chemometrics and Intelligent Laboratory Systems

Received Date: 5 March 2021

Revised Date: 20 April 2021
Accepted Date: 6 May 2021

Please cite this article as: P. Mishra, CT-GUI: a graphical user interface to perform calibration transfer
for multivariate calibrations, Chemometrics and Intelligent Laboratory Systems, https://doi.org/10.1016/
j.chemolab.2021.104338.

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© 2021 The Author(s). Published by Elsevier B.V.

 1 CT-GUI: a graphical user interface to perform calibration

2 transfer for multivariate calibrations

3 Puneet Mishra1

1
4 Food and Biobased Research, Wageningen University and Research, Bornse Weilanden 9,

5 6708 WG, Wageningen, The Netherlands.

6 1. Abstract

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7 A new MATLAB based graphical user interface integrating several multivariate calibration

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8 transfer approaches is presented. Several methods for standard-based and standard-free

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calibration transfer are integrated. A demonstration of the toolbox and functionalities of
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10 different approaches was judged using a calibration transfer case of the corn dataset. All
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11 methods were tested on the corn dataset and the results showed that the toolbox is ready to be
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12 used. The best feature of the toolbox is that it is a push-button toolbox that even non-expert

13 can use to achieve complex calibration transfer tasks. The CT-GUI toolbox is available at
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14 https://tinyurl.com/PMishra.
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15

16 Keywords: orthogonal projection; instrument transfer; model maintenance

17 2. Introduction
18
19 Multivariate chemometric calibrations are highly specific to the primary instrument

20 (spectrometers) on which the data was first collected and modelled [1-3]. Hence, simply

21 reusing a model made for an instrument on a new instrument is not possible as different

22 instruments have intrinsic differences such as different instrument components such as the

23 detector, illumination, difference in spectra range or resolution, or differences in the

24 surrounding environment in which the instrument is operated [2]. To deal with this challenge,
25 extensive development in the chemometrics domain have taken place and several calibration

26 transfer (CT) strategies are now available to transfer models from one instrument to another

27 [2, 3].

28 In the domain of the chemometrics two types of CT methods are available i.e., standard-

29 based [2] and standard-free [3]. The standard-based methods are fairly developed and widely

30 used in practice, while the standard-free methods are recent. The standard-based methods

31 such as direct standardization (DS) [4] and piece direct standardization (PDS) [5], requires

32 standard samples to be measured on both instruments to model instrumental differences

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33 and/or compensate for them [2]. By measuring the same standard sample on different

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34 instruments, it is assumed that the differences in the signals are due to

35
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the intrinsic differences in the instruments. The instrument difference can be modelled as the
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36 transfer function. The transfer function can be used to transform the data before any model
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37 application [4, 5]. However, in many scenarios, the measurement of standard samples on both
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38 instruments is not possible [6-8], for example, when instruments are in remote locations and

39 the primary instrument is damaged. Hence, there is an increasing trend towards the
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40 development of standard-free CT methods to support model sharing across different

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41 instruments. Recently, several approaches to perform standard-free CT have been proposed in

42 the literature [3]. Approaches range from techniques that require non-standard samples such

43 as the dynamic orthogonal projections (DOP) [9, 10] where the need for standard samples is

44 replaced by the measurement of new samples just on the slave instrument, domain adaption

45 (DA) techniques such as transfer component analysis (TCA) [11, 12] and parameter-free

46 calibration enhancement (PFCE) framework which allows updating of model based on some

47 new measurements from a different instrument [13].

48 Although there have been significant developments in the chemometrics domain related to

49 new CT methods [2, 3], the use of such methods is limited to highly skilled chemometricians
50 with competence in programming. Wider usage of such methods by non-experts requires

51 methods to be available in easy-to-use interfaces, where the CT can be performed with basic

52 or even no skills in programming. The best solution for non-expert users is the graphical user

53 interface (GUI), as it requires minimal programming skills as well reduces the time required

54 to adapt or standardize the codes from scratch. GUIs are gaining popularity and recently

55 several chemometric toolboxes have become available, such as the batch process modelling

56 and monitoring toolbox (MVBATCH) [14], the data pre-processing and multivariate

57 statistical process control toolbox (PreScreen) [15], the trilinear data discriminant analysis

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58 toolbox (TTWD-DA) [16], the multivariate calibration toolbox (TOMCAT) [17], the

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59 hyperspectral image analysis toolbox (HyperTools) [18], the multi-block analysis toolbox

60
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(MBA-GUI) [19], the batch effect correction toolbox (FRUITNIR-GUI) [12], the multivariate
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61 exploratory data analysis toolbox (MEDA) [20] and the N-Way toolbox [21]. Until now
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62 there is no dedicated GUI that integrates several CT techniques. A command-line toolbox

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63 called SAISIR [22] provides a subset of CT techniques but they are for highly skilled

64 programmers and a non-expert lacking programming skill may never implement them.
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65 The objective of this work is to provide a new MATLAB based graphical user interface
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66 integrating several multivariate CT approaches. Several methods for standard-based and

67 standard-free CT are integrated. A demonstration of the toolbox and functionalities of

68 different approaches was judged using a CT case of the corn dataset. All methods were tested

69 on the corn dataset and the results showed that the toolbox is ready to be used.

70 3. Software description

71 The Transfer-GUI was built utilizing the application builder in MATLAB version 2018b

72 (MathWorks, Natick, MA, USA). The application can be downloaded and installed in

73 MATLAB (preferred versions 2018b or higher) or can be used as a stand-alone executable or

74 can be run through the ‘.mlapp’ files in the MATLAB command line. If the user does not
75 have MATLAB version 2018b or greater then it is recommended to install the free MATLAB

76 runtime tool and run the app as a standalone. All the MATLAB functions can be downloaded

77 from: https://tinyurl.com/Pmishra2. The standalone application can be downloaded from:

78 https://tinyurl.com/PMishra. The free MATLAB runtime can be downloaded from:

79 https://nl.mathworks.com/products/compiler/matlab-runtime.html. The compatible runtime

80 for this toolbox is version 9.5 and 2018b. Before installing the standalone application the

81 MATLAB runtime environment should be installed.

82 To run the toolbox from the command line, the user should use the toolbox folder as the

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83 current folder and type ‘T1’ on the command line to start the main GUI interface. The GUI

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84 supports the input data formats.csv, ‘.xlsx’ and ‘.mat’. The input to the toolbox is the matrix

85 of spectra of size where

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is the number of samples and is the number for
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86 variables. The extra 1 is the first row of the matrix which are the variables (for examples
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87 wavelengths in the case of optical spectroscopy). The reference property matrix must be of
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88 size . The toolbox has three types of data pre-processing, i.e., smoothing, scatter

89 correction and normalization, and derivation, which it inherits from the wide collection
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90 available in MBA-GUI [19].

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91

92 4. Brief description of methods integrated

93 4.1. Direct standardisation

94 DS [4] relates the response of a standard sample measured with one instrument (R1) to its

95 response obtained on another instrument (R2) using a linear transformation matrix (F) as R1 =

96 R2 F, where F is a squared matrix with dimension equal to the number of wavelengths. The F

97 matrix is obtained as F = R2-1R1. For any new data acquisition, the spectra are transformed

98 with the F matrix such that the model made on the primary instrument can be directly used on
 99 the secondary instrument. In the GUI, DS is implemented by means of an in-house MATLAB

100 code.

101
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103 4.2. Piece wise direct standardisation
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105 In the DS method, the whole spectrum of the secondary instrument is used to fit each point of

106 the spectrum of the primary instrument. However, in most cases, the spectral variation is

107 present in localized regions. Hence, the new method PDS [5] was designed to map the local

108 variation in the secondary instrument with each point on the primary instrument. The PDS [5]

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109 transformation matrix is used to transform any new spectrum measured on a secondary

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110 instrument, thus allowing calibration model transfer. A key point to note is that unlike DS,

111
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which is almost parameter-free, the PDS approach requires to decide the optimal window size
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112 to map the local variation in the secondary instrument data. In the GUI, PDS is implemented
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113 by means of an in-house MATLAB code.

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114
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115 4.3. Dynamic orthogonal projection

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116 Dynamic orthogonal projection (DOP) is a model maintenance method developed to deal

117 with physical, chemical, and environmental effects in spectroscopic modelling [9]. The

118 approach is based on the correction of the calibration dataset based on the new reference

119 measurements performed in different physical, chemical, and environmental conditions. The

120 correction is performed using orthogonal projections based on the subspace defined by the

121 difference of the calibration spectra and the new condition spectra. The DOP method

122 estimates virtual standards, i.e., the spectra that should have been measured if the calibration

123 conditions had not varied. This is accomplished by means of linear combinations of the

124 original calibration data matrix, whose coefficients are calculated using

125 kernels centred on reference values. Once the virtual standards are prepared then the
126 difference spectra are calculated. The orthogonal basis for the difference spectra is estimated

127 by singular value decomposition (SVD) and finally, the original spectra are projected

128 orthogonally to that basis. This removes the external influences from the spectra and then the

129 model recalibrated on these data becomes insensitive to the differences (physical, chemical,

130 and environmental conditions). In the GUI, DOP is implemented by means of an in-house

131 function [10]; once the data are corrected, then a PLS regression model is built as described

132 previously. The codes for DOP were inherited from the previous published external effect

133 removal FRUIT-NIR GUI toolbox [12].

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135 4.4. Parameter free calibration enhancement

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The parameter-free calibration enhancement framework (PFCE) is a recently proposed
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138 method to update existing calibrations based on the measurements from new instruments or
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139 different measurement conditions [13]. The PFCE can be used in three scenarios i.e., non-

140 supervised PFCE (NS-PFCE), semi-supervised PFCE (SS-PFCE), and full-supervised PFCE
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141 (FS-PFCE). The NS-PFCE requires standard samples spectra from primary and secondary
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142 instrument to update the primary model by implementing a correlation constraint on the
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143 regression coefficients. The SS-PFCE and FS-PFCE methods integrate the spectra from the

144 second instrument and corresponding reference values to update the models [13]. The NS-

145 PFCE is like the DS approach to calibration transfer, as they both require the spectra from

146 primary and secondary instruments to model the difference. The SS-PFCE and FS-PFCE can

147 be considered like the DOP approach as they both require some new spectral and reference

148 measurements to update the models. The PFCE was integrated with the open codes provided

149 along with the manuscript [13]. While using the PFCE integrated into this toolbox, please

150 also cite the original manuscript i.e. [13].

151 5. Data used for demonstration

152 To demonstrate the functionalities of the toolbox the publicly available corn data set was used

153 (www.eigenvector.com/data/Corn). From the corn data set, data corresponding to two

154 spectrometers i.e., M5 and MP6 was used. The aim was to transfer the model from M5 to

155 MP6 spectrometer. The corn data set has 80 spectra of corn samples and corresponding

156 reference properties. To demonstrate the functionalities of the toolbox, the protein content

157 was used as the reference property. The 80 spectra were divided into calibration (60 %) and

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158 independent test set (40 %) using the Duplex algorithm. The calibration set was used for

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159 primary model development and calibration transfer, while the independent test set was used

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for evaluating the performance of transferred calibration. The mean spectra from the M5 and

161 Mp6 spectrometer are shown in Fig. 1. The differences in the mean spectra can be noted
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162 along with the whole spectral range, where the Mp6 spectrometer has a globally lower signal
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163 intensity compared to the M5 spectrometer. Such a difference in mean spectral response for
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164 the same samples indicates the intrinsic difference in the spectrometers, which should be
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165 carefully dealt with while transferring the model from one spectrometer to another. A
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166 summary of the reference protein content is shown in Table 1. The exact partitioned data is

167 also provided with the toolbox such that user ay replicate the analysis and enhance their

168 understanding of toolbox functionalities.

169
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171 Fig. 1:Mean spectra of corn from M5 and Mp6 spectrometer.
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173 Table 1: A summary of reference protein content in calibration and test set.
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Property of interest Calibration Test

Protein (%) 8.59 ± 0.48 8.78 ± 0.51
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174
175
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176 6. Demonstration

177 The starting interface of the toolbox is shown in Fig. 2. The interface provides options to load

178 data from two instruments. Further, several pre-processing approaches can be explored to

179 enhance the data. Later, from the drop-down menu, a relevant CT method can be selected and

180 used.
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181

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Fig. 2: The starting interface of the toolbox. This interface allows user to upload data and
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183 pre-process it and select the relevant calibration transfer or model updating approach.
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184 An example of running the DS calibration transfer and general outputs from the toolbox are
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185 shown in Fig. 3, 4, and 5. The DS CT provides a plot for optimal latent variable selection

186 where the PLS models with (bottom row Fig. 3) and without CT are optimized (top row Fig.
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187 3). For example, the PLS model without CT suggests 9 LVs (Latent Variables) for model
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188 calibration, while the PLS after DS-CT suggest only 8 LVs to optimize the model sufficient

189 to be used on a new instrument. Hence, 8 LVs can be used to calibrate the final model. The

190 outputs of the final model calibrated based on 8 LVs are shown in Fig. 4A and B. After the

191 model calibration, the test set can be loaded, and the model can be deployed. A summary of

192 the results of the test set for corn data is shown in Fig. 4C. It can be noticed that after the DS-

193 CT the RMSE (Root Mean Squared Error) for the calibration (Fig. 4B) and test set (Fig. 4C)

194 were similar ~0.14 %.

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196 Fig. 3: A summary of latent variables optimization routine for direct standardization
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197 calibration transfer. PLS model (A) Explained variance in response variable as a function of
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198 latent variables, and (B) mean square error as a function of latent variables. DS corrected
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199 PLS model (C) Explained variance in response variable as a function of latent variables, and
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200 (D) mean square error as a function of latent variables. The user can use the (D) to select the
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201 optimal number of latent variables for final model.

202

203
204 Fig. 4:A summary of the model calibration and test for the direct standardization calibration

205 transfer. (A) PLS model without calibration transfer, (B) PLS model after calibration

206 transfer, and (C) transferred model used on an independent test set.
207 The CT methods also provide an extra plot presenting the regression vector of the final model

208 (Fig. 5A) and the difference between the regression vectors before and after CT (Fig. 5B).

209 The regression vector of the final models can be used for interpretation of the model, while

210 the difference vector can be used to understand the main spectral regions carrying the

211 differences in the spectral response of two instruments.

212

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213
214 Fig. 5: (A) The regression vector of the final model, and (B) the difference between the
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215 regression vector before and after calibration transfer.

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217 To demonstrate that all integrated methods are fully functional, the corn data was analyzed
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218 with each technique. A summary of the results for all the techniques is shown in Table 2. It

219 can be noted that all techniques attained similar RMSEP (~0.14 %) for predicting protein

220 content in corn. In this data set, all CT methods performed similar, however, while

221 performing the CT on new data set, the user may explore different techniques to find the best

222 suited for their data.

223 Table 2: A summary of performance of different methods integrated in toolbox for corn data

224 set.

Methods Latent variables RMSEP (%)

DS 8 0.14
PDS (window size 11) 9 0.13
DOP 8 0.14
 Non-supervised PFCE 8 0.14
Semi-supervised PFCE 8 0.13
Fully-supervised PFCE 8 0.13
225

226 7. When to use which technique

227 In the GUI, 4 main techniques are integrated for CT and model maintenance. Different

228 techniques have intrinsic properties and can perform better in different cases. In particular,

229 the methods that model the global differences such as the DS and NS-PFCE, are suitable for

230 cases when the differences between different instruments are expected to be dominated

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231 globally compared to the local difference. The global differences are encountered in the cases

232 when the CT is usually performed between different modalities of instruments, such as

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transferring a model from a high-resolution lab-based spectrometer to the handheld portable
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234 spectrometer. On other hand, when the differences are local such as usually encountered in
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235 the case of the identical instrument, the methods modelling the local differences (such as
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236 PDS) are suitable. Further, the methods such as DS, PDS and NS-PFCE, requires the spectra

237 of the standard samples from primary as well as a secondary instrument. However, it may not
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238 be feasible in many practical cases such as when the primary spectrometer is damaged or is
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239 based in a remote location. In that case, the methods such as DOP, SS-PFCE and FS-PFCE

240 can be used. However, a main drawback of the DOP, SS-PFCE and FS-PFCE methods is that

241 they require both the spectra and the reference measurements measured for the new

242 instrument.

243 8. Conclusion

244 A new GUI for calibration transfer was presented. The toolbox functionalities were

245 demonstrated on the corn data set. The result showed that the toolbox is fully functional, and

246 all methods are ready to be used. On the corn data set all integrated CT techniques performed
247 similarly. The user may explore the toolbox and find the best-suited technique for their CT

248 challenge. An exemplary tutorial video to use the GUI can be accessed at: CT-GUI quick test

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250 . In the case of difficulty in software usage, the user can always post the comment in the
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251 YouTube video related to CT-GUI and the developer of toolbox will support the user in
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252 resolving the issue.

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253 9. Independent testing

254
255 Name: Dr. Lalit Mohan Kandpal
256 Job: Research scientist
257 Affiliation: Ghent University, Belgium
258 Email: LalitMohan.Kandpal@UGent.be
259 Phone: +32465759700
260
261
262 “Dr. Lalit Mohan Kandpal in Precision soil & crop engineering group, Department of

263 Environment, Ghent University, B-9000 Gent, Belgium. I have tested the “CTGUI” graphical

264 user-friendly interface based on MATLAB for the analysis of soil chemical data, and it

265 appears to function as the authors described. When analysing the soil data with spectral

266 sensor, it is important to standardize tailored procedure and retrieve results that can answer
267 the analytical problem. Further, when the model needs to be deployed in the field, then very

268 often the models made on laboratory instruments are required to be transferred to portable

269 handheld field instruments. This is precisely what CTGUI does.

270 The toolbox according to the link provided has two options i.e., command line tools as well

271 as the stand-alone tool. The main benefit of the standalone tool is that it does not require

272 MATLAB software to run on computer. I have tested the standalone tool with the MATLAB

273 2018b runtime tool as well as command line on the MATLAB 2020b. The GUI is working

274 well in both the MATLAB versions. Further, I have also performed the analysis according to

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275 the tutorial video provided with the toolbox at:

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276 https://www.youtube.com/watch?v=fI1EnrlUwV4. I was able to replicate all the analysis as

277 demonstrated in the tutorial video.

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278 The main benefit of the toolbox is that it provides most used CT techniques such as direct
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279 standardisation, piecewise direct standardisation to be easily used by even non-experts.

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280 Furthermore, the toolbox also integrates recent model updating approaches such as parameter

281 free calibration enhancement framework which will benefit users of spectroscopy in multiple
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282 situations. From my side, I am confident that this toolbox will serve an important purpose for
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283 transferring and updating spectral models.”

284

285 10. References

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289 [2] J.J. Workman, A Review of Calibration Transfer Practices and Instrument Differences in
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291 [3] B. Malli, A. Birlutiu, T. Natschläger, Standard-free calibration transfer - An evaluation of

292 different techniques, Chemometrics and Intelligent Laboratory Systems, 161 (2017) 49-60.

293 [4] Y. Wang, D.J. Veltkamp, B.R. Kowalski, Multivariate instrument standardization,
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296 Infrared Spectrometers, Applied Spectroscopy, 46 (1992) 764-771.

297 [6] P. Mishra, R. Nikzad-Langerodi, Partial least square regression versus domain invariant
298 partial least square regression with application to near-infrared spectroscopy of fresh fruit,
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308 [10] P. Mishra, J.M. Roger, D.N. Rutledge, E. Woltering, Two standard-free approaches to

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313 [12] P. Mishra, J.M. Roger, F. Marini, A. Biancolillo, D.N. Rutledge, FRUITNIR-GUI: A
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319 on correlation constraint, Analytica Chimica Acta, 1142 (2021) 169-178.

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335 [19] P. Mishra, J.M. Roger, D.N. Rutledge, A. Biancolillo, F. Marini, A. Nordon, D. Jouan-
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Highlights
 A free GUI for calibration transferred is develop
 GUI can be used as command line or standalone application
 Standard based and standard free methods are integrated

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Declaration of interests

☒ The authors declare that they have no known competing financial interests or personal relationships
that could have appeared to influence the work reported in this paper.

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