A significant part of the uniformity degradation in the acquired hyperspectral images can be attributed to the coregistration distortions and spectrally and spatially dependent resolution arising from the misalignments and the operation principle of the spectrograph based hyperspectral imaging system. The aim of this study was the development and validation of a practical method for characterization of the geometric coregistration distortions and position dependent resolution. The proposed method is based on modeling the imaging system response to several affordable reference objects. The results of the characterization can be used for calibration of the acquired images or as a tool for assessment of the expected errors in various hyperspectral imaging systems.
© 2013 OSA
In a basic scheme of a line-scan hyperspectral imaging system (HIS) the observed sample is illuminated by a broadband light source. The diffused or transmitted light, containing information on the observed sample, is collected by the input optics, then passed through a narrow slit, and finally dispersed across the detector array forming one spatial slice of the hyperspectral image. For proper interpretation of the recorded information either an absolute relation between the physical properties of the observed sample and the recorded image or at least instrument-level uniformity with respect to the spectral and spatial position is required. Due to the optical properties and aberrations of the integrated lens (e.g. astigmatism, distortion, chromatic aberration, etc.), and aberrations arising from the dispersing element, the imaging system response is strongly spectrally and spatially dependent . In an ideal image, free of geometric coregistration errors, the spectral and the spatial information would be aligned with the image columns (spatial channels) and rows (spectral channels), respectively. However, due to the higher order effects the recorded image is geometrically distorted. Speaking in relative terms, the recorded image appears wrapped in the spectral direction due to change of the dispersion angle with the spatial position (smile). Similar effect, arising from the wavelength-dependent magnification, is observed in the spatial direction (keystone). Images can be additionally distorted in both directions by rotational and angular misalignment between the spectrograph and the camera. On top of the geometric distortions the uniformity of the recorded image is further degraded by a spectrally and spatially dependent point spread function (PSF). Therefore, a simple global linear model (scaling and shifting of the image) is insufficient for the proper spectral and spatial calibration of the HIS.
Considering that the artifacts arising from the geometric misalignments and position variant PSF are well known issues in the field of remote sensing, the problem is surprisingly rarely addressed in the field of chemical imaging. To the best of our knowledge, there is only one publication  studying and dealing with the geometric coregistration problem, which was conducted in the field of Raman spectroscopy. The study has shown that even minor geometric misalignments lead to significant nonlinear intensity errors in the acquired spectra, which degrade the subsequent hyperspectral image analysis. The findings were in agreement with the studies made in the field of remote sensing, where numerous methods were proposed to both analyze and alleviate the impact of the problem [3–6]. However, these methods are specific to the recorded data, employed equipment and challenges in the field of remote sensing, and usually discuss only the spectral calibration.
Polder et al.  proposed a set of practical procedures suitable for characterization of several laboratory HIS setups. The spectral calibration was performed by finding the polynomial relation between measured peak locations of several known spectra and corresponding real spectral line wavelengths. Spectral resolution was reported as the full width at half maximum (FWHM) of a laser spectral line at 670 nm. The spatial resolution was assessed in terms of FWHM at three wavelengths by several methods. Most reliable results were obtained by calculating the derivative of the b-spline interpolated grey levels of a black-to-white step edge. The image position variant spectral response function (SRF) is usually estimated by stepping trough the spectral range by means of a spectrally tunable light source ([8, 9]). Unfortunately, this approach requires a calibrated monochromator and a relatively complex measurement setup. Analogous approach was used for the spatial calibration by observing a distant, physically thin, light source at predetermined positions . The proposed practical method  for mitigation of the geometric coregistration problem in a Raman imaging spectrograph, utilized a feature-based image registration. The required control points were extracted from a pair of reference images corresponding to a neon light source and patterned white-illumination. Unfortunately, the SRF and the spatial response function (SiRF) were not assessed in this work. Most popular methods for the measurement of the optical system line spread function (LSF), closely related to the SiRF, are based on precise sub-pixel shifting of the calibration object [11, 12]. While this method is straightforward and accurate, it requires a precise mechanical actuator. Latter can pose a problem either when it is necessary to characterize an optical assembly prior to integration into the final setup or when scanning is performed on a system lacking the ability of precise positioning, e.g. conveyor belt.
In summary, the previously published methods either do not consider the complete spatial-spectral dependence of the HIS or require complex measurement setups, which render them impractical. To alleviate this problem, we propose a novel method based on modeling of the HIS response to a scene exhibiting well-defined spectral and spatial features. For a reliable and unambiguous modeling, spatial and spectral features were retrieved by acquisition and analysis of images corresponding to different spectral reference lamps and a spatial reference object. The proposed method requires a relatively simple measurement setup and does not depend on any special equipment.
Let represent the true object defined in object coordinates (θ, λ), where θ is a spatial position and λ a wavelength. Firstly, the geometric properties of the HIS are captured by mapping the true object into the image space by a forward tuning function. Secondly, presence of the blur is modeled by convolving the transformed object and the PSF of the HIS. Assuming the 2D PSF is separable it can be broken into a pair of 1D line spread functions, namely the spectral response function (SRF) and the spatial response function (SiRF). SRF and SiRF functions take into account the properties of the entire HIS, i.e. the lens, spectrograph and camera. Therefore, the acquired image I(u,w) of size U × W pixels can be estimated within error ε as:Fig. 1, where each contains information varying either in the direction of the SRF or the SiRF, Eq. (1) can be expressed as a system of two equations, each describing the spatial or the spectral direction:
The image (SA) of the spectral reference object (gS) provides a good definition of the properties in the spectral direction and is vastly insensitive to the distortions in the spatial direction, while the opposite holds true for the image (SiA) of the spatial reference object (gSi). In general, the SRF and SiRF are aligned with the spatial and the spectral axis of the spectrograph and not necessarily with the columns and rows of the acquired image. However, to lower the computational complexity of the proposed method, the alignment of the spatial and spectral axes between the spectrograph and the camera is assumed. The assumption holds if the initial geometric coregistration errors are small, which is realistic, since the proposed method is used after the proper adjustments are made by other, sufficiently accurate procedures . Furthermore, the SRF and SiRF are position variant. Therefore, the Eq. (2) and Eq. (3) should be directly computed only for small regions, where the local invariance can be adopted.
The first goal of the characterization is the assessment of the forward (υ,ω) = (TS(θ,λ),TSi(θ,λ)) and of the corresponding inverse tuning function (θ,λ) = (ZS(υ,ω),ZSi(υ,ω)). The first is used to estimate the image of a given object, while the second is required for a physically meaningful interpretation of the acquired image. The tuning functions are determined by establishing a correspondence between the features in the object space and the corresponding positions in the acquired image. For this purpose, the feature locations have to be extracted from the acquired image. Furthermore, the quality of HIS is also defined by its resolution, therefore the position dependent response functions SRF(υ,ω) and SiRF(υ,ω) are also determined. With respect to the HIS properties and technological limitations of the reference object design, solving the two equations, namely Eq. (2) and Eq. (3), requires a different approach.
2.1 Spectral feature extraction and SRF characterization
Since the atomic emission spectral lines are significantly narrower than the width of the instrument’s SRF, these can be considered as shifted Dirac delta functions. Assuming locally invariant SRF and considering the delayed delta function shifting role with respect to the convolution, the measured response to a single spectral line is a good approximation of the SRF. In the majority of publications SRF is modeled as a Gaussian function. However, for the studied HIS, such model exhibited poor fit of the acquired data. Significantly better results were produced using the symmetric normalized Voigt profile V(ω-w0;γL,γG), defined as a convolution of the centered Gaussian and Lorentzian broadening functions. Therefore, spectral response of the HIS to a single spectral line, centered at a position w0 = TS(θ,λ0), is completely defined by two spectrally and spatially variant SRF parameters (γL,γG). Using a fast approximation formula proposed in  this model retains global parameterization and reasonable computational efficiency.
Coverage of the utilized spectral range by a single spectral reference source is limited. Therefore, separate spectra of L different sources, each contributing Jl unique spectral lines, were simultaneously modeled. A given j-th spectral line in the spectrum of l-th reference lamp is defined by its wavelength λ0,l,j and intensity. By modeling the spectral line with delta function, transforming it by forward spectral tuning function, and modeling intensity αl,j, the Ts(gS(θ,λ)) in Eq. (2) is substituted by αl,j∙δu(ω-w0,l,j,u). Using the Voigt profile as a SRF model in Eq. (2), and taking into account the convolution rule of SRF and shifted delta function, the modeled spectrum SM,l,u of the l-th reference lamp corresponding to a spatial channel u of SA,l can be written as a sum of responses to the individual spectral lines, i.e. shifted Voigt profiles αl,j∙V(ω-w0,l,j,u,γG(u,w0,l,j,u),γL(u,w0,l,j,u)). Approximating the integral in Eq. (2) over a rectangular area of size δu × δw by the rectangle rule , and adding a polynomial model of the baseline shift, the final spectrum model can be written as:15] based on the Fischer’s definition of the correlation coefficient between two arrays containing the intensity values of the modeled sM(w) = SM,l,u(w) and the acquired sA(w) = SA,l,u(w) spectra in arbitrary spatial channel u can be written as
The three utilized spectral reference lamps (L = 3) shown in Fig. 2 provided 55 useful spectral lines. The most informative spectral range and the corresponding spectral lines were identified for each lamp. Three mercury lines of the Hg(Ar) lamp in the range from 527 nm to 588 nm were used and the Ne-lamp provided further 28 spectral lines in the range from 565 nm to 772 nm. Since the Hg(Ar) lamp exhibited a large intensity contrast between the argon and the mercury spectral lines, the additional Ar lamp was utilized in the range from 732 nm to 990 nm, providing 24 spectral lines. The accurate wavelengths of all the spectral lines were taken from the NIST spectral database .
Computation of the optimal parameters was performed by a nested approach. Parameters defining the properties of the HIS (bG, bL, bS) were optimized by outer Broyden-Fletcher-Goldfarb-Shanno (BFGS)  nonlinear optimization method. This gradient-based iterative quasi-Newton method exhibits quadratic convergence and employs the observed behavior of the dissimilarity χS and its gradient for construction of the Hessian matrix approximation and step size selection. In each BFGS iteration the optimal auxiliary parameters αl,j and βl,k,u, capturing the unknown experimental variations (HIS independent), were computed by the constrained linear least-squares imposing the non-negativity of the spectral line intensities. Initial approximation of bS were computed by a linear fit between the real and the acquired positions of the distinct spectral peaks (Hg:546.10 nm, Ne:671.70 nm, Ar:763.51 nm, 965.78 nm). While the initial SRF parameters bG and bL were set to values fitting a single Ar peak at the central part of the acquired image (Ar:763.51 nm). Prior to optimization the parameters were scaled to improve convergence and aid the proper selection of stopping criterion. Furthermore, convergence to local minima was prevented by iteratively increasing the number of breaks employed by the subsequent runs of the optimization. The number of breaks KB and KG act as regularization parameters. For values less than four the model exhibited underfitting. Between five and seven the optimization problem was properly regularized and best results were achieved. Further increasing the number of breaks led to overfitting. Since the computation time increases with the number of breaks, both KB and KG were set to five. Optimal parameters for a single spectrum were computed in approximately 11 s on a current generation personal computer.
The elements of the weight arrays µl(w), corresponding to the lamp specific informative spectral range were set to unit and left zero otherwise. In the HIS under study, the baseline shift was mainly contributed by the thermal drift of the camera sensor. The approximate shape of the baseline was assessed by recording an image of white reference material illuminated by a halogen broadband light and a series of images corresponding to the camera dark current. The frequency at which the dark frames were captured was low enough that the camera drift was measurable. For each frame a difference between the corresponding dark frame and the first dark frame in the series was computed. This difference was further divided by the difference between the white frame and the first dark frame in the series. The resulting series of images represented the time-lapse of baseline drift for each spatial channel. By fitting each baseline in the series it was determined that a baseline can be approximated by second order polynomial. Since the weights were nonzero only within narrow spectral bands, baseline was locally modeled by a first order polynomial (K = 1).
2.2 Spatial feature extraction and nonparametric SiRF characterization
The spatial reference object can be designed to suit the task at hand and, unlike the spectral lines, the modeled features can be well separated. Due to the manufacturing limitations the delta function approximation of these features is hard to achieve in an affordable reference object. Furthermore, in contrast to the SRF characterization, modeling the spatial resolution is significantly more demanding due to the SiRF complexity. However, reliable and computationally straightforward results were obtained by using a series of black-to-white step edges. Each spatial profile of the acquired spatial reference image at a given spectral channel w, may be interpreted as a sequence of blurred edges of alternating orientations. The model of the single edge with transition located at the image position u0 is written as a Heaviside step function H(υ-u0) modulated by a multiplicative cM and an additive term cA, arising from uneven illumination, temperature drift of the sensor and the reflected light. Therefore, in Eq. (3), the term TSi(gSi(θ,λ)) is substituted by the edge model at the wavelength λEq. (10) has to be integrated over the rectangular area of size δu × δw. Using the rectangle rule of integral approximation and taking into account the wavelength invariant intensity, the acquired profile of a single e-th edge of the spectral channel w can be modeled within error εSi as:
Since the SiRF model is nonparametric it was, under the approximation of local invariance, fitted to a number NR of small (2∙∆uR + 1) × (2∙∆wR + 1) sized image regions Rr centered at (uR,r,wR,r). A region and corresponding variables are shown in Fig. 3. The two keys for selecting the region denoted by index r were capturing the information relevant to the convolution of the SiRF and keeping the edge er, approximately in the center of the region. The spatial region size ∆uR was chosen to be the rounded half of the average distance between two adjacent edge approximations:Eq. (11), the optimal parameters defining SiRF and edge positions were assessed by minimizing the sum of squared fit errors:
The optimization of the main parameters (u0,r, ρr, σr, µG r) was performed by a nonlinear constrained sequential quadratic programming (SQP)  algorithm, while the auxiliary parameters cM,r and cA,r were computed by a pseudo-inverse. At each iteration of the SQP method an approximation of the Hessian of the Lagrangian function is made using the BFGS update method. Step direction is determined by a quadratic programing solution of a subproblem, which is formed using the approximated Hessian of the Lagrangian. The step size is determined by a line search procedure. The smoothness of SiRF was implicitly enforced by setting M = 3 and imposing the lower limit of the parameters σm,r>0.5. The optimization problem was further constrained by solving the Eq. (12) and limiting the weights to nonnegative values (ρm,r≥0). Initial values of the edge positions were set to match the corresponding region centers u0,r = uR,r. while the parameters σm,r, ρm,r and υm,r were determined by fitting the given edge with simplified Gaussian SiRF model. According to the earlier described region size selection criterion, ∆wR and ∆uR were set to 16 and 2, respectively. Optimal parameters for a single region were computed in approximately 0.9 s.
2.3 Global modeling of the computed parameters
The parameters were actually computed only on a mesh of points formed by spectral lines and spatial edges. Therefore, the final step of the characterization is regularization and computation of global tuning function and interpolation functions for the SRF and the SiRF. Starting with the spectral direction, the first step is the definition of features in the image space. This is accomplished by inserting values of the optimized parameters into the constraint equation for each spatial channel, resulting in a 2D grid of points (u,w0,l,j,u). By assigning the values of the target properties to each point of the grid, three sets of data are formed: one for the spectral tuning function λ(u, w0,l,j,u), and two for the SRF shape parameters γG(u,w0,l,j,u) and γL(u,w0,l,j,u). By fitting 2D polynomial surfaces to each of the data sets, the interpolation functions (ΓG, ΓL) and the inverse spectral tuning function ZS were computed:
Similar grid was assembled for the image of the spatial reference object by combining the edge positions and their corresponding region centers. Using the true edge positions (θ0,e) the correspondence pairs θ0,e(u0,r, wR,r) were formed and the inverse spatial tuning function ZSi was obtained by a procedure analogous to the computation of the ZS:
2.4 Hyperspectral imaging system and experimental setup
Calibration and validation images were acquired by a hyperspectral imaging system, shown in Fig. 4(a), consisting of a near infrared enhanced MV1-D1312(l)-160-CL-12 camera (Photonfocus) with 1312 × 1082 light sensitive pixels, an ImSpector V10E (from 400 nm to 1000 nm) spectrograph (Specim Ltd, Finland), and S23-f/2.4 lens (Specim Ltd, Finland). The broadband illumination source comprised a research QTH lamp housing (Newport, Oriel Instruments – model: 66881), and a radiometric power supply (Newport, Oriel Instruments – model: 69931). The spectral reference and validation images were recordings of the Hg(Ar), Ar, Ne, and Kr pen spectral reference lamps (Newport, Oriel instruments) models: 6035, 6030, 6032, 6031 respectively. Since a significant portion of the energy emitted by these lamps is in a form of ultraviolet light, optical 525 nm long-pass filter (Edmund Optics, model: NT64-634) was used to attenuate higher energy radiation, preventing hazards and unwanted effects of the light induced fluorescence of organic contaminants (mainly cellulose dust particles). The modulated light was dispersed by a tilted solid thermoplastic diffuse reflectance standard (T, Spectralon, Labsphere) and a thin diffuser (D) placed on the imaging plane. Despite the modeling of the multiplicative and additive effects in Eq. (4), care was taken to ensure a reasonably homogeneous illumination to satisfy the premise of minimal spatial variation of the spectral reference images. By replacing filtered gas emission lamps with broadband light source, and placing the spatial reference object on the imaging plane the system was prepared for the acquisition of the spatial reference image. The employed spatial reference object was a custom laser-machined 150 µm thick stainless-steel mask, shown in Fig. 4(b), with overall manufacturing accuracy of ± 8 µm. Prior to modeling or analysis all the acquired images were corrected by point-to-point subtraction of the dark image and division by the difference between the bright and the dark image. With regards to the position dependent signal-to-noise ratio, the spectral axis was cropped to the spectral range from 527 nm to 980 nm (W = 581 pixel). Likewise, due to the design of the studied HIS, the spatial image dimension was cropped to cover approximately 155 mm wide range (U = 1000 pixel).
3. Results and validation of the proposed characterization method
In a perfect HIS we expect that spectra at different spatial channels are mutually aligned and relation between the image spectral positions ω and their corresponding wavelengths λ can be described by a first order polynomial model λ = zS,1∙ω + zS,0 + ES. In such case, the only contribution to the fit error would be the spatially and spectrally independent noise ES. However, due to the coregistration errors, the first order polynomial model has to be expanded by a term that includes spectral and spatial dependence of the inverse tuning function: λ = zS,1∙ω + zS,0 + ES + δZS(υ,ω). The parameters zS,1 and zS,0 were assessed by a first order polynomial fit between the true wavelengths of the spectral lines λ0,l,j and their corresponding locations w0,l,j,u in all spatial channels of the acquired image (zS,1 = 0.8004, zS,0 = 524.3097). Example of the estimated spectral line positions is shown in Figs. 5(a) and 5(b). The position dependent residual δZS(υ,ω) is shown in Fig. 5(c). Likewise, the relation between true spatial position θ and the corresponding spatial position in the acquired image υ can be written as θ = zSi,1∙υ + zSi,0 + E0 + δZSi(υ,ω). The parameters zSi,1 and zSi,0 were assessed by a first order polynomial fit between the true edge positions θ0,e and their corresponding locations u0,r in all regions Rr of the acquired image (zSi,1 = 0.1525, zSi,0 = 0.6108). Distribution of the extracted edge positions and the residual δZSi, are presented in Figs. 5(d)-5(f).
The SRF, shown in Fig. 6, exhibits a significant variation with wavelength, starting as a Gaussian at short wavelengths and becoming increasingly influenced by the Lorentzian broadening at the near infrared (NIR). The maximum spectral half width at half maximum (HWHM) of the SRF was 2.17 nm assuming an average dispersion of:0.8 nm/pixel. Spatial resolution is the highest in the central part of the image. While the SiRF, depicted in Fig. 7, shows some variance with spatial position, the main variability is with respect to the wavelength. With increasing deviation towards shorter wavelengths, the complex structure and asymmetry of the SiRF becomes evident, while in the opposite direction the symmetry of the SiRF improves, but the resolution is lower. Both can be observed in Fig. 8.
Accuracy of the characterization method was assessed by analyzing the validation image of Kr spectral reference source. Firstly, the forward tuning function and the SRF model were validated by predicting the acquired validation image, shown in Fig. 9(a), by the computed characterization model. Secondly, the positions of four well resolved spectral lines in the acquired validation image were extracted by fitting the SRF model to the acquired intensity profiles of the emission lines. The extracted positions wV,j,u of j-th spectral line at spatial channel u were then transformed into corresponding wavelengths λV,j,u by the inverse tuning function. The wavelength prediction error was calculated as δλV,j,u = λV,j,u-λV,0,j, where λV,0,j are the true wavelengths of the spectral lines. For comparison, additional spectral calibration was performed according to the method proposed by Polder et.al . The spectral line pixel positions were extracted from each spatial channel of the acquired Hg(Ar) reference lamp image. The relation between pixel locations and the true wavelengths was modeled by a third order polynomial fit. For the purpose of validation, the extracted pixel positions of the four well resolved Kr spectral lines were transformed by the calculated polynomial fit and compared to the corresponding true wavelengths. The prediction error statistics of the two methods for each of the four selected Kr spectral lines is presented in Table 1.
Likewise, the spatial validation image shown in Fig. 9(b), was produced by imaging the reference object displaced by a known shift. Quantitative assessment was made by finding the image-wise edge positions and calculating their expected locations in the object space. Analogically to the spectral direction, the 30 equally distributed edges covering the entire spatial region were located by locally fitting the modeled edge response to each of the 581 spectral channels resulting in a total of 17430 validation points. The residual misalignments, shown in Fig. 10, were computed as a difference between the expected and the true edge positions in the object space. The mean residual misalignment for all the validation points was 0.001 mm, with the standard deviation of 0.005 mm. Speaking in pixel-size terms, the mean error was 0.007 pixel and the standard deviation was 0.05 pixel. The validation shows that the expected error was in the range of 1/10 of a pixel, which is comparable to the spatial reference object uncertainty specified by the manufacturer.
The computed forward tuning function can be used for calibration of the acquired image by means of geometric image transform . First, a pixel grid (θq, λq) is formed in the object space. Each pixel q is then transformed by the forward tuning function into the acquired image space (υq,ωq) = (TS(θq, λq), TSi(θq, λq)). Finally, the intensities of the object space image are computed by bicubic interpolation. Results of the validation image calibration are displayed in Fig. 11.
Prior work has demonstrated the significant impact of the errors arising from poor uniformity of the acquired images on the accuracy of the subsequent hyperspectral image analysis. Various methods were proposed for the assessment and/or correction of the effects arising from the operation principle of the spectrograph based hyperspectral imaging system. However, the majority of these methods require equipment often not present on the application site or the characterization is based on a small number of image locations, effectively ignoring the spectral-spatial dependency. Moreover, many of the spectral lines emitted by the standard reference sources are unresolvable by the moderate spectral resolution of the imaging spectrographs. Consequently, the simple estimation of the spectral line position by its center of gravity is inaccurate. This significantly limits the number of well resolved spectral lines useful for the calibration, and thereby the degree of modeling, and consequently the accuracy of the fitting. We have alleviated this problem by using spectral matching method, which allowed taking into account all the significant spectral lines in the observed range and the spectral resolution of the device. Furthermore, a simple visual inspection suggested asymmetry of the spatial response function (SiRF). This was an important finding, as the edges extracted by the popular gradient based edge detection algorithms would be inevitably biased. Therefore, we proposed an extension of the SiRF model allowing greater flexibility. The results of the proposed characterization method can be used for calibration of the acquired images and/or as a tool for quantization of the expected errors in various hyperspectral imaging techniques. Furthermore, we expect, the proposed characterization of the SRF and SiRF can be used in future work for development of hyperspectral image restoration methods based on previously published work on hyperspectral image deconvolution [20, 21].
This work was supported by the Slovenian Research Agency (ARRS) under grants L2-4072, J7-2246 and L2-2023, by Sensum, Computer Vision Systems, and by the European Union, European Social Fund.
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