Publications
See a list of publications below or visit the Photonics academic staff page and click on a particular member of staff to access their personal web page, which includes a list of their own publications.
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Journal articleMurray RT, Runcorn TH, Guha S, et al., 2017,
High average power parametric wavelength conversion at 3.31–3.48 μm in MgO:PPLN
, Optics Express, Vol: 25, Pages: 6421-6430, ISSN: 1094-4087We present results of high average power mid-infrared (mid-IR) generation employingsynchronized nanosecond pulsed ytterbium and erbium fiber amplifier systems using periodicallypoled lithium niobate. We generate greater than 6 W of mid-IR radiation tunable in wavelengthbetween 3.31–3.48μm, at power conversion efficiencies exceeding 75%, with near diffractionlimited beam quality (M2= 1.4). Numerical modeling is used to verify the experimental resultsin differing pump depletion regimes.
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Journal articleWoodward RI, Murray RT, Phelan CF, et al., 2017,
Characterization of the second- and third-order nonlinear optical susceptibilities of monolayer MoS2 using multiphoton microscopy
, 2D Materials, Vol: 4, ISSN: 2053-1583We report second- and third-harmonic generation in monolayer MoS2 as a tool for imaging and accurately characterizing the material's nonlinear optical properties under 1560 nm excitation. Using a surface nonlinear optics treatment, we derive expressions relating experimental measurements to second- and third-order nonlinear sheet susceptibility magnitudes, obtaining values of $| {\chi }_{{\rm{s}}}^{(2)}| \ =2.0\times {10}^{-20}$ m2 V−1 and, for the first time for monolayer MoS2, $| {\chi }_{{\rm{s}}}^{(3)}| =1.7\times {10}^{-28}$ m3 V−2. These sheet susceptibilities correspond to effective bulk nonlinear susceptibility values of $| {\chi }_{{\rm{b}}}^{(2)}| =2.9\ \times {10}^{-11}$ m V−1 and $| {\chi }_{{\rm{b}}}^{(3)}| =2.4\times {10}^{-19}$ m2 V−2, accounting for the sheet thickness. Experimental comparisons between MoS2 and graphene are also performed, demonstrating ~3.4 times stronger third-order sheet nonlinearity in monolayer MoS2, highlighting the material's potential for nonlinear photonics in the telecommunications C band.
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Journal articleChakraborty BK, Bhuyan MK, Kumar S, 2017,
Combining image and global pixel distribution model for skin colour segmentation
, Pattern Recognition Letters, Vol: 88, Pages: 33-40, ISSN: 0167-8655Skin colour detection in unconstrained and natural environment is a critical research problem. Skin regions show slightly different chrominance properties for different ambient conditions. Accuracy of detection is mostly affected either due to background colour similarity with the skin and/or poor illumination condition. To address this specific issue, a novel skin detection method is proposed by utilizing the information of pixel distribution in an image for a particular colour space. In our method, a local skin distribution model (LSDM) is derived from the image pixel distribution model using pixels from the facial region as reference. Finally, a combined skin distribution model is obtained by fusing the LSDM with the global skin colour distribution model. Subsequently, a dynamic region growing (DRG) method is proposed to allow the skin regions to grow dynamically. Our proposed DRG minimizes the overall detection error. Experimental results show that proposed skin detection method can more accurately segment out the skin-coloured regions. We obtained total detection error of 12.87% for a standard database. This improvement is due to the fact that both local and global skin colour information are used for skin segmentation.
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Journal articleBotiz I, Codescu M-A, Farcau C, et al., 2017,
Convective self-assembly of pi-conjugated oligomers and polymers
, JOURNAL OF MATERIALS CHEMISTRY C, Vol: 5, Pages: 2513-2518, ISSN: 2050-7526 -
Journal articleVan de Pette M, Abbas A, Feytout A, et al., 2017,
Visualizing changes in Cdkn1c expression links early life adversity to imprint mis-regulation in adults
, Cell Reports, Vol: 31, Pages: 1090-1099, ISSN: 2211-1247Imprinted genes are regulated according to parental origin and can influence embryonic growth and metabolism and confer disease susceptibility.Here we designed sensitive allele-specific reporters to non-invasively monitor imprinted Cdkn1cexpression in mice and showed that expression was modulated by environmental factors encounteredin utero.Acute exposure to chromatin modifyingdrugs resulted in de-repression of paternally inherited (silent) Cdkn1calleles in embryos that was temporary and resolved after birth.In contrast, deprivation of maternal dietary proteinin uteroprovoked permanent de-repression of imprinted Cdkn1cexpression that was sustained into adulthood and occurred through a folate-dependent mechanism of DNA methylation loss.Given the function of imprinted genes in regulating behavior and metabolic processes in adults, these results establish imprinting deregulation as a credible mechanism linking early life adversity to later-life outcomes.Furthermore,Cdkn1c-luciferasemice offer non-invasivetools to identify factors that disrupt epigenetic processes and strategies to limit their long-term impact.
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Journal articleSparks H, Gorlitz F, Kelly D, et al., 2017,
Characterisation of new gated optical image intensifiers for fluorescence lifetime imaging
, Review of Scientific Instruments, Vol: 88, ISSN: 1089-7623We report the characterisation of gated optical image intensifiers for fluorescence lifetime imaging (FLIM), evaluating the performance of several different prototypes that culminate in a new design that provides improved spatial resolution conferred by the addition of a magnetic field to reduce the lateral spread of photoelectrons on their path between the photocathode and microchannel plate, and higher signal to noise ratio conferred by longer time gates. We also present a methodology to compare thesesystems and their capabilities, including the quantitative readouts of Förster resonant energy transfer (FRET).
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Journal articleFrench PMW, Görlitz F, Kelly D, et al., 2017,
Open source high content analysis utilizing automated fluorescence lifetime imaging microscopy
, Jove-Journal of Visualized Experiments, Vol: 119, ISSN: 1940-087XWe present an open source high content analysis instrument utilizing automated fluorescence lifetime imaging (FLIM) for assaying protein interactions using Förster resonance energy transfer (FRET) based readouts of fixed or live cells in multiwell plates. This provides a means to screen for cell signaling processes read out using intramolecular FRET biosensors or intermolecular FRET of protein interactions such as oligomerization or heterodimerization, which can be used to identify binding partners. We describe herethe functionality of this automated multiwell plate FLIM instrumentation and present exemplar data from our studies of HIV Gag protein oligomerization and a time course of a FRET biosensor in live cells. A detailed description of the practical implementation is then provided with reference to a list of hardware components and a description of the open source data acquisition software written in μ Manager. The application of FLIMfit, an open source MATLAB-based client for the OMERO platform, to analyze arrays of multiwell plate FLIM data is also presented. The protocols for imaging fixed and live cells are outlined and a demonstration of an automated multiwell plate FLIM experiment using cells expressing fluorescent protein-based FRET constructs is presented. This is complemented by a walk-through of the data analysis for this specific FLIM FRET data set.
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Journal articlePerdios L, Lowe AR, Saladino G, et al., 2017,
Conformational transition of FGFR kinase activation revealed by site-specific unnatural amino acid reporter and single molecule FRET
, Scientific Reports, Vol: 7, ISSN: 2045-2322Protein kinases share significant structural similarity; however, structural features alone are insufficient to explain their diverse functions. Thus, bridging the gap between static structure and function requires a more detailed understanding of their dynamic properties. For example, kinase activation may occur via a switch-like mechanism or by shifting a dynamic equilibrium between inactive and active states. Here, we utilize a combination of FRET and molecular dynamics (MD) simulations to probe the activation mechanism of the kinase domain of Fibroblast Growth Factor Receptor (FGFR). Using genetically-encoded, site-specific incorporation of unnatural amino acids in regions essential for activation, followed by specific labeling with fluorescent moieties, we generated a novel class of FRET-based reporter to monitor conformational differences corresponding to states sampled by non phosphorylated/inactive and phosphorylated/active forms of the kinase. Single molecule FRET analysis in vitro, combined with MD simulations, shows that for FGFR kinase, there are populations of inactive and active states separated by a high free energy barrier resulting in switch-like activation. Compared to recent studies, these findings support diversity in features of kinases that impact on their activation mechanisms. The properties of these FRET-based constructs will also allow further studies of kinase dynamics as well as applications in vivo.
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Conference paperGörlitz F, Corcoran DS, Sparks H, et al., 2017,
Mapping molecular function to biological nanostructure: Combining structured illumination microscopy with fluorescence lifetime imaging
We report the enhancement of spatial resolution and sensitivity of wide-field time-gated imaging and the combination with SIM to map molecular function using FRET to biological nanostructure below the conventional diffraction limit.
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Conference paperKerridge-Johns WR, Damzen MJ, 2017,
Vortex mode generation from coupled anti-resonant ring lasers
Vortex modes with controllable handedness were generated by coupling two laser cavities through a common Nd:YVO4 gain medium inside an anti-resonant ring. This design is applicable to both isotropic and anisotropic gain media.
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Conference paperParali U, Thomas GM, Minassian A, et al., 2017,
Wavelength tunable passively Q-switched Alexandrite laser with direct diode-pumping at 635 nm
, 5th International Conference on Photonics, Optics and Laser Technology (PHOTOPTICS), Publisher: SCITEPRESS, Pages: 82-89We report on a wavelength tunable passively Q-switched Alexandrite laser directly red-diode-pumped at 635 nm. Passive Q-switching was achieved with a semiconductor saturable absorber mirror (SESAM) and wavelength tuning with a birefringent tuner. The pulse repetiton rate was variable on the pump power and wavelength and a maximum 27 kHz rate was achieved in fundamental TEM00 mode. The maximum average output power obtained was 41 mW. The Q-switched wavelength tuning band was studied between 740 nm and 755 nm. To the best of our knowledge, this is the first time that tunable TEM00 passive Q-switched operation of a diode-pumped Alexandrite laser has been achieved. The results obtained in this study can be significantly further optimised for performance. A new cavity configuration for this optimisation is described. Future work is expected to lead to the development of higher power, more efficient tunable passive Q-switched (and potentially passive mode-locked) diode-pumped Alexandrite la (More)
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Conference paperRuncorn T, Murray RT, Taylor JR, 2017,
Microjoule Nanosecond 560 nm Source by SHG of a Combined Yb-Raman Fiber Amplifier
, Pages: ATu1A-7 -
Conference paperMurray RT, Runcorn T, Guha S, et al., 2017,
Fibre MOPA Pumped MIR Parametric Wavelength Conversion
, Pages: AM2A-1 -
Book chapterCasey D, Wylie D, Neil M, 2017,
Optical techniques and microtools for subcellular delivery and sampling
, LIGHT ROBOTICS STRUCTURE-MEDIATED NANOBIOPHOTONICS, Publisher: ELSEVIER SCIENCE BV, Pages: 287-311, ISBN: 978-0-7020-7096-9 -
Conference paperKumar S, Bhuyan MK, Chakraborty BK, 2016,
Uncorrelated multiview discriminant locality preserving projection analysis for multiview facial expression recognition
Recently several multi-view learning-based methods have been proposed, and they are found to be more efficient in many real world applications. However, existing multi-view learning-based methods are not suitable for finding discriminative directions if the data is multi-modal. In such cases, Locality Preserving Projection (LPP) and/or Local Fisher Discriminant Analysis (LFDA) are found to be more appropriate to capture discriminative directions. Furthermore, existing methods show that imposing uncorrelated constraint onto the common space improves classification accuracy of the system. Hence inspired from the above findings, we propose an Uncorrelated Multi-view Discriminant Locality Preserving Projection (UMvDLPP)-based approach. The proposed method searches a common uncorrelated discriminative space for multiple observable spaces. Moreover, the proposed method can also handle the multimodal characteristic, which is inherently embedded in multi-view facial expression recognition (FER) data. Hence, the proposed method is effectively more efficient for multi-view FER problem. Experimental results show that the proposed method outperforms state-of-the-art multi-view learning-based methods.
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Conference paperChakraborty BK, Bhuyan MK, Kumar S, 2016,
Fusion-based skin detection using image distribution model
Skin colour detection under poor or varying illumination condition is a big challenge for various image processing and human-computer interaction applications. In this paper, a novel skin detection method utilizing image pixel distribution in a given colour space is proposed. The pixel distribution of an image can provide a better localization of the actual skin colour distribution of an image. Hence, a local skin distribution model (LSDM) is derived using the image pixel distribution model and its similarity with the global skin distribution model (GSDM). Finally, a fusionbased skin model is obtained using both the GSDM and the LSDM. Subsequently, a dynamic region growing method is employed to improve the overall detection rate. Experimental results show that proposed skin detection method can significantly improve the detection accuracy in presence of varying illumination conditions.
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Journal articleMcCall MW, Gratus J, Kinsler P, et al., 2016,
On spacetime transformation optics: temporal and spatial dispersion
, New Journal of Physics, Vol: 18, ISSN: 1367-2630The electromagnetic implementation of cloaking, the hiding ofobjectsfrom sight by di-verting and reassembling illuminating electromagnetic fields has now been with us ten years,while the notion of hidingeventsis now five. Both schemes as initially presented neglectedthe inevitable dispersion that arises when a designed medium replaces vacuum under trans-formation. Here we define a transformation design protocol that incorporates both spacetimetransformations and dispersive material responses in a natural and rigorous way. We showhow this methodology is applied to an event cloak designed to appear as a homogeneousand isotropic butdispersivemedium. The consequences for spacetime transformation de-sign in dispersive materials are discussed, and some parameter and bandwidth constraintsidentified.
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Journal articleThomas GM, Minassian A, Sheng X, et al., 2016,
Diode-pumped Alexandrite lasers in Q-switched and cavity-dumped Q-switched operation
, Optics Express, Vol: 24, Pages: 27212-27224, ISSN: 1094-4087We present the first study of Q-switched Alexandrite lasers under continuous-wave diode-pumping with operation up to 10 kHz repetition rates in TEM00, with spatial quality M2 1.15. With a pulsed-diode dual-end-pumped design, pulse energy is scaled to a record level of 3 mJ. We also demonstrate, for the first time, cavity-dumped Q-switching of diode-pumped Alexandrite lasers under continuous-wave and pulsed diode-pumping, up to 10 kHz. Pulse energy of 510 μJ is demonstrated with 3 ns pulse duration and 170 kW peak power, in TEM00 with M2 < 1.2. Second harmonic generation of the cavity-dumped Q-switched pulses was used to generate UV wavelength 379 nm with conversion efficiency of 47 %.
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Journal articleMaioli V, Chennell G, Sparks H, et al., 2016,
Time-lapse 3-D measurements of a glucose biosensor in multicellular spheroids by light sheet fluorescence microscopy in commercial 96-well plates
, Scientific Reports, Vol: 6, ISSN: 2045-2322Light sheet fluorescence microscopy has previously been demonstrated on a commercially available inverted fluorescence microscope frame using the method of oblique plane microscopy (OPM). In this paper, OPM is adapted to allow time-lapse 3-D imaging of 3-D biological cultures in commercially available glass-bottomed 96-well plates using a stage-scanning OPM approach (ssOPM). Time-lapse 3-D imaging of multicellular spheroids expressing a glucose Förster resonance energy transfer (FRET) biosensor is demonstrated in 16 fields of view with image acquisition at 10 minute intervals. As a proof-of-principle, the ssOPM system is also used to acquire a dose response curve with the concentration of glucose in the culture medium being varied across 42 wells of a 96-well plate with the whole acquisition taking 9 min. The 3-D image data enable the FRET ratio to be measured as a function of distance from the surface of the spheroid. Overall, the results demonstrate the capability of the OPM system to measure spatio-temporal changes in FRET ratio in 3-D in multicellular spheroids over time in a multi-well plate format.
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Journal articleKerridge-Johns WR, Damzen MJ, 2016,
Analytical model of tunable Alexandrite lasing under diode end-pumping with experimental comparison
, Journal of the Optical Society of America B, Vol: 33, Pages: 2525-2534, ISSN: 0740-3224An analytical model is formulated to support understanding and underpin experimental development of laser action in the promising diode end-pumped Alexandrite system. Closed form solutions are found for output power, threshold, and slope efficiency that for the first time incorporate the combined effects of laser ground state absorption and excited state absorption (laser ESA), along with pump excited state absorption (pump ESA), in the case of an end-pumping geometry. Comparison is made between model predictions and experimental results from a fiber-delivered diode end-pumped Alexandrite laser system, showing the impact of wavelength tuning, crystal temperature, laser output coupling, and intracavity loss. The model is broadly applicable to other quasi-three-level lasers with combined laser and pump ESA. A condition for bistable operation is also formulated.
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Journal articleCortés E, Huidobro PA, Sinclair HG, et al., 2016,
Plasmonic nanoprobes for stimulated emission depletion nanoscopy
, ACS Nano, Vol: 10, Pages: 10454-10461, ISSN: 1936-0851Plasmonic nanoparticles influence the absorption and emission processes of nearby emitters due to local enhancements of the illuminating radiation and the photonic density of states. Here, we use the plasmon resonance of metal nanoparticles in order to enhance the stimulated depletion of excited molecules for super-resolved nanoscopy. We demonstrate stimulated emission depletion (STED) nanoscopy with gold nanorods with a long axis of only 26 nm and a width of 8 nm. These particles provide an enhancement of up to 50% of the resolution compared to fluorescent-only probes without plasmonic components irradiated with the same depletion power. The nanoparticle-assisted STED probes reported here represent a ∼2 × 103 reduction in probe volume compared to previously used nanoparticles. Finally, we demonstrate their application toward plasmon-assisted STED cellular imaging at low-depletion powers, and we also discuss their current limitations.
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Journal articleChandaria VV, McGinty J, Nowlan NC, 2016,
Characterising the effects of in vitro mechanical stimulation on morphogenesis of developing limb explants
, Journal of Biomechanics, Vol: 49, Pages: 3635-3642, ISSN: 1873-2380Mechanical forces due to fetal movements play an important role in joint shape morphogenesis, and abnormalities of the joints relating to abnormal fetal movements can have long-term health implications. While mechanical stimulation during development has been shown to be important for joint shape, the relationship between the quantity of mechanical stimulation and the growth and shape change of developing cartilage has not been quantified. In this study, we culture embryonic chick limb explants in vitro in order to reveal how the magnitude of applied movement affects key aspects of the developing joint shape. We hypothesise that joint shape is affected by movement magnitude in a dose-dependent manner, and that a movement regime most representative of physiological fetal movements will promote characteristics of normal shape development. Chick hindlimbs harvested at seven days of incubation were cultured for six days, under either static conditions or one of three different dynamic movement regimes, then assessed for joint shape, cell survival and proliferation. We demonstrate that a physiological magnitude of movement in vitro promotes the most normal progression of joint morphogenesis, and that either under-stimulation or over-stimulation has detrimental effects. Providing insight into the optimal level of mechanical stimulation for cartilage growth and morphogenesis is pertinent to gaining a greater understanding of the etiology of conditions such as developmental dysplasia of the hip, and is also valuable for cartilage tissue engineering.
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Journal articleFriddin MS, Bolognesi G, Elani Y, et al., 2016,
Optically assembled droplet interface bilayer (OptiDIB) networks from cell-sized microdroplets
, Soft Matter, Vol: 12, Pages: 7731-7734, ISSN: 1744-6848We report a new platform technology to systematically assemble droplet interface bilayer (DIB) networks in user-defined 3D architectures from cell-sized droplets using optical tweezers. Our OptiDIB platform is the first demonstration of optical trapping to precisely construct 3D DIB networks, paving the way for the development of a new generation of modular bio-systems.
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Journal articleMargineanu A, Chan JJ, Kelly DJ, et al., 2016,
Corrigendum: Screening for protein-protein interactions using Förster resonance energy transfer (FRET) and fluorescence lifetime imaging microscopy (FLIM).
, Scientific Reports, Vol: 6, ISSN: 2045-2322 -
Journal articleWarren SC, Kim Y, Stone JM, et al., 2016,
Adaptive multiphoton endomicroscopy through a dynamically deformed multicore optical fiber using proximal detection
, Optics Express, Vol: 24, Pages: 21474-21484, ISSN: 1094-4087This paper demonstrates multiphoton excited fluorescenceimaging through a polarisation maintaining multicore fiber (PM-MCF)while the fiber is dynamically deformed using all-proximal detection.Single-shot proximal measurement of the relative optical path lengths of allthe cores of the PM-MCF in double pass is achieved using a Mach-Zehnderinterferometer read out by a scientific CMOS camera operating at 416 Hz.A non-linear least squares fitting procedure is then employed to determinethe deformation-induced lateral shift of the excitation spot at the distal tip ofthe PM-MCF. An experimental validation of this approach is presented thatcompares the proximally measured deformation-induced lateral shift infocal spot position to an independent distally measured ground truth. Theproximal measurement of deformation-induced shift in focal spot position isapplied to correct for deformation-induced shifts in focal spot positionduring raster-scanning multiphoton excited fluorescence imaging.
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Conference paperChakraborty BK, Bhuyan MK, Kumar S, 2016,
A Weighted Skin Probability Map for skin color segmentation
, Pages: 2133-2136Skin color segmentation is important for several image processing, and computer vision applications. But, the accuracy of a color-based skin detection method is affected by the presence of some skin-like colors in the background regions. So, probabilistic approaches are more suitable for the skin detection as compared to hard decision-based approaches. A Skin Probability Map (SPM) of an image provides the probability of a pixel belonging to skin region. It is observed that the accuracy of a SPM-based skin detection method also depend on the chosen colorspace for the SPM. In this paper, a novel Weighted Skin Probability Map (WSPM) is proposed for the skin color segmentation. The WSPM is represented as a weighted sum of the SPMs obtained from different color spaces. Experimental results based on standard databases show that replacing the single colorspace-based SPMs with the proposed WSPM can reduce the overall detection errors significantly.
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Conference paperChakraborty BK, Bhuyan MK, Kumar S, 2016,
Adaptive propagation-based skin segmentation method for color images
Segmentation of skin regions from color images has many important Computer Vision applications. But, accuracy of existing skin detection methods are severely affected by the color similarity between the background and actual skin regions. Probabilistic approaches using skin probability maps (SPMs) can solve this problem to an extent. In this paper, a novel method has been proposed which uses seeded region growing method. Region growing is implemented by an adaptive cost propagation and neighborhood analysis scheme. The initial seeds are obtained from the SPM. It is observed from the experimental results that the proposed method can perform better compared to the existing skin segmentation methods for different illumination and background conditions.
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Conference paperKumar S, Bhuyan MK, Chakraborty BK, 2016,
An efficient face model for facial expression recognition
Existing facial expression recognition (FER) algorithms aim to extract discriminative features from a face. These discriminative features can be extracted only from the informative regions of a face. In this view, several face models are proposed which are mainly intended to extract geometrical features from a face, and hence these models may not be suitable for extract discriminative texture features from a face. We proposed a novel face model based on projection analysis of a face. Our proposed projection analysis evaluates the distribution of informative regions of a face. This is done by projecting the expressive face images onto their corresponding neutral images. Hence, the proposed face model can efficiently extract distinctive texture features from a face. Additionally, the proposed face model can extract geometrical features as well. The performance of the proposed face model is evaluated on MUG datasets which shows that the proposed face model outperforms several existing face models. Also, the proposed face model can give a recognition accuracy of 97.3% which is significantly better than the performance of state-of-the-art face models.
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Journal articleKumar S, Bhuyan MK, Chakraborty BK, 2016,
Extraction of informative regions of a face for facial expression recognition
, IET Computer Vision, Vol: 10, Pages: 567-576, ISSN: 1751-9632The aim of facial expression recognition (FER) algorithms is to extract discriminative features of a face. However, discriminative features for FER can only be obtained from the informative regions of a face. Also, each of the facial subregions have different impacts on different facial expressions. Local binary pattern (LBP) based FER techniques extract texture features from all the regions of a face, and subsequently the features are stacked sequentially. This process generates the correlated features among different expressions, and hence affects the accuracy. This research moves toward addressing these issues. The authors' approach entails extracting discriminative features from the informative regions of a face. In this view, they propose an informative region extraction model, which models the importance of facial regions based on the projection of the expressive face images onto the neural face images. However, in practical scenarios, neutral images may not be available, and therefore the authors propose to estimate a common reference image using Procrustes analysis. Subsequently, weighted-projection-based LBP feature is derived from the informative regions of the face and their associated weights. This feature extraction method reduces miss-classification among different classes of expressions. Experimental results on standard datasets show the efficacy of the proposed method.
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Conference paperGore DM, French P, O'Brart D, et al., 2016,
NC-1059 peptide-assisted transepithelial riboflavin penetration in an ex-vivo rabbit corneal model
, Annual Meeting of the Association-for-Research-in-Vision-and-Ophthalmology (ARVO), Publisher: ASSOC RESEARCH VISION OPHTHALMOLOGY INC, ISSN: 0146-0404
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