Arun K. Gupta

Functional markers based molecular characterization and cloning of resistance gene analogs encoding NBS-LRR disease resistance proteins in finger millet (Eleusine coracana)

Magnaporthe grisea, the blast fungus is one of the main pathological threats to finger millet crop worldwide. A systematic search for the blast resistance gene analogs was carried out, using functional molecular markers. Three-fourths of the recognition-dependent disease resistance genes (R-genes) identified in plants encodes nucleotide binding site (NBS) leucine-rich repeat (LRR) proteins. NBS-LRR homologs have only been isolated on a limited scale from Eleusine coracana. Genomic DNA sequences sharing homology with NBS region of resistance gene analogs were isolated and characterized from resistant genotypes of finger millet using PCR based approach with primers designed from conserved regions of NBS domain. Attempts were made to identify molecular markers linked to the resistance gene and to differentiate the resistant bulk from the susceptible bulk. A total of 9 NBS-LRR and 11 EST-SSR markers generated 75.6 and 73.5% polymorphism respectively amongst 73 finger millet genotypes. NBS-5, NBS-9, NBS-3 and EST-SSR-04 markers showed a clear polymorphism which differentiated resistant genotypes from susceptible genotypes. By comparing the banding pattern of different resistant and susceptible genotypes, five DNA amplifications of NBS and EST-SSR primers (NBS-05504, NBS-09711, NBS-07688, NBS-03509 and EST-SSR-04241) were identified as markers for the blast resistance in resistant genotypes. Principal coordinate plot and UPGMA analysis formed similar groups of the genotypes and placed most of the resistant genotypes together showing a high level of genetic relatedness and the susceptible genotypes were placed in different groups on the basis of differential disease score. Our results provided a clue for the cloning of finger millet blast resistance gene analogs which not only facilitate the process of plant breeding but also molecular characterization of blast resistance gene analogs from Eleusine coracana.

Wavelet-modified maximum average correlation height filter for rotation invariance that uses chirp encoding in a hybrid digital-optical correlator

We discuss and implement a wavelet-modified maximum average correlation height (MACH) filter for 0 degrees -360 degrees in-plane rotations in a hybrid digital-optical correlator. Use of a wavelet transform improves the performance of the MACH filter by reducing the number of filters that are required to identify a target rotated at any angle between 0 degrees and 360 degrees in-plane rotations and enhances the autocorrelation peak intensity significantly. The output of a hybrid digital-optical correlator contains two autocorrelation peaks and a strong dc. Using a chirp function with the wavelet-modified MACH filter, the correlation signals are focused in three different planes. Thus placing a peak-capturing CCD camera at a particular plane, only one autocorrelation peak is recorded, discarding the strong dc and other autocorrelation peaks. A signal-to-noise ratio has been calculated as a metric of goodness of the proposed wavelet-modified MACH filter.

Differential modal Zernike wavefront sensor employing a computer-generated hologram: a proposal

The process of Zernike mode detection with a Shack-Hartmann wavefront sensor is computationally extensive. A holographic modal wavefront sensor has therefore evolved to process the data optically by use of the concept of equal and opposite phase bias. Recently, a multiplexed computer-generated hologram (CGH) technique was developed in which the output is in the form of bright dots that specify the presence and strength of a specific Zernike mode. We propose a wavefront sensor using the concept of phase biasing in the latter technique such that the output is a pair of bright dots for each mode to be sensed. A normalized difference signal between the intensities of the two dots is proportional to the amplitude of the sensed Zernike mode. In our method the number of holograms to be multiplexed is decreased, thereby reducing the modal cross talk significantly. We validated the proposed method through simulation studies for several cases. The simulation results demonstrate simultaneous wavefront detection of lower-order Zernike modes with a resolution better than lambda/50 for the wide measurement range of +/-3.5lambda with much reduced cross talk at high speed.

Binary differential joint-transform correlator based on a ferroelectric-liquid-crystal electrically addressed spatial light modulator

We implement a binary differential joint-transform correlator for real-time single- and multiple-target recognition applications. In a real-time situation the input scene is captured using a CCD or thermal camera. The obtained joint power spectrum is first differentiated and then binarized. The subset median threshold method was used to get the threshold value for binarization. The binarized joint power spectrum is displayed over a ferroelectric-liquid-crystal spatial light modulator and is Fourier-transformed optically to obtain the correlation peaks. Differential processing of the joint power spectrum removes the zero-order spectra (dc) and hence improves the detection efficiency. Experiments taking single as well as multiple input images have been performed. The parameters for a performance measure have also been calculated. Single and multiple targets with added Gaussian noise have also been used to check the correlation outputs. Computer simulation and experimental results are presented.

Log-polar transform-based wavelet-modified maximum average correlation height filter for distortion invariance in a hybrid digital-optical correlator

We discuss and implement a log-polar transform-based distortion-invariant filter for automatic target recognition applications. The log-polar transform is a known space-invariant image representation used in several image vision systems to eliminate the effects of scale and rotation in an image. For in-plane rotation invariance and scale invariance, a log-polar transform-based filter was synthesized. In cases of in-plane rotation invariance, peaks shift horizontally, and in cases of scale invariance, peaks shift vertically. To achieve out-of-plane rotation invariance, log-polar images were used to train the wavelet-modified maximum average correlation height (WaveMACH) filter. The designed filters were implemented in the hybrid digital-optical correlation scheme. It was observed that, for a certain range of rotation and scale differences, the correlation signals merge with the strong dc. To solve this problem a shift was introduced in the log-polar image of the target. The use of a chirp function for dc removal has also been discussed. Correlation peak height and peak-to-sidelobe ratio have been calculated as metrics of goodness of the log-polar transform-based WaveMACH filter. Experimental results are presented.

Hybrid digital-optical correlation employing a chirp-encoded simulated-annealing-based rotation-invariant and distortion-tolerant filter

The simulated annealing (SA) algorithm based on entropy optimization is a technique of synthesizing distortion-invariant matched filters capable of discriminating very similar images. The synthesis of rotation-invariant filters using modified SA-based filter equations and their tolerance to distortions are studied. The filters are trained with true class images rotated in-plane at 3 degrees intervals between 0 degrees and 360 degrees . A total of seven filters are required over the whole range for both CCD or thermal images. Optical correlation in a hybrid digital-optical correlator results in an unwanted zero-order dc along with two first-order (+/-1) correlation peaks. A chirp function multiplied with the filter separates out the three peaks to three different planes, and only one peak in focus is captured in a camera. The performance of the modified SA-based filter has been studied in comparison to the conventional SA filter as well as with other filters.

Propagation of optical vortices embedded with multiple wavefront singularities

Optical vortices with the embedded wavefront singularities have attracted intensive attentions in many branches of modern physics, due to their important applications in optical tweezers, quantum entangles, optical testing, atmospheric propagations, etc. In this paper, optical vortices are generated by new types of custom designed wavefronts and their propagation in free-space is reported. Huygens–Fresnel diffraction integral is directly solved using the Gauss–Legendre quadrature method to estimate the diffraction pattern at some arbitrary plane. The variation of vorticity is demonstrated under diffraction. Evolution of phase singularities in wavefronts as the wavefront propagate is predicted for various near field distances. Simulations reveal that the exchange of the nature of topological charge occurs at a finite distance. Experimentally, the wavefronts have been generated using the phase-only spatial light modulator and their far-field diffraction patterns are recorded. The experimental result has been validated with the numerical simulation.

An ocular wavefront sensor based on binary phase element: design and analysis

A modal wavefront sensor for ocular aberrations exhibits two main advantages compared to a conventional Shack–Hartmann sensor. As the wavefront is detected in the Fourier plane, the method is robust against local loss of information (e.g. local opacity of ocular lens as in the case of cataract), and is not dependent on the spatial distribution of wavefront sampling. We have proposed a novel method of wavefront sensing for ocular aberrations that directly detects the strengths of Zernike aberrations. A multiplexed Fourier computer-generated hologram has been designed as the binary phase element (BPE) for the detection of second-order and higher-order ocular aberrations (HOAs). The BPE design has been validated by comparing the simulated far-field pattern with the experimental results obtained by displaying it on a spatial light modulator. Simulation results have demonstrated the simultaneous wavefront detection with an accuracy better that ∼λ/30 for a measurement range of ±2.1λ with reduced cross-talk. Sensor performance is validated by performing a numerical experiment using the City data set for test waves containing second-order and HOAs and measurement errors of 0.065 µm peak-to-valley (PV) and 0.08 µm (PV) have been obtained, respectively.

A hybrid digital-optical correlator for automatic target recognition

Detection of rotationally distorted targets is a challenging task in pattern recognition applications. Recently, we proposed and implemented a wavelet-modified maximum average correlation height (MACH) filter for in-plane and out-of-plane rotation invariance in hybrid digital-optical correlator architecture. Use of wavelet transform improved the performance of the MACH filter by reducing the number of filters required for identifying a rotated target and enhancing the correlation peak intensity significantly. The output of a hybrid digital-optical correlator contains two autocorrelation peaks and a strong dc. To capture a desired single autocorrelation peak a chirp function with the wavelet-modified MACH filter was used. The influence of perturbations in hybrid digital-optical correlator has also been studied. Perturbations include, the effect of occlusion on input target, the effect of additive and multiplicative noise and their combined effect on input target, and the effect of occlusion of product function to be optically processed for obtaining the correlation outputs. The present paper reviews investigations on the hybrid digital-optical correlation scheme with special reference to the work carried out at the Photonics Division, IRDE Dehradun.

Nonlinear Optical Characterization of Borotellurite Glass of Composition 0.1BaO-0.4TeO2-0.5B2O3 by Z-Scan Method

Present work focuses on the study of nonlinear optical properties of borotellurite glass of composition 0.1BaO-0.4TeO2-0.5B2O3. Third order optical nonlinear coefficients of borotellurite glass have been investigated by using the standard z-scan method using 100 femtosecond Ti: sapphire laser at 1550 nm wavelength with repetition rate of 1 kHz. Nonlinear refractive index n2 was estimated to be 2.59 × 10−17 cm2/W. Nonlinear absorption coefficient β was found to be 0.3189 × 10−12 cm/W. Nonlinear susceptibility χ(3) has been calculated to be ~1.8329 × 10−14 esu.