Incoherent Correlation Research Articles

Streamlined boiling lysis DNA extraction for Gram-positive aquaculture pathogen Streptococcus agalactiae.

Accurate genetic analysis is essential for the detection of pathogens as it necessitates suitable DNA extraction methods tailored to specific microorganisms such as Gram-positive bacteria. This study examined several commercial and simplified DNA extraction methods for their suitability in isothermal downstream applications. Extracted DNA was assessed using spectrophotometry, electrophoresis, polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP) while its stability was inspected after five months of storage. The findings revealed variations in DNA yield, purity and integrity among the extraction methods. While extraction kits demonstrated high yield and purity, the in-house extraction techniques showed incoherent correlation between yield and purity, yet showed promise for a streamlined extraction process. The DNA acquired from all methods yielded positive amplification in PCR and LAMP. DNA extracted by kits exhibits prolonged stability than those obtained via boiling lysis. Both methods offer distinct advantages, with commercial kits providing longer stability and high-quality DNA while boiling lysis stands out for its simplicity, with shorter handling and processing periods. This study emphasizes selecting ideal extraction methods for Streptococcus agalactiae, in the prospect of aquaculture settings. In particular, successful LAMP reaction suggests that boiled extracts are feasible enough for detection, and suited for point-of-care (POC) testing where prompt detection of aquatic pathogens is often critical. Ultimately, the choice of method should be contemplated on a case-by-case basis such as the study goals, intended settings, and type of samples.

Dynamic 3D Fresnel incoherent correlation holography imaging based on single-shot mirrored phase-shifting technology.

Fresnel incoherent correlation holography (FINCH) records coaxial holograms for wide-field 3D imaging with incoherent light, but its temporal phase-shifting strategy makes dynamic imaging challenging. Here, we present a compact, portable single-shot mirrored phase-shifting (SSPMS) module that can be easily integrated into the FINCH system, achieving secondary modulation of self-interference beams to enable the simultaneous acquisition of four phase-shift holograms in a single exposure. Compared with previously reported methods that use diffraction gratings to spatially separate self-interference beams at specific angles, this module duplicates a laterally shifted mirrored beam using a simply modified Michelson interferometer, so the phase-shifting holograms obtained via this module are free from optical aberrations or higher-order diffracted light noises. The feasibility of the proposed method is experimentally demonstrated through imaging dynamic 3D grayscale scenes.

Phase recovery from Fresnel incoherent correlation holography using differential Zernike fitting.

Fresnel incoherent correlation holography (FINCH) was created to improve imaging resolution and 3D imaging capabilities using spatially incoherent illumination. The optical setup of a FINCH-based interferometer is closely related to a radial shearing interferometer, which measures the radial phase difference of an input wavefront. By using phase retrieval methodologies from lateral shearing interferometry, namely, differential Zernike fitting (DZF), we show that FINCH-based and radial shearing interferometry can be used for phase retrieval and adaptive optics (AO). In this paper, we describe the phase retrieval algorithm using least squares-based DZF and demonstrate a simple adaptive optics loop with an aberrated point spread function using wave optics simulation. We find that FINCH-based phase retrieval has the advantages of fast phase retrieval measurements, thanks to well-studied least squares-based phase reconstruction methods, improved resolution compared to the Shack-Hartmann-based wavefront sensing, and the simplified optical setup of radial shearing interferometry.

Single-pixel Fresnel incoherent correlation holography compressed imaging using a Trumpet network

Fresnel incoherent correlation holography (FINCH) can achieve high-precision and non-scanning 3D imaging. However, as a holographic imaging technology, the huge bandwidth requirements and the amount of holographic data transmitted have always been one of the important factors limiting its application. In addition, the hardware cost of pixel array-based CCD or CMOS imaging is very high under high resolution or specific wavelength conditions. Accordingly, a single-pixel Fresnel incoherent correlation holography (SP-FINCH) compressed imaging method is proposed, which replaces pixel array detector with single-pixel detector and designs a Trumpet network to achieve low-cost and high-resolution imaging. Firstly, a modified FINCH imaging system is constructed and data acquisition is carried out using a single-pixel detector. Secondly, a Trumpet network is constructed to directly map the relationship between one-dimensional sampled data and two-dimensional image in an end-to-end manner. Moreover, by comparing the reconstructed images using neural network with that using commonly used single-pixel reconstruction methods, the results indicate that the proposed SP-FINCH compressed imaging method can significantly improve the quality of image reconstruction at lower sampling rate and achieve imaging without phase-shifting operation. The proposed method has been shown to be feasible and advantageous through numerical simulations and optical experiment results.

Three-dimensional ranging system based on Fresnel incoherent correlation holography.

We proposed a three-dimensional (3D) ranging system based on Fresnel incoherent correlation holography (FINCH). Distinct from the displacement measurement based on coherent digital holography (DH), our system simultaneously achieves a 3D range measurement using incoherent illumination. The observation range is obtained by the holographic reconstruction, while the in-plane range is determined using the two-dimensional digital imaging correlation (2D-DIC) technique. Experimental results on the resolution target demonstrate precise 3D ranging determination and improved measurement accuracy.

Out-of-focus artifact removal for Fresnel incoherent correlation holography by deep learning

Fresnel incoherent correlation holography (FINCH) is a promising three-dimensional (3D) imaging method due to its incoherent illumination and inline optical configuration. However, due to information crosstalk, especially out-of-focus artifacts, the axial resolution of FINCH 3D imaging is limited, and the relationship between the artifacts and the reconstructed image is complex and nonlinear, which is difficult to obtain by traditional optical measurement methods. Here, inspired by the superiority of deep learning in nonlinear mapping over traditional physical methods, we propose and demonstrate a deep learning based out-of-focus artifact removal method for FINCH reconstruction, in which a out-of-focus segmentation convolutional neural network (CNN) is designed for obtaining accurate nonlinear relationship between the artifacts and the reconstructed image by training dataset and optimizing parameters, thereby eliminating information crosstalk in the reconstructed image. Both optical experiment and performance analysis demonstrate the effectiveness and superiority of the designed CNN in realizing out-of-focus artifacts removal. Importantly, this deep learning-based out-of-focus artifacts removal method will provide a useful strategy for realizing high quality 3D imaging of FINCH.

Fresnel incoherent compressive holography toward 3D videography via dual-channel simultaneous phase-shifting interferometry.

Fresnel incoherent correlation holography (FINCH) enables high-resolution 3D imaging of objects from several 2D holograms under incoherent light and has many attractive applications in motionless 3D fluorescence imaging. However, FINCH has difficulty implementing 3D imaging of dynamic scenes since multiple phase-shifting holograms need to be recorded for removing the bias term and twin image in the reconstructed scene, which requires the object to remain static during this progress. Here, we propose a dual-channel Fresnel noncoherent compressive holography method. First, a pair of holograms with π phase shifts obtained in a single shot are used for removing the bias term noise. Then, a physic-driven compressive sensing (CS) algorithm is used to achieve twin-image-free reconstruction. In addition, we analyze the reconstruction effect and suitability of the CS algorithm and two-step phase-shift filtering algorithm for objects with different complexities. The experimental results show that the proposed method can record hologram videos of 3D dynamic objects and scenes without sacrificing the imaging field of view or resolution. Moreover, the system refocuses images at arbitrary depth positions via computation, hence providing a new method for fast high-throughput incoherent 3D imaging.

Optimizing the temporal and spatial resolutions and light throughput of Fresnel incoherent correlation holography in the framework of coded aperture imaging

Fresnel incoherent correlation holography (FINCH) is a well-established digital holography technique for 3D imaging of objects illuminated by spatially incoherent light. FINCH has a higher lateral resolution of 1.5 times that of direct imaging systems with the same numerical aperture. However, the other imaging characteristics of FINCH, such as axial resolution, temporal resolution, light throughput, and signal-to-noise ratio (SNR), are lower than those of direct imaging systems. Different techniques were developed by researchers around the world to improve the imaging characteristics of FINCH while retaining the inherent higher lateral resolution of FINCH. However, most of the solutions developed to improve FINCH presented additional challenges. In this study, we optimized FINCH in the framework of coded aperture imaging. Two recently developed computational methods, such as transport of amplitude into phase based on the Gerchberg Saxton algorithm and Lucy–Richardson–Rosen algorithm, were applied to improve light throughput and image reconstruction, respectively. The above implementation improved the axial resolution, temporal resolution, and SNR of FINCH and moved them closer to those of direct imaging while retaining the high lateral resolution. A point spread function (PSF) engineering technique has been implemented to prevent the low lateral resolution problem associated with the PSF recorded using pinholes with a large diameter. We believe that the above developments are beyond the state-of-the-art of existing FINCH-scopes.

Single-pixel Fresnel incoherent correlation holography for 3D imaging

Fresnel incoherent correlation holography (FINCH) is an incoherent, non-scanning, and high-precision 3D imaging technique, but its area imaging characteristics limit the application of FINCH to some extent. Accordingly, we developed a single-pixel imaging method based on FINCH to realize 3D imaging. We utilized spatial light modulators (SLM) and loaded a measurement matrix on a digital micromirror array (DMD), thereby achieving phase modulation and compressed encoding simultaneously; one-dimensional data acquisition was achieved using a single-pixel camera. Finally, we combined the single-pixel reconstruction and phase-shifting algorithm to achieve incoherent correlation holography imaging with subsampling. The experimental results demonstrated that the proposed method could achieve comparable quality results at a sampling rate of 20 % compared to a 100 % sampling rate, and the method had good noise immunity. This not only avoided the limitations of area array sensors but also enabled high-fidelity imaging with a small data volume, which broadened the scope of research on the application of FINCH in the field of 3D imaging.

Edge enhancement in three-dimensional vortex imaging based on FINCH by Bessel-like spiral phase modulation.

Edge enhancement, as an important part of image processing, has played an essential role in amplitude-contrast and phase-contrast object imaging. The edge enhancement of three-dimensional (3D) vortex imaging has been successfully implemented by Fresnel incoherent correlation holography (FINCH), but the background noise and image contrast effects are still not satisfactory. To solve these issues, the edge enhancement of FINCH by employing Bessel-like spiral phase modulation is proposed and demonstrated. Compared with the conventional spiral phase modulated FINCH, the proposed technique can achieve high-quality edge enhancement 3D vortex imaging with lower background noise, higher contrast and resolution. The significantly improved imaging quality is mainly attributed to the effective sidelobes' suppression in the generated optical vortices with the Bessel-like modulation technique. Experimental results of the small circular aperture, resolution target, and the Drosophila melanogaster verify its excellent imaging performance. Moreover, we also proposed a new method for selective edge enhancement of 3D vortex imaging by breaking the symmetry of the spiral phase in the algorithmic model of isotropic edge enhancement. The reconstructed images of the circular aperture show that the proposed method is able to enhance the edges of the given objects selectively in any desired direction.

NONCOHERENT DATA TRANSFER BY USING ORTHOGONAL NOISE SIGNALS

The modern period of communications development is associated with the search and use of new broadband noise-like signals. One of the pressing problems in this area – large-power ensembles synthesis of broadband noise-like signals with good correlation and group properties. Another problem is the difficulty of isolating components from a mixture of several broadband noise-like signals under noise conditions, as well as the difficulty of reproducing such signals during correlation reception shape. The article discusses an incoherent correlation method of data transmission, based on the use of signals generated on the transmitter side by some noise generator. The noise signal is divided into parts (noise pulses) of a given duration. When the current noise pulse is transmitted, the next noise pulse is orthogonalized or collinearized depending on the transmitted data bit. On the receiver side, the mutual energy of the current and previous noise pulse is calculated. If this energy is less than the threshold, a decision is made to transmit zero, otherwise, to transmit one. Synchronization of the receiver and transmitter is carried out by changing the sign of the mutual energy of adjacent noise pulses.

Dipole instability in molecules irradiated by XUV pulses

We study the response of small covalent molecules to XUV laser pulses. The theoretical description relies on a real-time and real-space Time-Dependent Density Functional Theory (TDDFT) approach at the level of the local density approximation complemented by an efficient self-interaction correction. We observe the development of a dipole instability well after the laser pulse has died out. We find that this instability mechanism is robust with respect to ionic motion, to a wide variety of laser characteristics and to the inclusion of incoherent correlations at the level of a relaxation time ansatz. To rule out any potential numerical effects, we use two independent computational implementations of the TDDFT approach. A comparison of the various laser parameters together with the widely used model approach consisting in an instantaneous hole excitation shows the generic character of this instability in terms of the level depletion of a deep lying electron state. An experimental verification of the phenomenon is proposed in terms of a time-resolved measurement of the photoelectron spectrum.

Single-shot deep-learning based 3D imaging of Fresnel incoherent correlation holography

Fresnel incoherent correlation holography (FINCH) is a non-scanning and non-coherent light 3D imaging technology that has the potential of axial super-resolution imaging. However, the large depth-of-field artifacts of out-of-focus information greatly limits the axial resolution of FINCH. Here, we propose a single-shot deep-learning based 3D imaging method of FINCH. First, a hologram is collected and back propagated to obtain holograms at different back propagation distances. Subsequently, the designed network is used to identify and remove zero-order, conjugate, and defocused image from the hologram, thereby obtaining 3D information of the sample without phase-shifting operation. The experimental results demonstrate that the proposed method can effectively remove the interference of zero-order and conjugate image in back propagation hologram, and the imaging quality is comparable to that of multi-step phase-shifting based FINCH technology. In addition, clear focused images at different distances on the z-axis can be obtained without interference from defocused images at different back propagation distances, indicating that the proposed method can greatly improve temporal and axial resolution of 3D imaging for FINCH.

Enhanced resolution of edge enhancement in three-dimensional vortex imaging based on a modified Michelson interferometer

Edge enhancement is emerging as an essential technique for object recognition in recent years. The edge detection of three-dimensional (3D) imaging has been successfully demonstrated in Fresnel incoherent correlation holograph (FINCH) system; however, with a relatively low resolution which needs to be further improved to meet practical requirements. In this work, a modified Michelson interferometer system using a spatial light modulator (SLM) is proposed, which realizes 3D vortex imaging with high resolution and low background noise. Compared with the spiral phase modulated polarization multiplexing FINCH system, the resolution of this system has apparently improved from 50.80 lp mm−1 to 57.02 lp mm−1. The improvement is assumed to be ascribed to the inherently high luminous flux utilization configuration of the Michelson interferometer and the precision phase shifts. More importantly, the proposed system exhibits prominently improved performance of edge enhancement for different objects, including the standard resolution target and label-free biological living cells. The experimental results of the small watch parts also demonstrate its ability in 3D vortex imaging with edge detection. These results provide a promising strategy for high-quality 3D vortex imaging and edge enhancement, and might pave the way for future applications in the fields such as edge detection and pattern recognition.

Computational study of Na diffusion and conduction in P2- and O3-Na2x[NixTi1-x]O2 materials with machine-learning interatomic potentials

Sodium-ion batteries (SIBs) provide a feasible solution for large-scale energy storage applications of sustainable energy resources like wind and solar energy. Layered sodium nickel titanates (Na2x[NixTi1-x]O2) (SNTL) are considered a promising electrode material for SIBs since they can function as either a positive or negative electrode due to the coexistence of high redox potential element Ni (V = 3.7 V vs. Na/Na+) and low redox potential element Ti (V = 0.7 V vs. Na/Na+). There have been both experimental and computational studies on the family of Na2x[NixTi1-x]O2 materials, investigating their structures, electrochemical performance, electronic and ionic conductivity, etc. However, the current understanding of the Na migration mechanism is still very limited at an atomic level because of the restrictions of simulation methods: density-functional theory (DFT) simulation is restricted to a small length and time scale, whereas the conventional empirical interatomic potential (IP) is restricted by a limited accuracy. To solve this efficiency-versus-accuracy dilemma, herein we developed a neural network (NN)-based machine-learning interatomic potential (MLIP), which is trained using DFT data. Our MLIP demonstrates a DFT-approaching accuracy in terms of atomic forces. Moreover, the extracted Na self-diffusivity, ionic conductivity, and activation energy values from MLIP-MD simulation agree well with experimental data. In general, P2-SNTL demonstrates a higher Na self-diffusivity and ionic conductivity than O3-SNTL, mainly due to the larger bottleneck size through which Na ions migrate. We also employed the incoherent density correlation function to study the Na migration mechanism. The Singwi-Sjölander (SS) model and Chudley-Elliot (CE) model were used to fit the jump-diffusion behavior in P2- and O3-SNTL, respectively. The obtained jump distance values match well with the typical distance between the nearest Na sites in P2- and O3-SNTL, confirming that the hopping events happen mostly between neighboring Na sites in SNTL. The decrease of residence time and jump distance values with temperature is a result of higher ion mobility and level of delocalization, as validated by the nuclear density maps. In addition, our study also confirmed that both the “straight” and “curved” Na migration paths exist in O3-SNTL, in contrast to previous studies which only mention the “curved” migration path. In the end, our calculated Haven ratios have a value <1, indicating that it is more likely for the Na hopping events to occur via a concerted migration of several atoms other than the jump of an isolated atom.

Enhanced design of multiplexed coded masks for Fresnel incoherent correlation holography

Fresnel incoherent correlation holography (FINCH) is a well-established incoherent digital holography technique. In FINCH, light from an object point splits into two, differently modulated using two diffractive lenses with different focal distances and interfered to form a self-interference hologram. The hologram numerically back propagates to reconstruct the image of the object at different depths. FINCH, in the inline configuration, requires at least three camera shots with different phase shifts between the two interfering beams followed by superposition to obtain a complex hologram that can be used to reconstruct an object’s image without the twin image and bias terms. In general, FINCH is implemented using an active device, such as a spatial light modulator, to display the diffractive lenses. The first version of FINCH used a phase mask generated by random multiplexing of two diffractive lenses, which resulted in high reconstruction noise. Therefore, a polarization multiplexing method was later developed to suppress the reconstruction noise at the expense of some power loss. In this study, a novel computational algorithm based on the Gerchberg-Saxton algorithm (GSA) called transport of amplitude into phase (TAP-GSA) was developed for FINCH to design multiplexed phase masks with high light throughput and low reconstruction noise. The simulation and optical experiments demonstrate a power efficiency improvement of ~ 150 and ~ 200% in the new method in comparison to random multiplexing and polarization multiplexing, respectively. The SNR of the proposed method is better than that of random multiplexing in all tested cases but lower than that of the polarization multiplexing method.

Single-shot Fresnel incoherent correlation holography via deep learning based phase-shifting technology.

Fresnel incoherent correlation holography (FINCH) realizes non-scanning three-dimension (3D) images using spatial incoherent illumination, but it requires phase-shifting technology to remove the disturbance of the DC term and twin term that appears in the reconstruction field, thus increasing the complexity of the experiment and limits the real-time performance of FINCH. Here, we propose a single-shot Fresnel incoherent correlation holography via deep learning based phase-shifting (FINCH/DLPS) method to realize rapid and high-precision image reconstruction using only a collected interferogram. A phase-shifting network is designed to implement the phase-shifting operation of FINCH. The trained network can conveniently predict two interferograms with the phase shift of 2/3 π and 4/3 π from one input interferogram. Using the conventional three-step phase-shifting algorithm, we can conveniently remove the DC term and twin term of the FINCH reconstruction and obtain high-precision reconstruction through the back propagation algorithm. The Mixed National Institute of Standards and Technology (MNIST) dataset is used to verify the feasibility of the proposed method through experiments. In the test with the MNIST dataset, the reconstruction results demonstrate that in addition to high-precision reconstruction, the proposed FINCH/DLPS method also can effectively retain the 3D information by calibrating the back propagation distance in the case of reducing the complexity of the experiment, further indicating the feasibility and superiority of the proposed FINCH/DLPS method.

DMD-based optical pattern recognition using holograms generated with the Hartley transform

High-speed optical reconstruction of holographic and diffractive optical elements is widely used in encryption and recognition, 3D-displays, beam shaping, nanofabrication, visualization, etc. This paper proposes the use of amplitude holograms generated by the Hartley transform (HT) as filters in an incoherent correlator. The real computations using the HT are faster and less computationally intensive than the standard complex transforms. Generated holograms using HT and Fourier transform (FT) were compared. It is demonstrated that the diffraction efficiency of HT-based holograms is not inferior to the FT case. The reconstruction quality is better in metrics (NSTD, MSE, SNR, RMS contrast, SSIM) by 2–10%. An optical incoherent correlator based on two digital micromirror devices (DMDs) was constructed. DMDs have very high frame rates (up to 30 kHz) that provides its great potential for application in fast recognition problems. The object images were displayed on the first DMD. The holograms generated with the HT were binarized and displayed on the second DMD. The objects were successfully recognized. Thus, HT-based amplitude holograms can be successfully used instead of FT-based amplitude holograms.

Comparing farmers’ perceptions of climate change with meteorological data: A case study of livestock farmers in Eswatini’s lowveld region

This paper compared livestock farmers’ perceptions of climate change with meteorological data with the intent of understanding the predictors of farmers’ perceptions. Primary and secondary data sources were used. The sample size was 278 farmers. The data was analysed using descriptive and inferential statistics. The results showed that livestock farmers are mainly aged, married males that practiced mixed farming and reared mainly cattle and goats. The farmers’ perceptions were that the climate had changed notably with increased temperatures, decreased rainfall, delayed rain season and an increased intensity of drought. Climate trends indicated a significant decline in temperatures in the northern lowveld and an increase in the southern lowveld. There was pronounced rainfall variability and a significant decline in summer rainfall in the north. Comparison of climate trends with the farmers’ perceptions revealed some incoherent correlations regarding temperature in the north and annual rainfall throughout the lowveld. Age, education, experience, location, who managed the farm and the crops grown were found to be significant predictors of farmers’ perceptions using multinomial logistic regression. Focusing interventions on these bio-demographic variables will positively enhance farmers’ perception and adaptation. It is further recommended that future studies incorporate drought and floods in comparing trends and perceptions.

Roadmap of incoherent digital holography

This roadmap article focuses on spatially incoherent digital holography (IDH). Representative IDH methods such as optical scanning holography (OSH), Fresnel incoherent correlation holography (FINCH), coded aperture correlation holography (COACH), IDH with a Fresnel zone aperture, and IDH with an interferometer along with a state-of-the-art optical device are introduced as modern IDH methods. We describe these IDH techniques with applications of three-dimensional (3D) imagers, 3D thermography, and 3D microscopy.