Reconstruction Distance Research Articles

Total internal reflection of the mid-IR near single-cycle light bullet in LiF.

Mid-IR light bullets formation and self-reconstruction after total internal reflection in LiF is investigated experimentally and through numerical simulations. The experiment showed that spatial-temporal deformations of the wave packet in inhomogeneous wave on a reflecting interface can be neglected for this process and a near single-cycle light bullet can be formed or recovered after a distance determined by its energy loss for ionization and supercontinuum radiation. The estimation of the reconstruction distance by an empirical formula for self-focusing distance on the base of the peak power and the radius of the LB numerical simulation are in a good agreement with experimental data received.

Netrd: A library for network reconstruction and graph distances

Over the last two decades, alongside the increased availability of large network datasets, we have witnessed the rapid rise of network science. For many systems, however, the data we have access to is not a direct description of the underlying network. More and more, we see the drive to study networks that have been inferred or reconstructed from non-network data---in particular, using time series data from the nodes in a system to infer likely connections between them. Selecting the most appropriate technique for this task is a challenging problem in network science. Different reconstruction techniques usually have different assumptions, and their performance varies from system to system in the real world. One way around this problem could be to use several different reconstruction techniques and compare the resulting networks. However, network comparison is also not an easy problem, as it is not obvious how best to quantify the differences between two networks, in part because of the diversity of tools for doing so. The netrd Python package seeks to address these two parallel problems in network science by providing, to our knowledge, the most extensive collection of both network reconstruction techniques and network comparison techniques (often referred to as graph distances) in a single library (https://github.com/netsiphd/netrd). In this article, we detail the two main functionalities of the netrd package. Along the way, we describe some of its other useful features. This package builds on commonly used Python packages and is already a widely used resource for network scientists and other multidisciplinary researchers. With ongoing open-source development, we see this as a tool that will continue to be used by all sorts of researchers to come.

Autofocusing of in-line holography based on compressive sensing

Holographic reconstruction is affected by the phase-conjugate wave arising from the symmetry of the complex field. Compressive sensing (CS) has been used in in-line digital holography (DH) to eliminate noise, especially the interference from twin images. Herein, CS with total variation regularization combining autofocusing is presented. It provides an autofocusing function from a single-exposure hologram and obtains reconstructed objects without twin image noise. A series of images at a fixed interval within a reconstruction distance are processed using a two-step iterative shrinkage/thresholding algorithm in CS. It can calculate the focus distance in a larger range around the focal plane using twin-image-free reconstruction, so it can achieve a higher focusing accuracy than traditional focusing methods, including the Laplace operator, absolute gradient operator, and Tamura coefficient. The proposed method is a simple combination of algorithms and a powerful extension that can effectively improve simulated and experimental image quality and handle difficult datasets, which existing algorithms cannot.

Autofocusing in digital holography using eigenvalues.

A new autofocusing algorithm for digital holography is proposed based on the eigenvalues of the images reconstructed at different distances in the measurement volume. An image quality metric evaluated based on the distribution of its eigenvalues is compared in function of the reconstruction distance to identify the location of the focal plane. The proposed automatic focal plane detection algorithm is capable of working with amplitude objects, phase objects, and mixed type objects. A performance comparison of the proposed algorithm with some previously reported representative algorithms is provided. The simulation and experimental results demonstrate the practical applicability of the proposed algorithm.

A comparative study of the lengths of different reconstruction routes used after thoracic esophagectomy

A challenge in esophageal reconstruction after esophagectomy is that the distance from the neck to the abdomen must be replaced with a long segment obtained from the gastrointestinal tract. The success or failure of the reconstruction depends on the blood flow to the reconstructed organ and the tension on the anastomotic site, both of which depend on the reconstruction distance. There are three possible esophageal reconstruction routes: posterior mediastinal, retrosternal, and subcutaneous. However, there is still no consensus as to which route is the shortest. The length of each reconstruction route was retrospectively compared using measurements obtained during surgery, where the strategy was to pull up the gastric conduit through the shortest route. The proximal reference point was defined as the left inferior border of the cricoid cartilage and the distal reference point was defined as the superior border of the duodenum arising from the head of the pancreas. This study involved 112 Japanese patients with esophageal cancer (102 men, 10 women). The mean distances of the posterior mediastinal, retrosternal, and subcutaneous routes were 34.7 ± 2.37cm, 32.4 ± 2.24cm, and 36.3 ± 2.27cm, respectively. The retrosternal route was significantly shorter than the other two routes (both p < 0.0001) and shorter by 2.31cm on average than the posterior mediastinal route. The retrosternal route was longer than the posterior mediastinal route in only 5 patients, with a difference of less than 1cm. The retrosternal route was the shortest for esophageal reconstruction in living Japanese patients.

Interior Sound Field Subjective Evaluation Based on the 3D Distribution of Sound Quality Objective Parameters and Sound Source Localization.

Controlling low frequency noise in an interior sound field is always a challenge in engineering, because it is hard to accurately localize the sound source. Spherical acoustic holography can reconstruct the 3D distributions of acoustic quantities in the interior sound field, and identify low-frequency sound sources, but the ultimate goal of controlling the interior noise is to improve the sound quality in the interior sound field. It is essential to know the contributions of sound sources to the sound quality objective parameters. This paper presents the mapping methodology from sound pressure to sound quality objective parameters, where sound quality objective parameters are calculated from sound pressure at each specific point. The 3D distributions of the loudness and sharpness are obtained by calculating each point in the entire interior sound field. The reconstruction errors of those quantities varying with reconstruction distance, sound frequency, and intersection angle are analyzed in numerical simulation for one- and two-monopole source sound fields. Verification experiments have been conducted in an anechoic chamber. Simulation and experimental results demonstrate that the sound source localization results based on 3D distributions of sound quality objective parameters are different from those based on sound pressure.

Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation

Ptychography is a lensless imaging method that allows for wavefront sensing and phase-sensitive microscopy from a set of diffraction patterns. Recently, it has been shown that the optimization task in ptychography can be achieved via automatic differentiation (AD). Here, we propose an open-access AD-based framework implemented with TensorFlow, a popular machine learning library. Using simulations, we show that our AD-based framework performs comparably to a state-of-the-art implementation of the momentum-accelerated ptychographic iterative engine (mPIE) in terms of reconstruction speed and quality. AD-based approaches provide great flexibility, as we demonstrate by setting the reconstruction distance as a trainable parameter. Lastly, we experimentally demonstrate that our framework faithfully reconstructs a biological specimen.

Optimal quantization for amplitude and phase in computer-generated holography.

Owing to the characteristics of existing spatial light modulators (SLMs), the computer-generated hologram (CGH) with continuous complex-amplitude is conventionally converted to a quantized amplitude-only or phase-only CGH in practical applications. The quantization of CGH significantly affects the holographic reconstruction quality. In this work, we evaluated the influence of the quantization for both amplitude and phase on the quality of holographic reconstructions by traversing method. Furthermore, we considered several critical CGH parameters, including resolution, zero-padding size, reconstruction distance, wavelength, random phase, pixel pitch, bit depth, phase modulation deviation, and filling factor. Based on evaluations, the optimal quantization for both available and future SLM devices is suggested.

Digital Holographic Microscopy Using a Spherical Reference Wave and Polarization Hologram

A reflective lensless on-axis digital holographic microscopic system with a spherical reference wave was developed and used to obtain a reconstructed image at several magnification levels. A polarization image camera (PIC) was used to suppress the direct current term and twin images of the on-axis digital holography (DH) microscope. The PIC was used in a parallel phase-shifting DH system without mechanical movement. Here, we show that the magnification can be adjusted by changing the ratio of the distance between the object and the PIC to that between the reference light and the PIC while maintaing a constant reconstruction distance.

Phase errors reduction in multi-angle illumination digital holographic microscopy

Synthetic aperture has been a common method in digital holographic microscopy resolution enhancement over the years. Multiangle illumination is one type of synthetic aperture methods. Reconstructed phase errors appeared when synthesizing aperture not considering the difference between different inclined incident beams' reconstruction distances. To reduce phase errors, this paper proposes a method using different reconstruction distances in inclined incident beams to achieve synthetic aperture resolution enhancement. A multiangle illumination reflectance digital holographic microscopy system is built to prove this method. The reconstruction distances can be calculated theoretically to compute the phase image. The phase image errors can be remarkably reduced by using the proposed method by analyzing the experimental result.

Noise-free quantitative phase imaging in Gabor holography with conditional generative adversarial network.

This paper shows that deep learning can eliminate the superimposed twin-image noise in phase images of Gabor holographic setup. This is achieved by the conditional generative adversarial model (C-GAN), trained by input-output pairs of noisy phase images obtained from synthetic Gabor holography and the corresponding quantitative noise-free contrast-phase image obtained by the off-axis digital holography. To train the model, Gabor holograms are generated from digital off-axis holograms with spatial shifting of the real image and twin image in the frequency domain and then adding them with the DC term in the spatial domain. Finally, the digital propagation of the Gabor hologram with Fresnel approximation generates a super-imposed phase image for the C-GAN model input. Two models were trained: a human red blood cell model and an elliptical cancer cell model. Following the training, several quantitative analyses were conducted on the bio-chemical properties and similarity between actual noise-free phase images and the model output. Surprisingly, it is discovered that our model can recover other elliptical cell lines that were not observed during the training. Additionally, some misalignments can also be compensated with the trained model. Particularly, if the reconstruction distance is somewhat incorrect, this model can still retrieve in-focus images.

Semisupervised Manifold Joint Hypergraphs for Dimensionality Reduction of Hyperspectral Image

In this letter, a new semisupervised dimensionality reduction (DR) method, termed geodesic-based manifold joint hypergraphs (GMJHs), is proposed for hyperspectral image (HSI). This method first builds a geodesic-based reconstruction model to discover the nonlinear similarity between two manifold reconstruction neighborhoods. Then, it implies the probabilistic relationship between unlabeled samples and each class via the geodesic-based reconstruction distance. With the probabilistic class relationship, a supervised hypergraph and an unsupervised hypergraph are constructed to represent the multivariate manifold relationship of samples. Finally, the supervised and unsupervised hypergraphs are jointed for learning optimal projection matrix and enhancing the intraclass compactness in low-dimensional embedding space. Experiments on two HSI data sets show that the proposed GMJH algorithm performs better performance than some state-of-the-art DR methods.

Axial displacement measurement with high resolution of particle movement based on compound digital holographic microscopy

In-line digital holographic particle imaging is gifted with high axial resolution but axial displacement of nearly-in-focus or in-focus particle is unable to be measured because of twin-image problem. Both in-focus and out-of-focus particles can be measured by off-axis digital holographic particle imaging but with poor axial resolution. These two make particle tracking in three-dimensional more complicated. This paper proposes a compound method of in-line and off-axis digital holographic microscopy to measure the axial displacement of both the in-focus and out-of-focus particle with improved resolution up to nanometer scale collectively. In the proposed compound digital holographic microscopy (CDHM), the critical reconstruction distance (CRD) is calculated. The twin image effect can be resolved by ensuring the reconstruction distance is larger than the CRD, then in-line digital holographic particle imaging can be effectively applied. If the reconstruction distance is smaller than the CRD, the ring pixels of optical path length (RPOPL) method is applied to improve resolution. The axial displacement of silica particles 5 μm and 10 μm in diameter fixed on the piezoelectric stage were successfully measured using CDHM method at resolution up to 4 nm (in-focus particle) and 2 nm (out-of-focus particle).

Digital lensless holographic microscopy: numerical simulation and reconstruction with ImageJ.

The description and validation of an ImageJ open-source plugin to numerically simulate and reconstruct digital lensless holographic microscopy (DLHM) holograms are presented. Two modules compose the presented plugin: the simulation module implements a discrete version of the Rayleigh-Somerfield diffraction formula, which allows the user to directly build a simulated hologram from a known phase and/or amplitude object by just introducing the geometry parameters of the simulated setup; the plugin's reconstruction module implements a discrete version of the Kirchhoff-Helmholtz diffraction integral, thus allowing the user to reconstruct DLHM holograms by introducing the parameters of the acquisition setup and the desired reconstruction distance. The plugin offers the two said modules within the robust environment provided by a complete set of built-in tools for image processing available in ImageJ. While the simulation module has been validated through the evaluation of the forecasted lateral resolution of a DLHM setup in terms of the numerical aperture, the reconstruction module is tested by means of reconstructing experimental DLHM holograms of biological samples.

Sizing calibration in digital lensless holographic microscopy via iterative Talbot self-imaging

In this work, an iterative method to calibrate the length measurements in digital lensless holographic microscopy (DLHM) is presented. In DLHM, the correct sizing is controlled by the accurate knowledge of the illumination wavelength, the digital camera specifications, and the source-to-screen distance. While the two formers are provided by the manufacturers, the latter has to be somehow measured, usually by mechanical means. As an alternative for performing that key measurement in DLHM, the Talbot self-imaging effect, and hence the Talbot distance, is used as a measurement tool in this work. Amplitude reconstructions of a monolayer of self-organized spheres of polystyrene produce the self-imaging phenomenon, with the Talbot distance controlled by the illuminating wavelength, the reconstruction distance, and the period of the monolayer. As the latter can be varied in DLHM by changing the source-to-screen distance while keeping fixed the wavelength and the camera specifications, the source-to-screen distance is iteratively varied until the correct Talbot distance is found. The proposed method has the advantages of i) increased sensitivity because of the axial quadratic dependency on transversal measurements, ii) not requiring in-focus images that demand the use of focusing criteria, and iii) can use non-approximated propagation methods to produce axial intensity profiles to determine the correct source-to-screen distance. The feasibility of the calibration method is tested by reconstructing a USAF 1951 test of resolution.

Distribution of Candidatus Liberibacter species in Eastern Africa, and the First Report of Candidatus Liberibacter asiaticus in Kenya

Huanglongbing (HLB) is a serious disease of Citrus sp. worldwide. In Africa and the Mascarene Islands, a similar disease is known as African citrus greening (ACG) and is associated with the bacterium Candidatus Liberibacter africanus (Laf). In recent years, Candidatus Liberibacter asiaticus (Las) associated with the severe HLB has been reported in Ethiopia. Thus, we aimed to identify the Liberibacter species affecting citrus, the associated vectors in Eastern Africa and their ecological distribution. We assessed the presence of generic Liberibacter in symptomatic leaf samples by quantitative PCR. Subsequently, we sequenced the 50 S ribosomal protein L10 (rplJ) gene region in samples positive for Liberibacters and identified the species by comparison with public sequence data using phylogenetic reconstruction and genetic distances. We detected generic Liberibacter in 26%, 21% and 66% of plants tested from Uganda, Ethiopia and Kenya, respectively. The rplJ sequences revealed the most prevalent Liberibacters in Uganda and Ethiopia were LafCl (22%) and Las (17%), respectively. We detected Las in Kenya for the first time from three sites in the coastal region. Finally, we modelled the potential habitat suitability of Las in Eastern Africa using MaxEnt. The projection showed large areas of suitability for the pathogen in the three countries surveyed. Moreover, the potential distribution in Eastern Africa covered important citrus-producing parts of Ethiopia, Kenya, Uganda and Tanzania, and included regions where the disease has not been reported. These findings will guide in the development of an integrated pest management strategy to ACG/HLB management in Africa.

Digital holographic microscopy for red blood cell imaging

Digital holographic microscopy (DHM) can obtain biological parameters and morphological information of cells by reconstructing holograms, which is different from traditional optical microscopy. The DHM is a three-dimensional imaging technology which is effective, non-contact and non-destructive. With the developments of the image sensor and the computing technology, it has made significant progress in the field of living cells detection, especially for red blood cell. Compared with the technologies which are widely used in the field of cell imaging such as con-focal laser scanning microscopy, scanning near-field optical microscopy and optical coherence tomography, the DHM has the advantages including wide FOV and high-resolution to achieve higher imaging and quality. This paper introduces the principle of recording and reconstruction of digital holography, and then analyzes the performance of three reconstruction algorithms using the Fresnel method, the convolution method and the angular spectrum method. The Fresnel method is suitable for the sample size larger than the image sensor. Both the convolution method and the angular spectrum method have an optimal reconstruction distance. When the reconstruction distance is different from the optimal distance, the resolution of the reconstructed image will decrease, and the angular spectrum method is better than the convolution method in overall performance. The DHM system for RBC measurements mainly adopts the convolution algorithm or the angular spectrum algorithm to implement numerical reconstruction. The systems of the in-line DHM, the off-axis DHM and the optical tweezers combining with off-axis DHM are introduced. These techniques use algorithms including Rayleigh-Sommerfeld back-propagation, the sharpness quantification, the watershed segmentation, the numerical refocusing and the thermal fluctuation to determine the focal plane position and obtain the best reconstruction distance of the RBCs, and further detect the shape change of the RBCs and extract the information of high-resolution blood vessel shape and blood flow velocity. These techniques can even achieve the dynamic tracking and measure three-dimensional volume of RBCs in real-time which is helpful for pathological studies such as diabetes, cardiovascular disease and Parkinson's disease. With its unique non-contact and non-destructive characteristics, the DHM realizes real-time and quantitative detection that is difficult to achieve with traditional three-dimensional microscopic imaging technologies.

Resolution and sampling analysis in digital in-line holography with spherical wave illumination

The resolution optimization and sampling strategies in practical digital in-line holography (DIH) with spherical wave illumination are analytically studied by optimizing system parameters. Optimal parameters of holographic recording, including illumination wavelength, numerical aperture of the spherical illumination wave, source-sensor distance, object–sensor distance, and sampling parameters of the sensor, for achievable resolution are worked out. A formula is derived to guide the DIH system design in general cases. Different sampling strategies associated with corresponding reconstruction waves (plane wave and spherical waves with various curvatures) are analyzed. The reason why recording with spherical wave and reconstructing with plane wave works well in practice is explained in detail. We also present how to determine the reconstruction distance and magnification to reconcile the curvature difference. The analysis is carried out mathematically and verified by simulated holograms. Optical experiments with U.S. Air Force resolution target are carried out based on the analysis for further verification.

Terahertz synthetic aperture in-line holography with intensity correction and sparsity autofocusing reconstruction

We demonstrate high-resolution and high-quality terahertz (THz) in-line digital holography based on the synthetic aperture method. The setup is built on a self-developed THz quantum cascade laser, and a lateral resolution better than 70 μm (∼λ) is achieved at 4.3 THz. To correct intensity differences between sub-holograms before aperture stitching, a practical algorithm with global optimization is proposed. To address the twin-image problem for in-line holography, a sparsity-based phase retrieval algorithm is applied to perform the high-quality reconstruction. Furthermore, a new autofocusing criterion termed “reconstruction objective function” is introduced to obtain the best in-focus reconstruction distance, so the autofocusing procedure and the reconstruction are unified within the same framework. Both simulation and experiment prove its accuracy and robustness. Note that all the methods proposed here can be applied to other wavebands as well. We demonstrate the success of this THz synthetic aperture in-line holography on biological and semiconductor samples, showing its potential applications in bioimaging and materials analysis.

Research on Experimental Parameters of Reflective Off-axis Digital Holography

Summarized the research status of digital holography microscopy technology. Aiming at the experimental parameters which influences the quality of hologram recurrent image, the recording and reconstruction process of hologram are analyzed, the reconstruction distance are calculated which based on the reflective off-axis digital holographic light path. The experiment records the hologram of standard resolution board and reconstruct it under different light intensity ratio. The results show that the object and reference light intensity ratio have a significant impact on the quality of hologram recurrent image. Besides, it’s the key to determining an appropriate recording distance and object and reference light intensity ratio of improving the quality of hologram. The result would provide theoretical basis and technical conditions for studying the reflective digital holography based on 3-D reconstruction.