Phase unwrapping using deep learning in holographic tomography.

Holographic tomography (HT) is a measurement technique that generates phase images, often containing high noise levels and irregularities. Due to the nature of phase retrieval algorithms within the HT data processing, the phase has to be unwrapped before tomographic reconstruction. Conventional algorithms lack noise robustness, reliability, speed, and possible automation. In order to address these problems, this work proposes a convolutional neural network based pipeline consisting of two steps: denoising and unwrapping. Both steps are carried out under the umbrella of a U-Net architecture; however, unwrapping is aided by introducing Attention Gates (AG) and Residual Blocks (RB) to the architecture. Through the experiments, the proposed pipeline makes possible the phase unwrapping of highly irregular, noisy, and complex experimental phase images captured in HT. This work proposes phase unwrapping carried out by segmentation with a U-Net network, that is aided by a pre-processing denoising step. It also discusses the implementation of the AGs and RBs in an ablation study. What is more, this is the first deep learning based solution that is trained solely on real images acquired with HT.

Method to analyze effects of low-level laser therapy on biological cells with a digital holographic microscope.

Low-level laser therapy (LLLT) is a therapeutic tool that uses the photobiochemical interaction between light and tissue. Its effectiveness is controversial due to a strong dependence on dosimetric parameters. In this work, we demonstrate that digital holographic microscopy is an effective label-free imaging technique to analyze the effects of LLLT on biological cells, and we propose the full methodology to create correct synthetic aperture phase maps for further extensive, highly accurate statistical analysis. The proposed methodology has been designed to provide a basis for many other biological experiments using quantitative phase imaging. We use SHSY-5Y and HaCaT cells irradiated with different doses of red light for the experiment. The analysis shows quantitative changes in cell dry mass density and the projected cell surface in response to different radiation doses.

Metrological Evaluation of the Demosaicking Effect on Colour Digital Image Correlation with Application in Monitoring of Paintings.

A modified 3D colour digital image correlation method (3D cDIC) is proposed for efficient displacement measurements of colour objects with natural texture. The method is using a separate analysis of correlation coefficient (sigma) value in the RGB channels of CCD cameras by utilising local information from the channel with the minimum sigma. In this way, merged U, V and W displacement maps are generated based on the local correlation quality. As the proposed method applies to colour filter array cameras, the images in RGB channels have to undergo a demosaicking procedure which directly influences the accuracy of displacement measurements. In the paper, the best performing demosaicking methods are selected. The metrological analysis of their influence on the results of canvas paintings investigations obtained by unmodified and modified 3D cDIC processing is presented.

Refractive Index Changes of Cells and Cellular Compartments Upon Paraformaldehyde Fixation Acquired by Tomographic Phase Microscopy.

Three-dimensional quantitative phase imaging is an emerging method, which provides the 3D distribution of the refractive index (RI) and the dry mass in live and fixed cells as well as in tissues. However, an insufficiently answered question is the influence of chemical cell fixation procedures on the results of RI reconstructions. Therefore, this work is devoted to systematic investigations on the RI in cellular organelles of live and fixed cells including nucleus, nucleolus, nucleoplasm, and cytoplasm. The research was carried out on four different cell lines using a common paraformaldehyde (PFA)-based fixation protocol. The selected cell types represent the diversity of mammalian cells and therefore the results presented provide a picture of fixation caused RI changes in a broader context. A commercial Tomocube HT-1S device was used for 3D RI acquisition. The changes in the RI values after the fixation process are detected in the reconstructed phase distributions and amount to the order of 10-3 . The RI values decrease and the observed RI changes are found to be different between various cell lines; however, all of them show the most significant loss in the nucleolus. In conclusion, our study demonstrates the evident need for standardized preparation procedures in phase tomographic measurements. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals LLC. on behalf of International Society for Advancement of Cytometry.

Roadmap on digital holography [Invited].

This Roadmap article on digital holography provides an overview of a vast array of research activities in the field of digital holography. The paper consists of a series of 25 sections from the prominent experts in digital holography presenting various aspects of the field on sensing, 3D imaging and displays, virtual and augmented reality, microscopy, cell identification, tomography, label-free live cell imaging, and other applications. Each section represents the vision of its author to describe the significant progress, potential impact, important developments, and challenging issues in the field of digital holography.

Holographic tomography: techniques and biomedical applications [Invited].

Holographic tomography (HT) is an advanced label-free optical microscopic imaging method used for biological studies. HT uses digital holographic microscopy to record the complex amplitudes of a biological sample as digital holograms and then numerically reconstruct the sample's refractive index (RI) distribution in three dimensions. The RI values are a key parameter for label-free bio-examination, which correlate with metabolic activities and spatiotemporal distribution of biophysical parameters of cells and their internal organelles, tissues, and small-scale biological objects. This article provides insight on this rapidly growing HT field of research and its applications in biology. We present a review summary of the HT principle and highlight recent technical advancement in HT and its applications.

Suitability analysis of holographic vs light field and 2D displays for subjective quality assessment of Fourier holograms.

Measuring the impact of compression on the reconstruction quality of holograms remains a challenge. A public subjectively-annotated holographic data set that allows for testing the performance of compression techniques and quality metrics is presented, in addition to a subjective visual quality assessment methodology. Moreover, the performance of the quality assessment procedures is compared for holographic, regular 2D and light field displays. For these experiments, a double-stimulus, multi-perspective, multi-depth testing methodology was designed and implemented. Analysis of the quality scores indicated that in the absence of a suitable holographic display and under the presented test conditions, non-holographic displays can be deployed to display numerically reconstructed holograms for visual quality assessment tasks.

Reconstruction method for extended depth-of-field optical diffraction tomography.

In the paper we present a novel method of extended depth-of-field limited-angle optical diffraction tomography, in which the change of a focal plane position is performed with a liquid focus-tunable lens. One sinogram is acquired for each state of a focus-tunable lens. After acquisition process is complete, all sinograms are independently reconstructed and stitched to form the final tomographic reconstruction. The presented solution effectively extends the applicability of the Rytov approximation to relatively thick samples and provides uniform resolution of 3D tomographic reconstructions. The method is also combined with Generalized Total Variation Iterative Constraint algorithm, which minimizes distortion of the results due to the limited angular range of acquired projections. The combined solution is dedicated to investigation of transparent and semi-transparent biological micro-structures, like cells and tissue slices.

Generalized total variation iterative constraint strategy in limited angle optical diffraction tomography.

Due to incompleteness of input data inherent to Limited Angle Tomography (LAT), specific additional constraints are usually employed to suppress image artifacts. In this work we demonstrate a new two-stage regularization strategy, named Generalized Total Variation Iterative Constraint (GTVIC), dedicated to semi-piecewise-constant objects. It has been successfully applied as a supplementary module for two different reconstruction algorithms: an X-ray type solver and a diffraction-wise solver. Numerical tests performed on a detailed phantom of a biological cell under conical illumination pattern show significant reduction of axial blurring in the reconstructed refractive index distribution after GTVIC is added. Analogous results were obtained with experimental data.

Accurate approach to capillary-supported optical diffraction tomography.

A new holographic data processing path for accurate quantitative tomographic reconstruction of 3D samples placed in a cylindrical capillary is proposed. The method considers strong unintentional focusing effects induced by the inner cylindrical boundary of the vessel: 1) introduction of cylindrical wave illumination of a sample, and 2) object wave deformation. The first issue is addressed by developing an arbitrary illumination tomographic reconstruction algorithm based on filtered backpropagation, while the second by a novel correction algorithm utilizing the optical rays analysis. Moreover, the processing path includes a novel holographic method for correction of spherical aberration related to refraction at a planar surface. Utility of the developed data processing path is proven with numerical simulations and experimental measurement of a specially prepared test sample.

Hybrid single-beam reconstruction technique for slow and fast varying wave fields.

An iterative single-beam wave field reconstruction technique that employs both non-paraxial, wave propagation based and paraxial deterministic phase retrieval techniques is presented. This approach overcomes two major obstacles that exist in the current state of the art techniques: iterative methods do not reconstruct slowly varying wave fields due to slow convergence and stagnation, and deterministic methods have paraxial limits, making the reconstructions of quickly varying object features impossible. In this work, a hybrid approach is reported that uses paraxial wave field corrections within iterative phase retrieval solvers. This technique is suitable for cases ranging from slow to fast varying wave fields, and unlike the currently available methods, can also reconstruct measurement objects with different regions of both slowly and quickly varying object features. It is further shown that this technique gives a higher accuracy than current single-beam phase retrieval techniques, and in comparison to the iterative methods, has a higher convergence speed.

Noise suppressed optical diffraction tomography with autofocus correction.

We propose a novel tomographic measurement approach that enables a noise suppressed characterization of microstructures. The idea of this work is based on a finding that coherent noise in the input phase data generates an artificial circular structure whose magnitude is the highest at the centre of tomographic reconstruction. This method decreases the noise level by applying an unconventional tomographic measurement configuration with an object deliberately shifted with respect to the rotation axis. This enables a spatial separation between the reconstructed sample structure and the area of the largest refractive index perturbations. The input phase data defocusing that is a by-product of the introduced modification is numerically corrected with an automatic focus correction algorithm. The proposed method is validated with simulations and experimental measurements of an optical microtip.

Multiwavefront digital holographic television.

This paper presents the full technology chain supporting wide angle digital holographic television from holographic capture of real world objects/scenes to holographic display with an extended viewing angle. The data are captured with multiple CCD cameras located around an object. The display system is based on multiple tilted spatial light modulators (SLMs) arranged in a circular configuration. The capture-display system is linked by a holographic data processing module, which allows for significant decoupling of the capture and display systems. The presented experimental results, based on the reconstruction of real world, variable in time scenes, illustrates imaging dynamics, viewing angle and quality.

Optimum plane selection criteria for single-beam phase retrieval techniques based on the contrast transfer function.

In this work, an optimum plane selection methodology is reported that can be applied to a wide range of single-beam phase retrieval techniques, based on the contrast transfer function. It is shown that the optimum measurement distances obtained by this method form a geometric series that maximizes the range of spatial frequencies to be recovered using a minimum number of planes. This allows a noise-robust phase reconstruction that does not rely on regularization techniques, i.e., an extensive search for a regularization parameter is avoided. Measurement systems that employ this optimization criteria give an instant deterministic noise-robust phase reconstruction with higher accuracy, and enable the phase retrieval of the entire object spectrum, including lower frequency components.

Capture and display mismatch compensation for real-time digital holographic interferometry.

Optical holographic interferometry (HI) is realized by two well-known techniques: double exposure holographic interferometry (DEHI) and real-time holographic interferometry (RTHI). However, the digital version of HI is typically realized numerically by DEHI. The main problem in digital implementation of RTHI is the lack of commercially available cameras and spatial light modulators with the same pixel size. This mismatch results in lateral and transversal magnifications of an object wavefront reconstruction. In real-time digital HI the reconstruction of an object in an initial state has to be superimposed on top of the loaded object. In this work, we present and analyze five approaches to overcome the mismatch problem, and the performance of these procedures is numerically quantified and compared. The experimental suitability of these approaches is investigated.

Application of 3D digital image correlation to track displacements and strains of canvas paintings exposed to relative humidity changes.

This paper introduces a methodology for tracking displacements in canvas paintings exposed to relative humidity changes. Displacements are measured by means of the 3D digital image correlation method that is followed by a postprocessing of displacement data, which allows the separation of local displacements from global displacement maps. The applicability of this methodology is tested on measurements of a model painting on canvas with introduced defects causing local inhomogeneity. The method allows the evaluation of conservation methods used for repairing canvas supports.

Degeneration of Fraunhofer diffraction on bacterial colonies due to their light focusing properties examined in the digital holographic microscope system.

The degeneration of Fraunhofer diffraction conditions in the optical system with converging spherical wave illumination for bacteria species identification based on diffraction patterns is analyzed by digital holographic methods. The obtained results have shown that the colonies of analyzed bacteria species act as biological lenses with the time-dependent light focusing properties, which are characterized and monitored by means of phase retrieval from sequentially captured digital holograms. This significantly affects the location of Fraunhofer patterns observation plane, which is continuously shifted across optical axis in time.

Accelerated single-beam wavefront reconstruction techniques based on relaxation and multiresolution strategies.

A previous Letter by Pedrini et al. [Opt. Lett. 30, 833 (2005)] proposed an iterative single-beam wavefront reconstruction algorithm that uses a sequence of interferograms recorded at different planes. In this Letter, the use of relaxation and multiresolution strategies is investigated in terms of accuracy and computational effort. It is shown that the convergence rate of the conventional iterative algorithm can be significantly improved with the use of relaxation techniques combined with a hierarchy of downsampled intensities that are used within a preconditioner. These techniques prove to be more robust, to achieve a higher accuracy, and to overcome the stagnation problem met in the iterative wavefront reconstruction.

Deformation measurements by digital image correlation with automatic merging of data distributed in time.

This paper presents a method to analyze 3D displacement data captured by digital image correlation (DIC) method over a long period of time. It allows monitoring of an object when a 3D DIC setup is not fixed in the same position between a consecutive series of measurements. An implementation of the data merging procedure is described and a proof of concept is provided using example measurements for both a numerical model and a real experiment in laboratory conditions. We evaluated the accuracy and discuss the main sources of errors. The obtained results prove the method is feasible for in situ long-term measurements and monitoring in industry and civil engineering.

Computation of highly off-axis diffracted fields using the band-limited angular spectrum method with suppressed Gibbs related artifacts.

The angular spectrum (AS) method is a popular solution to the Helmholtz equation without the use of approximations. Modified band-limited AS methods are of particular interest for the cases of high-off-axis and large distance propagation problems, because conventional AS methods are impractical due to requirements regarding memory and computational effort. However, these techniques make use of rectangular-shaped filters that introduce ringing artifacts in the calculated field that are related to the Gibbs phenomenon. This work proposes AS algorithms based on a smooth band-limiting filter for accurate field computation as well as techniques that evaluate only nonzero components of the field. This enables accurate field calculations with an acceptable level of computational effort that cannot be offered by current AS methods reported in the scientific literature.