On the holographic 3D tracking of in vitro cells characterized by a highly-morphological change

In-focus quantitative phase imaging from defocused off-axis holograms: synergistic reconstruction framework

Digital holographic microscopy (DHM) enables the three-dimensional (3D) reconstruction of quantitative phase distributions from a defocused hologram. Traditional computational algorithms follow a sequential approach in which one first reconstructs the complex amplitude distribution and later applies focusing algorithms to provide an in-focus phase map. In this work, we have developed a synergistic computational framework to compensate for the linear tilt introduced in off-axis DHM systems and autofocus the defocused holograms by minimizing a cost function, providing in-focus reconstructed phase images without phase distortions. The proposed computational tool has been validated in defocused holograms of human red blood cells and three-dimensional images of dynamic sperm cells.

Holobricks: modular coarse integral holographic displays

Here, we propose and demonstrate a modular holographic display system that allows seamless spatial tiling of multiple coarse integral holographic (CIH) displays called "holobricks". A holobrick is a self-contained CIH module enclosing a spatial light modulator (SLM), a scanner, and periscopic coarse integral optics. Modular CIH uses a coarse pitch and small area but high-bandwidth SLM in conjunction with periscopic coarse integral optics to form the angularly tiled 3D holograms with large viewing areas and fields of view. The creation of periscopic coarse integral optics prevents the optical system from being larger than the holographic image and allows the holographic fringe pattern to fill the entire face of the holobrick. Thus, multiple holobricks can be seamlessly abutted to form a scalable spatially tiled holographic image display capable of both wide field-of-view angle and arbitrary large-size area. We demonstrate an initial prototype that seamlessly tiles two holobricks each with 1024 × 768 pixels, 40° FOV, full color, 24 fps, displaying 2D, 3D holographic stereograms, and full parallax 3D CGI Fresnel holograms.

Holographic 3D particle reconstruction using a one-stage network

Volumetric reconstruction of a three-dimensional (3D) particle field with high resolution and low latency is an ambitious and valuable task. As a compact and high-throughput imaging system, digital holography (DH) encodes the 3D information of a particle volume into a two-dimensional (2D) interference pattern. In this work, we propose a one-stage network (OSNet) for 3D particle volumetric reconstruction. Specifically, by a single feed-forward process, OSNet can retrieve the 3D coordinates of the particles directly from the holograms without high-fidelity image reconstruction at each depth slice. Evaluation results from both synthetic and experimental data confirm the feasibility and robustness of our method under different particle concentrations and noise levels in terms of detection rate and position accuracy, with improved processing speed. The additional applications of 3D particle tracking are also investigated, facilitating the analysis of the dynamic displacements and motions for micro-objects or cells. It can be further extended to various types of computational imaging problems sharing similar traits.

Robust autofocusing method for multi-wavelength lensless imaging

Lensless imaging based on multi-wavelength phase retrieval becomes a promising technology widely used as it has simple acquisition, miniaturized size and low-cost setup. However, measuring the sample-to-sensor distance with high accuracy, which is the key for high-resolution reconstruction, is still a challenge. In this work, we propose a multi-wavelength criterion to realize autofocusing modulation, i.e., achieving much higher accuracy in determining the sample-to-sensor distance, compared to the conventional methods. Three beams in different spectrums are adopted to illuminate the sample, and the resulting holograms are recorded by a CCD camera. The patterns calculated by performing back propagation of the recorded holograms, with exhaustively searched sample-to-sensor distance value, are adopted to access the criterion. Image sharpness can be accessed and the optimal sample-to-sensor distance can be finely determined by targeting the valley of the curve given by the criterion. Through our novel multi-wavelength based autofocusing strategy and executing further phase retrieval process, high-resolution images can be finally retrieved. The applicability and robustness of our method is validated both in simulations and experiments. Our technique provides a useful tool for multi-wavelength lensless imaging under limited experimental conditions.

Focus prediction in digital holographic microscopy using deep convolutional neural networks

Deep artificial neural network learning is an emerging tool in image analysis. We demonstrate its potential in the field of digital holographic microscopy by addressing the challenging problem of determining the in-focus reconstruction depth of Madin-Darby canine kidney cell clusters encoded in digital holograms. A deep convolutional neural network learns the in-focus depths from half a million hologram amplitude images. The trained network correctly determines the in-focus depth of new holograms with high probability, without performing numerical propagation. This paper reports on extensions to preliminary work published earlier as one of the first applications of deep learning in the field of digital holographic microscopy.

Effect of tissue staining in quantitative phase imaging

Quantitative phase imaging (QPI) is an emerging modality, which enables the identification of abnormalities in tissue based on optical properties. QPI can be applied to any biological specimen due to its label-free imaging capability, but its use in stained tissue is unclear. Here, we study the variability of QPI with the staining dye. Several tissues such as brain, heart and lung were stained with hematoxylin and eosin, and their optical properties compared at 550 and 730 nm. Our results showed that phase and scattering coefficients varied when QPI was used at the absorption wavelength of the staining dye. We also found that the variation of optical properties was dependent on tissue morphology.

Optical properties of acute kidney injury measured by quantitative phase imaging

The diagnosis of acute kidney disease (AKI) has been examined mainly by histology, immunohistochemistry and western blot. Though these approaches are widely accepted in the field, it has an inherent limitation due to the lack of high-throughput and quantitative information. For a better understanding of prognosis in AKI, we present a new approach using quantitative phase imaging combined with a wide-field scanning platform. Through the phase-delay information from the tissue, we were able to predict a stage of AKI based on various optical properties such as light scattering coefficient and anisotropy. These optical parameters quantify the deterioration process of the AKI model of tissue. Our device would be a very useful tool when it is required to deliver fast feedback of tissue pathology or when diseases are related to mechanical properties such as fibrosis.

Wavefront-sensing-based autofocusing in microscopy

Massive image acquisition is required along the optical axis in the classical image-analysis-based autofocus method, which significantly decreases autofocus efficiency. A wavefront-sensing-based autofocus technique is proposed to increase the speed of autofocusing and obtain high localization accuracy. Intensities at different planes along the optical axis can be computed numerically after extracting the wavefront at defocus position with the help of the transport-of-intensity equation method. According to the focus criterion, the focal plane can then be determined, and after sample shifting to this plane, the in-focus image can be recorded. The proposed approach allows for fast, precise focus detection with fewer image acquisitions compared to classical image-analysis-based autofocus techniques, and it can be applied in commercial microscopes only with an extra illumination filter.

Digital holography as 3D tracking tool for assessing acoustophoretic particle manipulation

The integration of digital holography (DH) imaging and the acoustic manipulation of micro-particles in a microfluidic environment is investigated. The ability of DH to provide efficient 3D tracking of particles inside a microfluidic channel is exploited to measure the position of multiple objects moving under the effect of stationary ultrasound pressure fields. The axial displacement provides a direct verification of the numerically computed positions of the standing wave's node, while the particles' transversal movement highlights the presence of nodes in the planar direction. Moreover, DH is used to follow the aggregation dynamics of trapped spheres in such nodes by using aggregation rate metrics.

Label-free analysis of mononuclear human blood cells in microfluidic flow by coherent imaging tools

The investigation of the physical properties of peripheral blood mononuclear cells (PBMC) is of great relevance, as they play a key role in regulating human body health. Here we report the possibility to characterize human PBMC in their physiological conditions in a microfluidic-based measurement system. A viscoelastic polymer solution is adopted for 3D alignment of individual cells inflow. An optical signature (OS) acquisition of each flowing cell is performed using a wide angle light scattering apparatus. Besides, a quantitative phase imaging (QPI) holographic system is employed with the aim (i) to check the position in flow of individual cells using a holographic 3D cell tracking method; and (ii) to estimate their 3D morphometric features, such as their refractive index (RI). Results obtained by combining OS and QPI have been compared with literature values, showing good agreement. The results confirm the possibility to obtain sub-micrometric details of physical cell properties in microfluidic flow, avoiding chemical staining or fluorescent labelling.

Changes in optical properties of electroporated cells as revealed by digital holographic microscopy

Changes in optical and shape-related characteristics of B16F10 cells after electroporation were investigated using digital holographic microscopy (DHM). Bipolar rectangular pulses specific for electrochemotherapy were used. Electroporation was performed in an "off-axis" DHM set-up without using exogenous markers. Two types of cell parameters were monitored seconds and minutes after pulse train application: parameters addressing a specifically defined area of the cell (refractive index and cell height) and global cell parameters (projected area, optical phase shift profile and dry mass). The biphasic behavior of cellular parameters was explained by water and mannitol dynamics through the electropermeabilized cell membrane.

Tomographic flow cytometry by digital holography

High-throughput single-cell analysis is a challenging task. Label-free tomographic phase microscopy is an excellent candidate to perform this task. However, in-line tomography is very difficult to implement in practice because it requires a complex set-up for rotating the sample and examining the cell along several directions. We demonstrate that by exploiting the random rolling of cells while they are flowing along a microfluidic channel, it is possible to obtain in-line phase-contrast tomography, if smart strategies for wavefront analysis are adopted. In fact, surprisingly, a priori knowledge of the three-dimensional position and orientation of rotating cells is no longer needed because this information can be completely retrieved through digital holography wavefront numerical analysis. This approach makes continuous-flow cytotomography suitable for practical operation in real-world, single-cell analysis and with a substantial simplification of the optical system; that is, no mechanical scanning or multi-direction probing is required. A demonstration is given for two completely different classes of biosamples: red blood cells and diatom algae. An accurate characterization of both types of cells is reported, despite their very different nature and material content, thus showing that the proposed method can be extended by adopting two alternate strategies of wavefront analysis to many classes of cells.

Hybrid bright-field and hologram imaging of cell dynamics

Volumetric observation is essential for understanding the details of complex biological phenomena. In this study, a bright-field microscope, which provides information on a specific 2D plane, and a holographic microscope, which provides information spread over 3D volumes, are integrated to acquire two complementary images simultaneously. The developed system was successfully applied to capture distinct T-cell adhesion dynamics on inflamed endothelial layers, including capture, rolling, crawling, transendothelial migration, and subendothelial migration.

Precise measurement of orientations of transparent ellipsoidal particles through digital holographic microscopy

A method to measure the orientations of transparent ellipsoidal particles using digital holographic microscopy (DHM) is proposed in this study. This approach includes volumetric recording and numerical reconstruction at different depths. Distinctive light scatterings from an ellipsoid with different angles of orientation are analyzed. A focus function is applied to obtain a reconstructed image that contains a bright line parallel to the major axis of the projected particle, which provides in-plane orientation information. An intensity profile is collected along the major axis of the projected particle in the direction of the optical axis, and this profile is then utilized to measure the out-of-plane orientation of the ellipsoid. After being verified for an ellipsoid with known orientations, the proposed method is applied to ellipsoids suspended in a pipe flow with random orientations. This DHM method can extract the essential information of ellipsoids and therefore has great potential applications in particle dynamics.

Tile-Based Two-Dimensional Phase Unwrapping for Digital Holography Using a Modular Framework

A variety of physical and biomedical imaging techniques, such as digital holography, interferometric synthetic aperture radar (InSAR), or magnetic resonance imaging (MRI) enable measurement of the phase of a physical quantity additionally to its amplitude. However, the phase can commonly only be measured modulo 2π, as a so called wrapped phase map. Phase unwrapping is the process of obtaining the underlying physical phase map from the wrapped phase. Tile-based phase unwrapping algorithms operate by first tessellating the phase map, then unwrapping individual tiles, and finally merging them to a continuous phase map. They can be implemented computationally efficiently and are robust to noise. However, they are prone to failure in the presence of phase residues or erroneous unwraps of single tiles. We tried to overcome these shortcomings by creating novel tile unwrapping and merging algorithms as well as creating a framework that allows to combine them in modular fashion. To increase the robustness of the tile unwrapping step, we implemented a model-based algorithm that makes efficient use of linear algebra to unwrap individual tiles. Furthermore, we adapted an established pixel-based unwrapping algorithm to create a quality guided tile merger. These original algorithms as well as previously existing ones were implemented in a modular phase unwrapping C++ framework. By examining different combinations of unwrapping and merging algorithms we compared our method to existing approaches. We could show that the appropriate choice of unwrapping and merging algorithms can significantly improve the unwrapped result in the presence of phase residues and noise. Beyond that, our modular framework allows for efficient design and test of new tile-based phase unwrapping algorithms. The software developed in this study is freely available.

Optical signature of erythrocytes by light scattering in microfluidic flows

A camera-based light scattering approach coupled with a viscoelasticity-induced cell migration technique has been used to characterize the morphological properties of erythrocytes in microfluidic flows. We have obtained the light scattering profiles (LSPs) of individual living cells in microfluidic flows over a wide angular range and matched them with scattering simulations to characterize their morphological properties. The viscoelasticity-induced 3D cell alignment in microfluidic flows has been investigated by bright-field and holographic microscopy tracking, where the latter technique has been used to obtain precise cell alignment profiles in-flow. Such information allows variable cell probability control in microfluidic flows at very low viscoelastic polymer concentrations, obtaining cell measurements that are almost physiological. Our results confirm the possibility of precise, label-free analysis of individual living erythrocytes in microfluidic flows.

Precise measurement of three-dimensional positions of transparent ellipsoidal particles using digital holographic microscopy

The dynamic motions of various particles suspended in microscale flows are essential phenomena in the scientific and engineering fields. These motions can be precisely measured by using 3D quantitative flow visualization techniques. Moreover, most cells and particles in nature possess a nonspherical shape. Digital holographic microscopy (DHM) is employed to measure the 3D positional information of transparent ellipsoidal particles. Both in-plane and out-of-plane positional information are obtained by analyzing the distinctive light scattering from the microsized ellipsoidal particles. The performance of the 3D position measurement method is experimentally verified for ellipsoidal particles seeded in a planar surface and a microtube. This DHM technique exhibits promising potential in the dynamic analysis of ellipsoidal particles and cells suspended in various microscale fluid flows.

Review of quantitative phase-digital holographic microscopy: promising novel imaging technique to resolve neuronal network activity and identify cellular biomarkers of psychiatric disorders

Quantitative phase microscopy (QPM) has recently emerged as a new powerful quantitative imaging technique well suited to noninvasively explore a transparent specimen with a nanometric axial sensitivity. In this review, we expose the recent developments of quantitative phase-digital holographic microscopy (QP-DHM). Quantitative phase-digital holographic microscopy (QP-DHM) represents an important and efficient quantitative phase method to explore cell structure and dynamics. In a second part, the most relevant QPM applications in the field of cell biology are summarized. A particular emphasis is placed on the original biological information, which can be derived from the quantitative phase signal. In a third part, recent applications obtained, with QP-DHM in the field of cellular neuroscience, namely the possibility to optically resolve neuronal network activity and spine dynamics, are presented. Furthermore, potential applications of QPM related to psychiatry through the identification of new and original cell biomarkers that, when combined with a range of other biomarkers, could significantly contribute to the determination of high risk developmental trajectories for psychiatric disorders, are discussed.

Refocusing criterion via sparsity measurements in digital holography

Several automatic approaches have been proposed in the past to compute the refocus distance in digital holography (DH). However most of them are based on a maximization or minimization of a suitable amplitude image contrast measure, regarded as a function of the reconstruction distance parameter. Here we show that, by using the sparsity measure coefficient regarded as a refocusing criterion in the holographic reconstruction, it is possible to recover the focus plane and, at the same time, establish the degree of sparsity of digital holograms, when samples of the diffraction Fresnel propagation integral are used as a sparse signal representation. We employ a sparsity measurement coefficient known as Gini's index thus showing for the first time, to the best of our knowledge, its application in DH, as an effective refocusing criterion. Demonstration is provided for different holographic configurations (i.e., lens and lensless apparatus) and for completely different objects (i.e., a thin pure phase microscopic object as an in vitro cell, and macroscopic puppets) preparation.

Investigation of osteoblast cells behavior in polymeric 3D micropatterned scaffolds using digital holographic microscopy

The effect of micropatterned polymeric scaffolds on the features of the cultured cells at different time intervals after seeding was investigated by digital holographic microscopy. Both parallel and perpendicular walls, with different heights, were fabricated using two-photon lithography on photopolymers. The walls were subsequently coated with polypyrrole-based thin films using the matrix assisted pulsed laser evaporation technique. Osteoblast-like cells, MG-63 line, were cultured on these polymeric 3D micropatterned scaffolds. To analyze these scaffolds with/without cultured cells, an inverted digital holographic microscope, which provides 3D images, was used. Information about the samples' refractive indices and heights was obtained from the phase shift introduced in the optical path. Characteristics of cell adhesion, alignment, orientation, and morphology as a function of the wall heights and time from seeding were highlighted.

Fully automated digital holographic processing for monitoring the dynamics of a vesicle suspension under shear flow

We investigate the dynamics of a vesicle suspension under shear flow between plates using DHM with a spatially reduced coherent source. Holograms are grabbed at a frequency of 24 frames/sec. The distribution of the vesicle suspension is obtained after numerical processing of the digital holograms sequence resulting in a 4D distribution. Obtaining this distribution is not straightforward and requires special processing to automate the analysis. We present an original method that fully automates the analysis and provides distributions that are further analyzed to extract physical properties of the fluid. Details of the numerical implementation, as well as sample experimental results are presented.

Holographic tracking of living cells by three-dimensional reconstructed complex wavefronts alignment

We propose here a new three-dimensional (3D) holographic tracking method capable to track, simultaneously and in a single step, all the spatial coordinates of micro-objects. The approach is based on the enhanced correlation coefficient (ECC) maximization method but applied, for the first time to the best of our knowledge, directly on the holographic reconstructed complex wave fields. The key novelty of the proposed strategy is its ability to calculate simultaneously the 3D coordinates of cells, without decoupling the contribution of amplitude and phase. The proposed strategy is tested on living cells (i.e., NIH 3T3 mouse fibroblast) flowing into a microfluidic channel and compared with classical holographic tracking approach. Theoretical description and experimental validation of the proposed strategy are reported.

Four-dimensional motility tracking of biological cells by digital holographic microscopy

Three-dimensional profiling and tracking by digital holography microscopy (DHM) provide label-free and quantitative analysis of the characteristics and dynamic processes of objects, since DHM can record real-time data for microscale objects and produce a single hologram containing all the information about their three-dimensional structures. Here, we have utilized DHM to visualize suspended microspheres and microfibers in three dimensions, and record the four-dimensional trajectories of free-swimming cells in the absence of mechanical focus adjustment. The displacement of microfibers due to interactions with cells in three spatial dimensions has been measured as a function of time at subsecond and micrometer levels in a direct and straightforward manner. It has thus been shown that DHM is a highly efficient and versatile means for quantitative tracking and analysis of cell motility.

Particle tracking by full-field complex wavefront subtraction in digital holography microscopy

The 3D tracking of micro-objects, based on digital holography, is proposed through the analysis of the complex wavefront of the light scattered by the micro-samples. Exploiting the advantages of the off-axis full-field holographic interferometry, the tracking of multiple objects is achieved by a direct wavefront analysis at the focal plane overcoming the limitation of the conventional back focal plane interferometry in which only one object at a time can be tracked. Furthermore, the method proposed and demonstrated here is a step forward with respect to other holographic tracking tools. The approach is tested in two experiments, the first investigates the Brownian motion of particles trapped by holographic optical tweezers, while the second relates to the cell motility in a 3D collagen matrix, thus showing its usefulness for lab-on-chip systems in typical bioassay testing.

Sperm trajectories form chiral ribbons

We report the discovery of an entirely new three-dimensional (3D) swimming pattern observed in human and horse sperms. This motion is in the form of ‘chiral ribbons’, where the planar swing of the sperm head occurs on an osculating plane creating in some cases a helical ribbon and in some others a twisted ribbon. The latter, i.e., the twisted ribbon trajectory, also defines a minimal surface, exhibiting zero mean curvature for all the points on its surface. These chiral ribbon swimming patterns cannot be represented or understood by already known patterns of sperms or other micro-swimmers. The discovery of these unique patterns is enabled by holographic on-chip imaging of >33,700 sperm trajectories at >90–140 frames/sec, which revealed that only ~1.7% of human sperms exhibit chiral ribbons, whereas it increases to ~27.3% for horse sperms. These results might shed more light onto the statistics and biophysics of various micro-swimmers' 3D motion.

Imaging through scattering microfluidic channels by digital holography for information recovery in lab on chip

We tackle the problem of information recovery and imaging through scattering microfluidic chips by means of digital holography (DH). In many cases the chip can become opalescent due to residual deposits settling down the inner channel faces, biofilm formation, scattering particle uptake by the channel cladding or its damaging by corrosive substances, or even by condensing effect on the exterior channels walls. In these cases white-light imaging is severely degraded and no information is obtainable at all about the flowing samples. Here we investigate the problem of counting and estimating velocity of cells flowing inside a scattering chip. Moreover we propose and test a method based on the recording of multiple digital holograms to retrieve improved phase-contrast images despite the strong scattering effect. This method helps, thanks to DH, to recover information which, otherwise, would be completely lost.

Field-portable pixel super-resolution colour microscope

Based on partially-coherent digital in-line holography, we report a field-portable microscope that can render lensfree colour images over a wide field-of-view of e.g., >20 mm(2). This computational holographic microscope weighs less than 145 grams with dimensions smaller than 17×6×5 cm, making it especially suitable for field settings and point-of-care use. In this lensfree imaging design, we merged a colorization algorithm with a source shifting based multi-height pixel super-resolution technique to mitigate 'rainbow' like colour artefacts that are typical in holographic imaging. This image processing scheme is based on transforming the colour components of an RGB image into YUV colour space, which separates colour information from brightness component of an image. The resolution of our super-resolution colour microscope was characterized using a USAF test chart to confirm sub-micron spatial resolution, even for reconstructions that employ multi-height phase recovery to handle dense and connected objects. To further demonstrate the performance of this colour microscope Papanicolaou (Pap) smears were also successfully imaged. This field-portable and wide-field computational colour microscope could be useful for tele-medicine applications in resource poor settings.

Wide-field computational color imaging using pixel super-resolved on-chip microscopy

Lens-free holographic on-chip imaging is an emerging approach that offers both wide field-of-view (FOV) and high spatial resolution in a cost-effective and compact design using source shifting based pixel super-resolution. However, color imaging has remained relatively immature for lens-free on-chip imaging, since a 'rainbow' like color artifact appears in reconstructed holographic images. To provide a solution for pixel super-resolved color imaging on a chip, here we introduce and compare the performances of two computational methods based on (1) YUV color space averaging, and (2) Dijkstra's shortest path, both of which eliminate color artifacts in reconstructed images, without compromising the spatial resolution or the wide FOV of lens-free on-chip microscopes. To demonstrate the potential of this lens-free color microscope we imaged stained Papanicolaou (Pap) smears over a wide FOV of ~14 mm(2) with sub-micron spatial resolution.