High-resolution three-dimensional imaging of red blood cells parasitized by Plasmodium falciparum and in situ hemozoin crystals using optical diffraction tomography

Three-dimensional label-free observation of individual bacteria upon antibiotic treatment using optical diffraction tomography

Measuring alterations in bacteria upon antibiotic application is important for basic studies in microbiology, drug discovery, clinical diagnosis, and disease treatment. However, imaging and 3D time-lapse response analysis of individual bacteria upon antibiotic application remain largely unexplored mainly due to limitations in imaging techniques. Here, we present a method to systematically investigate the alterations in individual bacteria in 3D and quantitatively analyze the effects of antibiotics. Using optical diffraction tomography, in-situ responses of Escherichia coli and Bacillus subtilis to various concentrations of ampicillin were investigated in a label-free and quantitative manner. The presented method reconstructs the dynamic changes in the 3D refractive-index distributions of living bacteria in response to antibiotics at sub-micrometer spatial resolution.

Real-time cholesterol sorting in Plasmodium falciparum-erythrocytes as revealed by 3D label-free imaging

Cholesterol, a necessary component of animal cell membranes, is also needed by the lethal human malaria parasite Plasmodium falciparum. Because P. falciparum lacks a cholesterol synthesis pathway and malaria patients have low blood cholesterol, we speculated that it scavenges cholesterol from them in some way. We used time-lapse holotomographic microscopy to observe cholesterol transport in live P. falciparum parasites and structurally investigate erythrocyte membranes, both during and after P. falciparum invasion of human erythrocytes. After P. falciparum initially acquired free cholesterol or inner erythrocytic membrane-derived cholesterol, we observed budding lipid membranes elongating into the cytosol and/or membrane segments migrating there and eventually fusing with the parasite membranes, presumably at the parasitophorous vacuole membrane (PVM). Finally, the cholesterol-containing segments were seen to surround the parasite nucleus. Our imaging data suggest that a novel membrane transport system operates in the cytosol of P. falciparum-infected erythrocytes as a cholesterol import system, likely between the PVM and the erythrocyte membrane, and that this transportation process occurs during the live erythrocyte stages of P. falciparum.

A plasmonic route for the integrated wireless communication of subdiffraction-limited signals

Perfect lenses, superlenses and time-reversal mirrors can support and spatially separate evanescent waves, which is the basis for detecting subwavelength information in the far field. However, the inherent limitations of these methods have prevented the development of systems to dynamically distinguish subdiffraction-limited signals. Utilizing the physical merits of spoof surface plasmon polaritons (SPPs), we demonstrate that subdiffraction-limited signals can be transmitted on planar integrated SPP channels with low loss, low channel interference, and high gain and can be radiated with a very low environmental sensitivity. Furthermore, we show how deep subdiffraction-limited signals that are spatially coupled can be distinguished after line-of-sight wireless transmission. For a visualized demonstration, we realize the high-quality wireless communication of two movies on subwavelength channels over the line of sight in real time using our plasmonic scheme, showing significant advantages over the conventional methods.

Versatile transmission/reflection tomographic diffractive microscopy approach

Tomographic diffractive microscopy (TDM) has gained interest in recent years due to its ability to deliver high-resolution, three-dimensional images of unlabeled samples. It has been applied to transparent samples in transmission mode, as well as to surface studies in reflection mode. Mudry et al. [Opt. Lett.35, 1857 (2010)OPLEDP0146-959210.1364/OL.35.001857] introduced the concept of mirror-assisted TDM (MA-TDM), an elegant approach for achieving quasi-isotropic-resolution microscopic imaging, but which is still to be experimentally applied. In this work, we show that a simplified version of MA-TDM allows for transforming a reflective TDM setup into a more versatile instrument, also capable of observing transparent samples in transmission mode if using specific sample holders made out of a mirror and coated with a low-thickness transparent spacer.

Mitotic Chromosomes in Live Cells Characterized Using High-Speed and Label-Free Optical Diffraction Tomography

The cell nucleus is a three-dimensional, dynamic organelle organized into subnuclear compartments such as chromatin and nucleoli. The structure and function of these compartments are maintained by diffusion and interactions between related factors as well as by dynamic and structural changes. Recent studies using fluorescent microscopic techniques suggest that protein factors can access and are freely mobile in heterochromatin and in mitotic chromosomes, despite their densely packed structure. However, the physicochemical properties of the chromosome during cell division are not fully understood. In the present study, characteristic properties such as the refractive index (RI), volume of the mitotic chromosomes, and diffusion coefficient (D) of fluorescent probes inside the chromosome were quantified using an approach combining label-free optical diffraction tomography with complementary confocal laser-scanning microscopy and fluorescence correlation spectroscopy. Variations in these parameters correlated with osmotic conditions, suggesting that changes in RI are consistent with those of the diffusion coefficient for mitotic chromosomes and cytosol. Serial RI tomography images of chromosomes in live cells during mitosis were compared with three-dimensional confocal micrographs to demonstrate that compaction and decompaction of chromosomes induced by osmotic change were characterized by linked changes in chromosome RI, volume, and the mobilities of fluorescent proteins.

Three-Dimensional Shapes and Cell Deformability of Rat Red Blood Cells during and after Asphyxial Cardiac Arrest

Changes in microcirculation are believed to perform an important role after cardiac arrest. In particular, rheological changes in red blood cells (RBCs) have been observed during and after ischemic-reperfusion injury. Employing three-dimensional laser interferometric microscopy, we investigated three-dimensional shapes and deformability of RBCs during and after asphyxial cardiac arrest in rats at the individual cell level. Rat cardiac arrest was induced by asphyxia. Five rats were maintained for 7 min of no-flow time, and then, cardiopulmonary resuscitation (CPR) was started. Blood samples were obtained before cardiac arrest, during CPR, and 60 min after return of spontaneous circulation (ROSC). Quantitative phase imaging (QPI) techniques based on laser interferometry were used to measure the three-dimensional refractive index (RI) tomograms of the RBC, from which structural and biochemical properties were retrieved. Dynamic membrane fluctuations in the cell membrane were also quantitatively and sensitively measured in order to investigate cell deformability. Mean corpuscular hemoglobin, mean cell volume, mean corpuscular hemoglobin concentration, and red blood cell distribution width remained unchanged during CPR and after ROSC compared with those before cardiac arrest. QPI results revealed that RBC membrane fluctuations, sphericity, and surface area did not change significantly during CPR or after ROSC compared with initial values. In conclusion, no three-dimensional shapes and cell deformability changes in RBCs were detected.

High-resolution 3D refractive index microscopy of multiple-scattering samples from intensity images

Optical diffraction tomography (ODT) reconstructs a sample's volumetric refractive index (RI) to create high-contrast, quantitative 3D visualizations of biological samples. However, standard implementations of ODT use interferometric systems, and so are sensitive to phase instabilities, complex mechanical design, and coherent noise. Furthermore, their reconstruction framework is typically limited to weakly scattering samples, and thus excludes a whole class of multiple-scattering samples. Here, we implement a new 3D RI microscopy technique that utilizes a computational multi-slice beam propagation method to invert the optical scattering process and reconstruct high-resolution (NA > 1.0) 3D RI distributions of multiple-scattering samples. The method acquires intensity-only measurements from different illumination angles and then solves a nonlinear optimization problem to recover the sample's 3D RI distribution. We experimentally demonstrate the reconstruction of samples with varying amounts of multiple-scattering: a 3T3 fibroblast cell, a cluster of C. elegans embryos, and a whole C. elegans worm, with lateral and axial resolutions of ≤ 240 nm and ≤ 900 nm, respectively. The results of this work lays groundwork for future studies into using optical wavelengths to probe 3D RI distributions of highly scattering biological organisms.

Label-free bioanalysis of Leishmania infantum using refractive index tomography with partially coherent illumination

In this work, we report the use of refractive index (RI) tomography for quantitative analysis of unstained DH82 cell line infected with Leishmania infantum. The cell RI is reconstructed by using a modality of optical diffraction tomography technique that employs partially coherent illumination, thus enabling inherent compatibility with conventional wide-field microscopes. The experimental results demonstrate that the cell dry mass concentration (DMC) obtained from the RI allows for reliable detection and quantitative characterization of the infection and its temporal evolution. The RI provides important insight for studying morphological changes, particularly membrane blebbing linked to an apoptosis (cell death) process induced by the disease. Moreover, the results evidence that infected DH82 cells exhibit a higher DMC than healthy samples. These findings open up promising perspectives for clinical diagnosis of Leishmania.

Projection extrapolation routine for tight-frame limited-angle optical diffraction tomography

We propose a data-replenishment-type expansion of the modified Gerchberg-Papoulis (GP) algorithm for limited-angle optical diffraction tomography (LAODT), which prevents artifact buildup in the GP reconstructions of confined bulk objects tightly fitting the active field of view (FoV) of the LAODT microscope. Objects crossing the FoV borders are not considered. The method relies on a Fourier-based forward projector complementary to the GP solver with no additional constraints. Fourier space regridding errors are minimized by means of one-dimensional oversampling in the axial direction, which is demonstrated to be more efficient than standard projection padding. Verification of both synthetic and experimental sinograms confirms the ability of the procedure to deduce missing projection parts necessary for the correct reconstruction.

Physicochemical Properties of Nucleoli in Live Cells Analyzed by Label-Free Optical Diffraction Tomography

The cell nucleus is three-dimensionally and dynamically organized by nuclear components with high molecular density, such as chromatin and nuclear bodies. The structure and functions of these components are represented by the diffusion and interaction of related factors. Recent studies suggest that the nucleolus can be assessed using various protein probes, as the probes are highly mobile in this organelle, although it is known that they have a densely packed structure. However, physicochemical properties of the nucleolus itself, such as molecular density and volume when cellular conditions are changed, are not yet fully understood. In this study, physical parameters such as the refractive index (RI) and volume of the nucleoli in addition to the diffusion coefficient (D) of fluorescent probe protein inside the nucleolus are quantified and compared by combining label-free optical diffraction tomography (ODT) with confocal laser scanning microscopy (CLSM)-based fluorescence correlation spectroscopy (FCS). 3D evaluation of RI values and corresponding RI images of nucleoli in live HeLa cells successfully demonstrated varying various physiological conditions. Our complimentary method suggests that physical property of the nucleolus in live cell is sensitive to ATP depletion and transcriptional inhibition, while it is insensitive to hyper osmotic pressure when compared with the cytoplasm and nucleoplasm. The result demonstrates that the nucleolus has unique physicochemical properties when compared with other cellular components.

Malaria-Infected Red Blood Cell Analysis through Optical and Biochemical Parameters Using the Transport of Intensity Equation and the Microscope's Optical Properties

The accuracy, reliability, speed and cost of the methods used for malaria diagnosis are key to the diseases' treatment and eventual eradication. However, improvement in any one of these requirements can lead to deterioration of the rest due to their interdependence. We propose an optical method that provides fast detection of malaria-infected red blood cells (RBCs) at a lower cost. The method is based on the combination of deconvolution, topography and three-dimensional (3D) refractive index reconstruction of the malaria-infected RBCs by use of the transport of intensity equation. Using our method, healthy RBCs were identified by their biconcave shape, quasi-uniform spatial distribution of their refractive indices and quasi-uniform concentration of hemoglobin. The values of these optical and biochemical parameters were found to be in agreement with the values reported in the literature. Results for the malaria-infected RBCs were significantly different from those of the healthy RBCs. The topography of the cells and their optical and biochemical parameters enabled identification of their stages of infection. This work introduces a significant method of analyzing malaria-infected RBCs at a lower cost and without the use of fluorescent labels for the parasites.

Study of Optical Configurations for Multiple Enhancement of Microalgal Biomass Production

Microalga is a promising biomass feedstock to restore the global carbon balance and produce sustainable bioenergy. However, the present biomass productivity of microalgae is not high enough to be marketable mainly because of the inefficient utilization of solar energy. Here, we study optical engineering strategies to lead to a breakthrough in the biomass productivity and photosynthesis efficiency of a microalgae cultivation system. Our innovative optical system modelling reveals the theoretical potential (>100 g m⁻² day⁻¹) of the biomass productivity and it is used to compare the optical aspects of various photobioreactor designs previously proposed. Based on the optical analysis, the optimized V-shaped configuration experimentally demonstrates an enhancement of biomass productivity from 20.7 m⁻² day⁻¹ to 52.0 g m⁻² day⁻¹, under the solar-simulating illumination of 7.2 kWh m⁻² day⁻¹, through the dilution and trapping of incident energy. The importance of quantitative optical study for microalgal photosynthesis is clearly exhibited with practical demonstration of the doubled light utilization efficiencies.

Enhancement of optical resolution in three-dimensional refractive-index tomograms of biological samples by employing micromirror-embedded coverslips

Optical diffraction tomography (ODT) enables the reconstruction of the three-dimensional (3D) refractive-index (RI) distribution of a biological cell, which provides invaluable information for cellular and subcellular structures in a non-invasive manner. However, ODT suffers from an inferior axial resolution, due to the limited accessible angles imposed by the numerical aperture of the objective lens. In this study, we propose and experimentally demonstrate an approach to enhance the 3D reconstruction performance in ODT. By employing trapezoidal micromirrors, side scattered signals from the sample are measured for various side plane-wave-illumination angles. By combining the side scattered fields with the forward scattered fields, the axial resolution and 3D image quality of ODT are improved, without changing optical instruments. The feasibility and applicability of the proposed method are demonstrated by reconstructing the 3D RI distribution of a red blood cell and HeLa cells in hydrogel. We also present systematic analyses of the improved 3D imaging performance using numerical simulations and experimental measurements for the 3D transfer function, a point object, and a microsphere. The analyses demonstrate an improved axial resolution of 0.31 μm, 4.8 times smaller than that of the conventional method. The proposed method enables the non-invasive and accurate 3D imaging of 3D cultured cells, which is crucial for cell biology studies.

Axonal Transport, Phase-Separated Compartments, and Neuron Mechanics - A New Approach to Investigate Neurodegenerative Diseases

Many molecular and cellular pathogenic mechanisms of neurodegenerative diseases have been revealed. However, it is unclear what role a putatively impaired neuronal transport with respect to altered mechanical properties of neurons play in the initiation and progression of such diseases. The biochemical aspects of intracellular axonal transport, which is important for molecular movements through the cytoplasm, e.g., mitochondrial movement, has already been studied. Interestingly, transport deficiencies are associated with the emergence of the affliction and potentially linked to disease transmission. Transport along the axon depends on the normal function of the neuronal cytoskeleton, which is also a major contributor to neuronal mechanical properties. By contrast, little attention has been paid to the mechanical properties of neurons and axons impaired by neurodegeneration, and of membraneless, phase-separated organelles such as stress granules (SGs) within neurons. Mechanical changes may indicate cytoskeleton reorganization and function, and thus give information about the transport and other system impairment. Nowadays, several techniques to investigate cellular mechanical properties are available. In this review, we discuss how select biophysical methods to probe material properties could contribute to the general understanding of mechanisms underlying neurodegenerative diseases.

Combining Three-Dimensional Quantitative Phase Imaging and Fluorescence Microscopy for the Study of Cell Pathophysiology

Quantitative phase imaging (QPI) has emerged as one of the powerful imaging tools for the study of live cells in a non-invasive manner. In particular, multimodal approaches combining QPI and fluorescence microscopic techniques have been recently developed for superior spatiotemporal resolution as well as high molecular specificity. In this review, we briefly summarize recent advances in three-dimensional QPI combined with fluorescence techniques for the correlative study of cell pathophysiology. Through this review, biologists and clinicians can be provided with insights on this rapidly growing field of research and may find broader applications to investigate unrevealed nature in cell physiology and related diseases.

Machine learning-based in-line holographic sensing of unstained malaria-infected red blood cells

Accurate and immediate diagnosis of malaria is important for medication of the infectious disease. Conventional methods for diagnosing malaria are time consuming and rely on the skill of experts. Therefore, an automatic and simple diagnostic modality is essential for healthcare in developing countries that lack the expertise of trained microscopists. In the present study, a new automatic sensing method using digital in-line holographic microscopy (DIHM) combined with machine learning algorithms was proposed to sensitively detect unstained malaria-infected red blood cells (iRBCs). To identify the RBC characteristics, 13 descriptors were extracted from segmented holograms of individual RBCs. Among the 13 descriptors, 10 features were highly statistically different between healthy RBCs (hRBCs) and iRBCs. Six machine learning algorithms were applied to effectively combine the dominant features and to greatly improve the diagnostic capacity of the present method. Among the classification models trained by the 6 tested algorithms, the model trained by the support vector machine (SVM) showed the best accuracy in separating hRBCs and iRBCs for training (n = 280, 96.78%) and testing sets (n = 120, 97.50%). This DIHM-based artificial intelligence methodology is simple and does not require blood staining. Thus, it will be beneficial and valuable in the diagnosis of malaria.

Measurements of three-dimensional refractive index tomography and membrane deformability of live erythrocytes from Pelophylax nigromaculatus

Unlike mammalian erythrocytes, amphibian erythrocytes have distinct morphological features including large cell sizes and the presence of nuclei. The sizes of the cytoplasm and nuclei of erythrocytes vary significantly over different species, their environments, or pathophysiology, which makes hematological studies important for investigating amphibian species. Here, we present a label-free three-dimensional optical quantification of individual amphibian erythrocytes from frogs Pelophylax nigromaculatus (Rana nigromaculata). Using optical diffraction tomography, we measured three-dimensional refractive index (RI) tomograms of the cells, which clearly distinguished the cytoplasm and nuclei of the erythrocytes. From the measured RI tomograms, we extracted the relevant biochemical parameters of the cells, including hemoglobin contents and hemoglobin concentrations. Furthermore, we measured dynamic membrane fluctuations and investigated the mechanical properties of the cell membrane. From the statistical and correlative analysis of these retrieved parameters, we investigated interspecific differences between frogs and previously studied mammals.

Super-resolution three-dimensional fluorescence and optical diffraction tomography of live cells using structured illumination generated by a digital micromirror device

We present a multimodal approach for measuring the three-dimensional (3D) refractive index (RI) and fluorescence distributions of live cells by combining optical diffraction tomography (ODT) and 3D structured illumination microscopy (SIM). A digital micromirror device is utilized to generate structured illumination patterns for both ODT and SIM, which enables fast and stable measurements. To verify its feasibility and applicability, the proposed method is used to measure the 3D RI distribution and 3D fluorescence image of various samples, including a cluster of fluorescent beads, and the time-lapse 3D RI dynamics of fluorescent beads inside a HeLa cell, from which the trajectory of the beads in the HeLa cell is analyzed using spatiotemporal correlations.

Label-free, high-throughput detection of P. falciparum infection in sphered erythrocytes with digital holographic microscopy

Effective malaria treatment requires rapid and accurate diagnosis of infecting species and actual parasitemia. Despite the recent success of rapid tests, the analysis of thick and thin blood smears remains the gold standard for routine malaria diagnosis in endemic areas. For non-endemic regions, sample preparation and analysis of blood smears are an issue due to low microscopy expertise and few cases of imported malaria. Automation of microscopy results could be beneficial to quickly confirm suspected infections in such conditions. Here, we present a label-free, high-throughput method for early malaria detection with the potential to reduce inter-observer variation by reducing sample preparation and analysis effort. We used differential digital holographic microscopy in combination with two-dimensional hydrodynamic focusing for the label-free detection of P. falciparum infection in sphered erythrocytes, with a parasitemia detection limit of 0.01%. Moreover, the achieved differentiation of P. falciparum ring-, trophozoite- and schizont life cycle stages in synchronized cultures demonstrates the potential for future discrimination of even malaria species.

Cell Swelling Induced by the Antimalarial KAE609 (Cipargamin) and Other PfATP4-Associated Antimalarials

For an increasing number of antimalarial agents identified in high-throughput phenotypic screens, there is evidence that they target PfATP4, a putative Na⁺ efflux transporter on the plasma membrane of the human malaria parasite Plasmodium falciparum For several such "PfATP4-associated" compounds, it has been noted that their addition to parasitized erythrocytes results in cell swelling. Here we show that six structurally diverse PfATP4-associated compounds, including the clinical candidate KAE609 (cipargamin), induce swelling of both isolated blood-stage parasites and intact parasitized erythrocytes. The swelling of isolated parasites is dependent on the presence of Na⁺ in the external environment and may be attributed to the osmotic consequences of Na⁺ uptake. The swelling of the parasitized erythrocyte results in an increase in its osmotic fragility. Countering cell swelling by increasing the osmolarity of the extracellular medium reduces the antiplasmodial efficacy of PfATP4-associated compounds, consistent with cell swelling playing a role in the antimalarial activity of this class of compounds.

Label-free non-invasive quantitative measurement of lipid contents in individual microalgal cells using refractive index tomography

Microalgae are promising candidates for biofuel production due to their high lipid content. To facilitate utilization of the microalgae for biofuel, rapid quantification of the lipid contents in microalgae is necessary. However, conventional methods based on the chemical extraction of lipids require a time-consuming destructive extraction process. Here, we demonstrate label-free, non-invasive, rapid quantification of the lipid contents in individual micro-algal cells measuring the three-dimensional refractive index tomograms. We measure three-dimensional refractive index distributions within Nannochloropsis oculata cells and find that lipid droplets are identifiable in tomograms by their high refractive index. In addition, we alter N. oculata under nitrogen deficiency by measuring the volume, lipid weight, and dry cell weight of individual cells. Characterization of individual cells allows correlative analysis between the lipid content and size of individual cells.

Usage of density analysis based on micro-CT for studying lung injury associated with burn-blast combined injury

BACKGROUND

Burn-blast combined injury is a kind of injury caused by heat and blast at the same time. The lung injury after burn-blast combined injuries is of primary importance, and investigation of lung injury is needed in the clinical care of patients. Computed tomography (CT) is one of the standard tools used to observe the anatomical basis and pathophysiology of acute lung injury.

METHODS

We applied a method of fast 3D (three-dimensional) reconstruction to calculate the density value of the lung injury by CT analysis. Blast-injury group (BL group), burn-injury group (B group), burn-blast combined injury group (BBL group), and sham control group (C group) were established. Each group had 16 rats. The three-dimensional images of the lung tissue were obtained at 6h, 24h, and 48h according to the CT value. The average density of the whole lung, left lung, and right lung were measured. The lung tissues were paraffin-embedded and HE stained. Smith scoring was performed according to the pathological findings.

RESULTS

In the BBL group, the density of the lung tissue was higher than those of the BL group and B group (P<0.01). The lung tissue density values at 24h after injury were higher than those at 6h and 48h after injury (P<0.01). Pathological results confirmed the changes of density analysis of the lung tissue.

CONCLUSION

The results have indicated that density analysis through a CT scan can be used as a way to evaluate lung injury in a burn-blast injury.

Tomographic phase microscopy: principles and applications in bioimaging [Invited]

Tomographic phase microscopy (TPM) is an emerging optical microscopic technique for bioimaging. TPM uses digital holographic measurements of complex scattered fields to reconstruct three-dimensional refractive index (RI) maps of cells with diffraction-limited resolution by solving inverse scattering problems. In this paper, we review the developments of TPM from the fundamental physics to its applications in bioimaging. We first provide a comprehensive description of the tomographic reconstruction physical models used in TPM. The RI map reconstruction algorithms and various regularization methods are discussed. Selected TPM applications for cellular imaging, particularly in hematology, are reviewed. Finally, we examine the limitations of current TPM systems, propose future solutions, and envision promising directions in biomedical research.

Three-dimensional label-free imaging and analysis of Pinus pollen grains using optical diffraction tomography

The structure of pollen grains is related to the reproductive function of the plants. Here, three-dimensional (3D) refractive index maps were obtained for individual conifer pollen grains using optical diffraction tomography (ODT). The 3D morphological features of pollen grains from pine trees were investigated using measured refractive index maps, in which distinct substructures were clearly distinguished and analyzed. Morphological and physiochemical parameters of the pollen grains were quantified from the obtained refractive index (RI) maps and used to quantitatively study the interspecific differences of pollen grains from different strains. Our results demonstrate that ODT can assess the structure of pollen grains. This label-free and rapid 3D imaging approach may provide a new platform for understanding the physiology of pollen grains.

Dynamic spatial filtering using a digital micromirror device for high-speed optical diffraction tomography

Optical diffraction tomography (ODT) is an emerging microscopy technique for three-dimensional (3D) refractive index (RI) mapping of transparent specimens. Recently, the digital micromirror device (DMD) based scheme for angle-controlled plane wave illumination has been proposed to improve the imaging speed and stability of ODT. However, undesired diffraction noise always exists in the reported DMD-based illumination scheme, which leads to a limited contrast ratio of the measurement fringe and hence inaccurate RI mapping. Here we present a novel spatial filtering method, based on a second DMD, to dynamically remove the diffraction noise. The reported results illustrate significantly enhanced image quality of the obtained interferograms and the subsequently derived phase maps. And moreover, with this method, we demonstrate mapping of 3D RI distribution of polystyrene beads as well as biological cells with high accuracy. Importantly, with the proper hardware configuration, our method does not compromise the 3D imaging speed advantage promised by the DMD-based illumination scheme. Specifically, we have been able to successfully obtain interferograms at over 1 kHz speed, which is critical for potential high-throughput label-free 3D image cytometry applications.

Optical diffraction tomography with fully and partially coherent illumination in high numerical aperture label-free microscopy [Invited]

Quantitative label-free imaging is an important tool for the study of living microorganisms that, during the last decade, has attracted wide attention from the optical community. Optical diffraction tomography (ODT) is probably the most relevant technique for quantitative label-free 3D imaging applied in wide-field microscopy in the visible range. The ODT is usually performed using spatially coherent light illumination and specially designed holographic microscopes. Nevertheless, the ODT is also compatible with partially coherent illumination and can be realized in conventional wide-field microscopes by applying refocusing techniques, as it has been recently demonstrated. Here, we compare these two ODT modalities, underlining their pros and cons and discussing the optical setups for their implementation. In particular, we pay special attention to a system that is compatible with a conventional wide-field microscope that can be used for both ODT modalities. It consists of two easily attachable modules: the first for sample illumination engineering based on digital light processing technology; the other for focus scanning by using an electrically driven tunable lens. This hardware allows for a programmable selection of the wavelength and the illumination design, and provides fast data acquisition as well. Its performance is experimentally demonstrated in the case of ODT with partially coherent illumination providing speckle-free 3D quantitative imaging.

Structured illumination microscopy for dual-modality 3D sub-diffraction resolution fluorescence and refractive-index reconstruction

Though structured illumination (SI) microscopy is a popular imaging technique conventionally associated with fluorescent super-resolution, recent works have suggested its applicability towards sub-diffraction resolution coherent imaging with quantitative endogenous biological contrast. Here, we demonstrate that SI can efficiently integrate together the principles of fluorescent super-resolution and coherent synthetic aperture to achieve 3D dual-modality sub-diffraction resolution, fluorescence and refractive-index (RI) visualizations of biological samples. We experimentally demonstrate this framework by introducing a SI microscope capable of 3D sub-diffraction resolution fluorescence and RI imaging, and verify its biological visualization capabilities by experimentally reconstructing 3D RI/fluorescence visualizations of fluorescent calibration microspheres as well as alveolar basal epithelial adenocarcinoma (A549) and human colorectal adenocarcinmoa (HT-29) cells, fluorescently stained for F-actin. This demonstration may suggest SI as an especially promising imaging technique to enable future biological studies that explore synergistically operating biophysical/biochemical and molecular mechanisms at sub-diffraction resolutions.

Correlative three-dimensional fluorescence and refractive index tomography: bridging the gap between molecular specificity and quantitative bioimaging

Optical diffraction tomography (ODT) provides label-free three-dimensional (3D) refractive index (RI) measurement of biological samples. However, due to the nature of the RI values of biological specimens, ODT has limited access to molecular specific information. Here, we present an optical setup combining ODT with three-channel 3D fluorescence microscopy, to enhance the molecular specificity of the 3D RI measurement. The 3D RI distribution and 3D deconvoluted fluorescence images of HeLa cells and NIH-3T3 cells are measured, and the cross-correlative analysis between RI and fluorescence of live cells are presented.

Beyond Born-Rytov limit for super-resolution optical diffraction tomography

Optical diffraction tomography (ODT) using Born or Rytov approximation suffers from severe distortions in reconstructed refractive index (RI) tomograms when multiple scattering occurs or the scattering signals are strong. These effects are usually seen as a significant impediment to the application of ODT because multiple scattering is directly linked to an unknown object itself rather than a surrounding medium, and a strong scatter invalidates the underlying assumptions of the Born and Rytov approximations. The focus of this article is to demonstrate for the first time that multiple scattering and high material contrast, if handled aptly, can significantly improve the image quality of the ODT thanks to multiple scattering inside a sample. Experimental verification using various phantom and biological cells substantiates that we not only revealed the structures that were not observable using the conventional approaches but also resolved the long-standing problem of missing cones in the ODT.

Compensation of aberration in quantitative phase imaging using lateral shifting and spiral phase integration

We present a simple and effective method to eliminate system aberrations in quantitative phase imaging. Using spiral phase integration, complete information about system aberration is calculated from three laterally shifted phase images. The present method is especially useful when measuring confluent samples in which acquisition of background area is challenging. To demonstrate validity and applicability, we present measurements of various types of samples including microspheres, HeLa cells, and mouse brain tissue. Working conditions and limitations are systematically analyzed and discussed.

Illumination-related errors in limited-angle optical diffraction tomography

In the paper, the design and tolerances of optical systems and scanning components used in limited-angle optical diffraction tomography are analyzed in order to improve the performance of the measurement systems and to encourage the application of tomography as a standard method for quantitative analysis of 3D refractive index distribution in biological microstructures. The first part of the presented analysis consists of component selection for the scanning device and optical system in the illumination part of the setup and the influence of the illumination wavefront on reconstruction quality. In the second part, the sensitivity of the tomographic reconstruction quality to three representative measurement-related errors based on synthetic data is demonstrated. Finally, a configuration of the system, selected to minimize reconstruction errors, is proposed and alignment tolerances simulated using the Monte Carlo method are provided.

Morphometric analysis of erythrocytes from patients with thalassemia using tomographic diffractive microscopy

Complete blood count is the most common test to detect anemia, but it is unable to obtain the abnormal shape of erythrocytes, which highly correlates with the hematologic function. Tomographic diffractive microscopy (TDM) is an emerging technique capable of quantifying three-dimensional (3-D) refractive index (RI) distributions of erythrocytes without labeling. TDM was used to characterize optical and morphological properties of 172 erythrocytes from healthy volunteers and 419 erythrocytes from thalassemic patients. To efficiently extract and analyze the properties of erythrocytes, we developed an adaptive region-growing method for automatically delineating erythrocytes from 3-D RI maps. The thalassemic erythrocytes not only contained lower hemoglobin content but also showed doughnut shape and significantly lower volume, surface area, effective radius, and average thickness. A multi-indices prediction model achieved perfect accuracy of diagnosing thalassemia using four features, including the optical volume, surface-area-to-volume ratio, sphericity index, and surface area. The results demonstrate the ability of TDM to provide quantitative, hematologic measurements and to assess morphological features of erythrocytes to distinguish healthy and thalassemic erythrocytes.

Reconstructions of refractive index tomograms via a discrete algebraic reconstruction technique

Optical diffraction tomography (ODT) provides three-dimensional refractive index (RI) tomograms of a transparent microscopic object. However, because of the finite numerical aperture of objective lenses, ODT has a limited access to diffracted light and suffers from poor spatial resolution, particularly along the axial direction. To overcome the limitation of the quality of RI tomography, we present an algorithm that accurately reconstructs RI tomography of a specimen with discrete and uniform RI, using prior information about the RI levels. Through simulations and experiments on various samples, including microspheres, red blood cells, and water droplets, we show that the proposed method can precisely reconstruct RI tomograms of samples which have discrete and homogenous RI distributions in the presence of the missing information and noise.

Holographic tomography with object rotation and two-directional off-axis illumination

A hybrid system of holographic tomography, which utilizes rotation of a sample and two-directional, off-axis illumination is proposed. The applied type of illumination brings two major benefits. First, it offers theoretical potential for the resolution improvement with respect to conventional tomography. Second, it enables effective, numerical compensation of the defocus error, which is achieved with an accurate, noise-immune autofocusing. Hence, the main practical obstacle of hybrid tomography is removed and its high-resolution potential is put into practice. The utility of the proposed concept is experimentally demonstrated with the tomographic measurement of a photonic crystal fiber.

Melittin-induced alterations in morphology and deformability of human red blood cells using quantitative phase imaging techniques

Here, the actions of melittin, the active molecule of apitoxin or bee venom, were investigated on human red blood cells (RBCs) using quantitative phase imaging techniques. High-resolution real-time 3-D refractive index (RI) measurements and dynamic 2-D phase images of individual melittin-bound RBCs enabled in-depth examination of melittin-induced biophysical alterations of the cells. From the measurements, morphological, intracellular, and mechanical alterations of the RBCs were analyzed quantitatively. Furthermore, leakage of haemoglobin (Hb) inside the RBCs at high melittin concentration was also investigated.

Generalized image deconvolution by exploiting the transmission matrix of an optical imaging system

Intact optical information of an object delivered through an imaging system is deteriorated by imperfect optical elements and unwanted defects. Image deconvolution has been widely exploited as a recovery technique due to its practical feasibility, and operates by assuming linear shift-invariant property of the imaging system. However, shift invariance does not rigorously hold in all imaging situations and is not a necessary condition for solving an inverse problem of light propagation. Several improved deconvolution techniques exploiting spatially variant point spread functions have been proposed in previous studies. However, the full characterization of an optical imaging system for compensating aberrations has not been considered. Here, we present a generalized method to solve the linear inverse problem of coherent light propagations without any regularization method or constraint on shift invariance by fully measuring the transmission matrix of the imaging system. Our results show that severe aberrations produced by a tilted lens or an inserted disordered layer can be corrected properly only by the proposed generalized image deconvolution. This work generalizes the theory of image deconvolution, and enables distortion-free imaging under general imaging condition.

Holographic deep learning for rapid optical screening of anthrax spores

Establishing early warning systems for anthrax attacks is crucial in biodefense. Despite numerous studies for decades, the limited sensitivity of conventional biochemical methods essentially requires preprocessing steps and thus has limitations to be used in realistic settings of biological warfare. We present an optical method for rapid and label-free screening of Bacillus anthracis spores through the synergistic application of holographic microscopy and deep learning. A deep convolutional neural network is designed to classify holographic images of unlabeled living cells. After training, the network outperforms previous techniques in all accuracy measures, achieving single-spore sensitivity and subgenus specificity. The unique "representation learning" capability of deep learning enables direct training from raw images instead of manually extracted features. The method automatically recognizes key biological traits encoded in the images and exploits them as fingerprints. This remarkable learning ability makes the proposed method readily applicable to classifying various single cells in addition to B. anthracis, as demonstrated for the diagnosis of Listeria monocytogenes, without any modification. We believe that our strategy will make holographic microscopy more accessible to medical doctors and biomedical scientists for easy, rapid, and accurate point-of-care diagnosis of pathogens.

Holographic deep learning for rapid optical screening of anthrax spores

Establishing early warning systems for anthrax attacks is crucial in biodefense. Despite numerous studies for decades, the limited sensitivity of conventional biochemical methods essentially requires preprocessing steps and thus has limitations to be used in realistic settings of biological warfare. We present an optical method for rapid and label-free screening of Bacillus anthracis spores through the synergistic application of holographic microscopy and deep learning. A deep convolutional neural network is designed to classify holographic images of unlabeled living cells. After training, the network outperforms previous techniques in all accuracy measures, achieving single-spore sensitivity and subgenus specificity. The unique "representation learning" capability of deep learning enables direct training from raw images instead of manually extracted features. The method automatically recognizes key biological traits encoded in the images and exploits them as fingerprints. This remarkable learning ability makes the proposed method readily applicable to classifying various single cells in addition to B. anthracis, as demonstrated for the diagnosis of Listeria monocytogenes, without any modification. We believe that our strategy will make holographic microscopy more accessible to medical doctors and biomedical scientists for easy, rapid, and accurate point-of-care diagnosis of pathogens.

Identification of non-activated lymphocytes using three-dimensional refractive index tomography and machine learning

Identification of lymphocyte cell types are crucial for understanding their pathophysiological roles in human diseases. Current methods for discriminating lymphocyte cell types primarily rely on labelling techniques with magnetic beads or fluorescence agents, which take time and have costs for sample preparation and may also have a potential risk of altering cellular functions. Here, we present the identification of non-activated lymphocyte cell types at the single-cell level using refractive index (RI) tomography and machine learning. From the measurements of three-dimensional RI maps of individual lymphocytes, the morphological and biochemical properties of the cells are quantitatively retrieved. To construct cell type classification models, various statistical classification algorithms are compared, and the k-NN (k = 4) algorithm was selected. The algorithm combines multiple quantitative characteristics of the lymphocyte to construct the cell type classifiers. After optimizing the feature sets via cross-validation, the trained classifiers enable identification of three lymphocyte cell types (B, CD4+ T, and CD8+ T cells) with high sensitivity and specificity. The present method, which combines RI tomography and machine learning for the first time to our knowledge, could be a versatile tool for investigating the pathophysiological roles of lymphocytes in various diseases including cancers, autoimmune diseases, and virus infections.

Tomographic active optical trapping of arbitrarily shaped objects by exploiting 3D refractive index maps

Optical trapping can manipulate the three-dimensional (3D) motion of spherical particles based on the simple prediction of optical forces and the responding motion of samples. However, controlling the 3D behaviour of non-spherical particles with arbitrary orientations is extremely challenging, due to experimental difficulties and extensive computations. Here, we achieve the real-time optical control of arbitrarily shaped particles by combining the wavefront shaping of a trapping beam and measurements of the 3D refractive index distribution of samples. Engineering the 3D light field distribution of a trapping beam based on the measured 3D refractive index map of samples generates a light mould, which can manipulate colloidal and biological samples with arbitrary orientations and/or shapes. The present method provides stable control of the orientation and assembly of arbitrarily shaped particles without knowing a priori information about the sample geometry. The proposed method can be directly applied in biophotonics and soft matter physics.

Controlling the three-dimensional behaviour of arbitrarily shaped and oriented particles with optical tweezers is a challenging task. Here, Kim and Park use tomographic active trapping to manipulate non-spherical particles and particle ensembles as well as biological cells.

Measurements of morphological and biophysical alterations in individual neuron cells associated with early neurotoxic effects in Parkinson's disease

Parkinson's disease (PD) is a common neurodegenerative disease. However, therapeutic methods of PD are still limited due to complex pathophysiology in PD. Here, optical measurements of individual neurons from in vitro PD model using optical diffraction tomography (ODT) are presented. By measuring 3D refractive index distribution of neurons, morphological and biophysical alterations in in-vitro PD model are quantitatively investigated. It was found that neurons show apoptotic features in early PD progression. The present approach will open up new opportunities for quantitative investigation of the pathophysiology of various neurodegenerative diseases. © 2017 International Society for Advancement of Cytometry.

Refractive index tomograms and dynamic membrane fluctuations of red blood cells from patients with diabetes mellitus

In this paper, we present the optical characterisations of diabetic red blood cells (RBCs) in a non-invasive manner employing three-dimensional (3-D) quantitative phase imaging. By measuring 3-D refractive index tomograms and 2-D time-series phase images, the morphological (volume, surface area and sphericity), biochemical (haemoglobin concentration and content) and mechanical (membrane fluctuation) parameters were quantitatively retrieved at the individual cell level. With simultaneous measurements of individual cell properties, systematic correlative analyses on retrieved RBC parameters were also performed. Our measurements show there exist no statistically significant alterations in morphological and biochemical parameters of diabetic RBCs, compared to those of healthy (non-diabetic) RBCs. In contrast, membrane deformability of diabetic RBCs is significantly lower than that of healthy, non-diabetic RBCs. Interestingly, non-diabetic RBCs exhibit strong correlations between the elevated glycated haemoglobin in RBC cytoplasm and decreased cell deformability, whereas diabetic RBCs do not show correlations. Our observations strongly support the idea that slow and irreversible glycation of haemoglobin and membrane proteins of RBCs by hyperglycaemia significantly compromises RBC deformability in diabetic patients.

Antibacterial Activities of Graphene Oxide-Molybdenum Disulfide Nanocomposite Films

Two-dimensional (2D) nanomaterials, such as graphene-based materials and transition metal dichalcogenide (TMD) nanosheets, are promising materials for biomedical applications owing to their remarkable cytocompatibility and physicochemical properties. On the basis of their potent antibacterial properties, 2D materials have potential as antibacterial films, wherein the 2D nanosheets are immobilized on the surface and the bacteria may contact with the basal planes of 2D nanosheets dominantly rather than contact with the sharp edges of nanosheets. To address these points, in this study, we prepared an effective antibacterial surface consisting of representative 2D materials, i.e., graphene oxide (GO) and molybdenum disulfide (MoS₂), formed into nanosheets on a transparent substrate for real device applications. The antimicrobial properties of the GO-MoS₂ nanocomposite surface toward the Gram-negative bacteria Escherichia coli were investigated, and the GO-MoS₂ nanocomposite exhibited enhanced antimicrobial effects with increased glutathione oxidation capacity and partial conductivity. Furthermore, direct imaging of continuous morphological destruction in the individual bacterial cells having contacts with the GO-MoS₂ nanocomposite surface was characterized by holotomographic (HT) microscopy, which could be used to detect the refractive index (RI) distribution of each voxel in bacterial cell and reconstruct the three-dimensional (3D) mapping images of bacteria. In this regard, the decreases in both the volume (67.2%) and the dry mass (78.8%) of bacterial cells that came in contact with the surface for 80 min were quantitatively measured, and releasing of intracellular components mediated by membrane and oxidative stress was observed. Our findings provided new insights into the antibacterial properties of 2D nanocomposite film with label-free tracing of bacterial cell which improve our understanding of antimicrobial activities and opened a window for the 2D nanocomposite as a practical antibacterial film in biomedical applications.

Time-multiplexed structured illumination using a DMD for optical diffraction tomography

We present a time-multiplexing structured illumination control technique for optical diffraction tomography (ODT). Instead of tilting the angle of illumination, time-multiplexed sinusoidal illumination is exploited using a digital micromirror device (DMD). The present method effectively eliminates unwanted diffracted beams from binary DMD patterns, which deteriorates the image quality of the ODT in the previous binary Lee hologram method. We experimentally show the feasibility and advantage of the present method by reconstructing three-dimensional refractive index distributions of various samples and comparing with a conventional Lee hologram method.

Rapid 3D Refractive-Index Imaging of Live Cells in Suspension without Labeling Using Dielectrophoretic Cell Rotation

A major challenge in the field of optical imaging of live cells is achieving rapid, 3D, and noninvasive imaging of isolated cells without labeling. If successful, many clinical procedures involving analysis and sorting of cells drawn from body fluids, including blood, can be significantly improved. A new label-free tomographic interferometry approach is presented. This approach provides rapid capturing of the 3D refractive-index distribution of single cells in suspension. The cells flow in a microfluidic channel, are trapped, and then rapidly rotated by dielectrophoretic forces in a noninvasive and precise manner. Interferometric projections of the rotated cell are acquired and processed into the cellular 3D refractive-index map. Uniquely, this approach provides full (360°) coverage of the rotation angular range around any axis, and knowledge on the viewing angle. The experimental demonstrations presented include 3D, label-free imaging of cancer cells and three types of white blood cells. This approach is expected to be useful for label-free cell sorting, as well as for detection and monitoring of pathological conditions resulting in cellular morphology changes or occurrence of specific cell types in blood or other body fluids.

Quantitative phase imaging for medical diagnosis

Optical microscopy is an indispensable diagnostic tool in modern healthcare. As a prime example, pathologists rely exclusively on light microscopy to investigate tissue morphology in order to make a diagnosis. While advances in light microscopy and contrast markers allow pathologists to visualize cells and tissues in unprecedented detail, the interpretation of these images remains largely subjective, leading to inter- and intra-observer discrepancy. Furthermore, conventional microscopy images capture qualitative information which makes it difficult to automate the process, reducing the throughput achievable in the diagnostic workflow. Quantitative Phase Imaging (QPI) techniques have been advanced in recent years to address these two challenges. By quantifying physical parameters of cells and tissues, these systems remove subjectivity from the disease diagnosis process and allow for easier automation to increase throughput. In addition to providing quantitative information, QPI systems are also label-free and can be easily assimilated into the current diagnostic workflow in the clinic. In this paper we review the advances made in disease diagnosis by QPI techniques. We focus on the areas of hematological diagnosis and cancer pathology, which are the areas where most significant advances have been made to date. [Image adapted from Y. Park, M. Diez-Silva, G. Popescu, G. Lykotrafitis, W. Choi, M. S. Feld, and S. Suresh, Proc. Natl. Acad. Sci. 105, 13730-13735 (2008).].

Three-dimensional label-free imaging and quantification of lipid droplets in live hepatocytes

Lipid droplets (LDs) are subcellular organelles with important roles in lipid storage and metabolism and involved in various diseases including cancer, obesity, and diabetes. Conventional methods, however, have limited ability to provide quantitative information on individual LDs and have limited capability for three-dimensional (3-D) imaging of LDs in live cells especially for fast acquisition of 3-D dynamics. Here, we present an optical method based on 3-D quantitative phase imaging to measure the 3-D structural distribution and biochemical parameters (concentration and dry mass) of individual LDs in live cells without using exogenous labelling agents. The biochemical change of LDs under oleic acid treatment was quantitatively investigated, and 4-D tracking of the fast dynamics of LDs revealed the intracellular transport of LDs in live cells.

Automated Detection of P. falciparum Using Machine Learning Algorithms with Quantitative Phase Images of Unstained Cells

Malaria detection through microscopic examination of stained blood smears is a diagnostic challenge that heavily relies on the expertise of trained microscopists. This paper presents an automated analysis method for detection and staging of red blood cells infected by the malaria parasite Plasmodium falciparum at trophozoite or schizont stage. Unlike previous efforts in this area, this study uses quantitative phase images of unstained cells. Erythrocytes are automatically segmented using thresholds of optical phase and refocused to enable quantitative comparison of phase images. Refocused images are analyzed to extract 23 morphological descriptors based on the phase information. While all individual descriptors are highly statistically different between infected and uninfected cells, each descriptor does not enable separation of populations at a level satisfactory for clinical utility. To improve the diagnostic capacity, we applied various machine learning techniques, including linear discriminant classification (LDC), logistic regression (LR), and k-nearest neighbor classification (NNC), to formulate algorithms that combine all of the calculated physical parameters to distinguish cells more effectively. Results show that LDC provides the highest accuracy of up to 99.7% in detecting schizont stage infected cells compared to uninfected RBCs. NNC showed slightly better accuracy (99.5%) than either LDC (99.0%) or LR (99.1%) for discriminating late trophozoites from uninfected RBCs. However, for early trophozoites, LDC produced the best accuracy of 98%. Discrimination of infection stage was less accurate, producing high specificity (99.8%) but only 45.0%-66.8% sensitivity with early trophozoites most often mistaken for late trophozoite or schizont stage and late trophozoite and schizont stage most often confused for each other. Overall, this methodology points to a significant clinical potential of using quantitative phase imaging to detect and stage malaria infection without staining or expert analysis.