Reflection phase microscopy using spatio-temporal coherence of light

High space-time bandwidth product imaging in low coherence quantitative phase microscopy

Current low coherence quantitative phase microscopy (LC-QPM) systems suffer from either reduced field of view (FoV) or reduced temporal resolution due to the short temporal coherence (TC) length of the light source. Here, we propose a hybrid, experimental and numerical approach to address this core problem associated with LC-QPM. We demonstrate high spatial resolution and high phase sensitivity in LC-QPM at high temporal resolution. High space-time bandwidth product is achieved by employing incoherent light source for sample illumination in QPM to increase the spatial resolution and single-shot Hilbert spiral transform (HST) based phase recovery algorithm to enhance the temporal resolution without sacrificing spatial resolution during the reconstruction steps. The high spatial phase sensitivity comes by default due to the use of incoherent light source in QPM which has low temporal coherence length and does not generate speckle noise and coherent noise. The spatial resolution achieved by the HST is slightly inferior to the temporal phase-shifting (TPS) method when tested on a specimen but surpasses that of the single-shot Fourier transform (FT) based phase recovery method. Contrary to HST method, FT method requires high density fringes for lossless phase recovery, which is difficult to achieve in LC-QPM over entire FoV. Consequently, integration of HST algorithm with LC-QPM system makes an attractive route. Here, we demonstrate scalable FoV and resolution in single-shot LC-QPM and experimentally corroborate it on a test object and on both live and fixed biological specimen such as MEF, U2OS and human red blood cells (RBCs). LC-QPM system with HST reconstruction offer high-speed single-shot QPM imaging at high phase sensitivity and high spatial resolution enabling us to study sub-cellular dynamic inside U2OS for extended duration (3 h) and observe high-speed (50 fps) dynamics of human RBCs. The experimental results validate the effectiveness of the present approach and will open new avenues in the domain of biomedical imaging in the future.

Three-dimensional imaging in reflection phase microscopy with minimal axial scanning

Reflection phase microscopy is a valuable tool for acquiring three-dimensional (3D) images of objects due to its capability of optical sectioning. The conventional method of constructing a 3D map is capturing 2D images at each depth with a mechanical scanning finer than the optical sectioning. This not only compromises sample stability but also slows down the acquisition process, imposing limitations on its practical applications. In this study, we utilized a reflection phase microscope to acquire 2D images at depth locations significantly spaced apart, far beyond the range of optical sectioning. By employing a numerical propagation, we successfully filled the information gap between the acquisition layers, and then constructed complete 3D maps of objects with substantially reduced number of axial scans. Our experimental results also demonstrated the effectiveness of this approach in enhancing imaging speed while maintaining the accuracy of the reconstructed 3D structures. This technique has the potential to improve the applicability of reflection phase microscopy in diverse fields such as bioimaging and material science.

Mapping nanoscale topographic features in thick tissues with speckle diffraction tomography

Resolving three-dimensional morphological features in thick specimens remains a significant challenge for label-free imaging. We report a new speckle diffraction tomography (SDT) approach that can image thick biological specimens with ~500 nm lateral resolution and ~1 μm axial resolution in a reflection geometry. In SDT, multiple-scattering background is rejected through spatiotemporal gating provided by dynamic speckle-field interferometry, while depth-resolved refractive index maps are reconstructed by developing a comprehensive inverse-scattering model that also considers specimen-induced aberrations. Benefiting from the high-resolution and full-field quantitative imaging capabilities of SDT, we successfully imaged red blood cells and quantified their membrane fluctuations behind a turbid medium with a thickness of 2.8 scattering mean-free paths. Most importantly, we performed volumetric imaging of cornea inside an ex vivo rat eye and quantified its optical properties, including the mapping of nanoscale topographic features of Dua's and Descemet's membranes that had not been previously visualized.

Thermo-optical measurements using quantitative phase microscopy

Quantitative phase microscopy (QPM) literally images the quantitative phase shift associated with image contrast, where the phase shift can be altered by laser heating. In this study, the thermal conductivity and thermo-optic coefficient (TOC) of a transparent substrate are simultaneously determined by measuring the phase difference induced by an external heating laser using a QPM setup. The substrates are coated with a 50-nm-thick titanium nitride film to photothermally generate heat. Then, the phase difference is semi-analytically modeled based on the heat transfer and thermo-optic effect to simultaneously extract the thermal conductivity and TOC. The measured thermal conductivity and TOC agree reasonably well, indicating the potential for measuring the thermal conductivities and TOCs of other transparent substrates. The concise setup and simple modeling differentiate the advantages of our method from other techniques.

Partially coherent broadband 3D optical transfer functions with arbitrary temporal and angular power spectra

Optical diffraction tomography is a powerful technique to produce 3D volumetric images of biological samples using contrast produced by variations in the index of refraction in an unlabeled specimen. While this is typically performed with coherent illumination from a variety of angles, interest has grown in partially coherent methods due to the simplicity of the illumination and the computation-free axial sectioning provided by the coherence window of the source. However, such methods rely on the symmetry or discretization of a source to facilitate quantitative analysis and are unable to efficiently handle arbitrary illumination that may vary asymmetrically in angle and continuously in the spectrum, such as diffusely scattered or thermal sources. A general broadband theory may expand the scope of illumination methods available for quantitative analysis, as partially coherent sources are commonly available and may benefit from the effects of spatial and temporal incoherence. In this work, we investigate partially coherent tomographic phase microscopy from arbitrary sources regardless of angular distribution and spectrum by unifying the effects of spatial and temporal coherence into a single formulation. This approach further yields a method for efficient computation of the overall systems' optical transfer function, which scales with O(n ³), down from O(mn ⁴) for existing convolutional methods, where n ³ is the number of spatial voxels in 3D space and m is the number of discrete wavelengths in the illumination spectrum. This work has important implications for enabling partially coherent 3D quantitative phase microscopy and refractive index tomography in virtually any transmission or epi-illumination microscope.

Highly sensitive quantitative phase microscopy and deep learning aided with whole genome sequencing for rapid detection of infection and antimicrobial resistance

Current state-of-the-art infection and antimicrobial resistance (AMR) diagnostics are based on culture-based methods with a detection time of 48-96 h. Therefore, it is essential to develop novel methods that can do real-time diagnoses. Here, we demonstrate that the complimentary use of label-free optical assay with whole-genome sequencing (WGS) can enable rapid diagnosis of infection and AMR. Our assay is based on microscopy methods exploiting label-free, highly sensitive quantitative phase microscopy (QPM) followed by deep convolutional neural networks-based classification. The workflow was benchmarked on 21 clinical isolates from four WHO priority pathogens that were antibiotic susceptibility tested, and their AMR profile was determined by WGS. The proposed optical assay was in good agreement with the WGS characterization. Accurate classification based on the gram staining (100% recall for gram-negative and 83.4% for gram-positive), species (98.6%), and resistant/susceptible type (96.4%), as well as at the individual strain level (100% sensitivity in predicting 19 out of the 21 strains, with an overall accuracy of 95.45%). The results from this initial proof-of-concept study demonstrate the potential of the QPM assay as a rapid and first-stage tool for species, strain-level classification, and the presence or absence of AMR, which WGS can follow up for confirmation. Overall, a combined workflow with QPM and WGS complemented with deep learning data analyses could, in the future, be transformative for detecting and identifying pathogens and characterization of the AMR profile and antibiotic susceptibility.

Demystifying speckle field interference microscopy

Dynamic speckle illumination (DSI) has recently attracted strong attention in the field of biomedical imaging as it pushes the limits of interference microscopy (IM) in terms of phase sensitivity, and spatial and temporal resolution compared to conventional light source illumination. To date, despite conspicuous advantages, it has not been extensively implemented in the field of phase imaging due to inadequate understanding of interference fringe formation, which is challenging to obtain in dynamic speckle illumination interference microscopy (DSI-IM). The present article provides the basic understanding of DSI through both simulation and experiments that is essential to build interference microscopy systems such as quantitative phase microscopy, digital holographic microscopy and optical coherence tomography. Using the developed understanding of DSI, we demonstrated its capabilities which enables the use of non-identical objective lenses in both arms of the interferometer and opens the flexibility to use user-defined microscope objective lens for scalable field of view and resolution phase imaging. It is contrary to the present understanding which forces us to use identical objective lenses in conventional IM system and limits the applicability of the system for fixed objective lens. In addition, it is also demonstrated that the interference fringes are not washed out over a large range of optical path difference (OPD) between the object and the reference arm providing competitive edge over low temporal coherence light source based IM system. The theory and explanation developed here would enable wider penetration of DSI-IM for applications in biology and material sciences.

Numerical analysis of the effect of reduced temporal coherence in quantitative phase microscopy and tomography

We present the numerical analysis of the effect of the temporarily partially coherent illumination on the phase measurement accuracy in digital holography microscopy (DHM) and optical diffraction tomography (ODT), as reconstruction algorithms tend to assume purely monochromatic conditions. In the regime of reduced temporal coherence, we simulate the hologram formation in two different optical setups, representing classical off-axis two-beam and grating common-path configurations. We consider two ODT variants: with sample rotation and angle-scanning of illumination. Besides the coherence degree of illumination, our simulation considers the influence of the sample normal dispersion, shape of the light spectrum, and optical parameters of the imaging setup. As reconstruction algorithms we employ Fourier hologram method and first-order Rytov approximation with direct inversion and nonnegativity constraints. Quantitative evaluation of the measurement results deviations introduced by the mentioned error sources is comprehensively analyzed, for the first time to the best of our knowledge. Obtained outcomes indicate low final DHM/ODT reconstruction errors for the grating-assisted common-path configuration. Nevertheless, dispersion and asymmetric spectrum introduce non-negligible overestimated refractive index values and noise, and should be thus carefully considered within experimental frameworks.

Label-Free Dynamic Imaging of Chromatin in Live Cell Nuclei by High-Speed Scattering-Based Interference Microscopy

Chromatin is a DNA-protein complex that is densely packed in the cell nucleus. The nanoscale chromatin compaction plays critical roles in the modulation of cell nuclear processes. However, little is known about the spatiotemporal dynamics of chromatin compaction states because it remains difficult to quantitatively measure the chromatin compaction level in live cells. Here, we demonstrate a strategy, referenced as DYNAMICS imaging, for mapping chromatin organization in live cell nuclei by analyzing the dynamic scattering signal of molecular fluctuations. Highly sensitive optical interference microscopy, coherent brightfield (COBRI) microscopy, is implemented to detect the linear scattering of unlabeled chromatin at a high speed. A theoretical model is established to determine the local chromatin density from the statistical fluctuation of the measured scattering signal. DYNAMICS imaging allows us to reconstruct a speckle-free nucleus map that is highly correlated to the fluorescence chromatin image. Moreover, together with calibration based on nanoparticle colloids, we show that the DYNAMICS signal is sensitive to the chromatin compaction level at the nanoscale. We confirm the effectiveness of DYNAMICS imaging in detecting the condensation and decondensation of chromatin induced by chemical drug treatments. Importantly, the stable scattering signal supports a continuous observation of the chromatin condensation and decondensation processes for more than 1 h. Using this technique, we detect transient and nanoscopic chromatin condensation events occurring on a time scale of a few seconds. Label-free DYNAMICS imaging offers the opportunity to investigate chromatin conformational dynamics and to explore their significance in various gene activities.

Multimode fiber as a tool to reduce cross talk in Fourier-domain full-field optical coherence tomography

Fourier-domain full-field optical coherence tomography (FD-FF-OCT) is an emerging tool for high-speed eye imaging. However, cross-talk formation in images limits the imaging depth. To this end, we have recently shown that reducing spatial coherence with a fast deformable membrane can suppress the noise but over a limited axial range and with substantial data processing. Here, we demonstrate that a multimode fiber with carefully chosen parameters enables cross-talk-free imaging over a long axial range and without significant artifacts. We also show that it can be used to image the human retina and choroid in vivo with exceptional contrast.

In vivo visualization of butterfly scale cell morphogenesis in Vanessa cardui

Many organisms exhibit functional micro- and nanoscale materials with structural definition and performance that challenge synthetic fabrication techniques, yet we know little about the processes that enable their formation. Using butterfly scales as a model system for functional biomaterials, we establish a timeline of scale formation and quantify relevant structural parameters for developing painted lady butterflies. We overcome challenges of previous efforts by imaging structure formation directly in living organisms, which allows us to continuously observe the evolving wing tissue and the fine details of individual scale cells. Visualization of scale structure formation in live butterflies forms the basis for modeling the underlying biomechanical processes and opens avenues for their translation into advanced fabrication strategies.

During metamorphosis, the wings of a butterfly sprout hundreds of thousands of scales with intricate microstructures and nano-structures that determine the wings’ optical appearance, wetting characteristics, thermodynamic properties, and aerodynamic behavior. Although the functional characteristics of scales are well known and prove desirable in various applications, the dynamic processes and temporal coordination required to sculpt the scales’ many structural features remain poorly understood. Current knowledge of scale growth is primarily gained from ex vivo studies of fixed scale cells at discrete time points; to fully understand scale formation, it is critical to characterize the time-dependent morphological changes throughout their development. Here, we report the continuous, in vivo, label-free imaging of growing scale cells of Vanessa cardui using speckle-correlation reflection phase microscopy. By capturing time-resolved volumetric tissue data together with nanoscale surface height information, we establish a morphological timeline of wing scale formation and gain quantitative insights into the underlying processes involved in scale cell patterning and growth. We identify early differences in the patterning of cover and ground scales on the young wing and quantify geometrical parameters of growing scale features, which suggest that surface growth is critical to structure formation. Our quantitative, time-resolved in vivo imaging of butterfly scale development provides the foundation for decoding the processes and biomechanical principles involved in the formation of functional structures in biological materials.

The effect of pupil transmittance on axial resolution of reflection phase microscopy

A reflection phase microscope (RPM) can be equipped with the capability of depth selection by employing a gating mechanism. However, it is difficult to achieve an axial resolution close to the diffraction limit in real implementation. Here, we systematically investigated the uneven interference contrast produced by pupil transmittance of the objective lens and found that it was the main cause of the practical limit that prevents the axial resolution from reaching its diffraction limit. Then we modulated the power of illumination light to obtain a uniform interference contrast over the entire pupil. Consequently, we could achieve an axial resolution fairly close to the diffraction limit set by the experimental conditions.

High-throughput spatial sensitive quantitative phase microscopy using low spatial and high temporal coherent illumination

High space-bandwidth product with high spatial phase sensitivity is indispensable for a single-shot quantitative phase microscopy (QPM) system. It opens avenue for widespread applications of QPM in the field of biomedical imaging. Temporally low coherence light sources are implemented to achieve high spatial phase sensitivity in QPM at the cost of either reduced temporal resolution or smaller field of view (FOV). In addition, such light sources have low photon degeneracy. On the contrary, high temporal coherence light sources like lasers are capable of exploiting the full FOV of the QPM systems at the expense of less spatial phase sensitivity. In the present work, we demonstrated that use of narrowband partially spatially coherent light source also called pseudo-thermal light source (PTLS) in QPM overcomes the limitations of conventional light sources. The performance of PTLS is compared with conventional light sources in terms of space bandwidth product, phase sensitivity and optical imaging quality. The capabilities of PTLS are demonstrated on both amplitude (USAF resolution chart) and phase (thin optical waveguide, height ~ 8 nm) objects. The spatial phase sensitivity of QPM using PTLS is measured to be equivalent to that for white light source and supports the FOV (18 times more) equivalent to that of laser light source. The high-speed capabilities of PTLS based QPM is demonstrated by imaging live sperm cells that is limited by the camera speed and large FOV is demonstrated by imaging histopathology human placenta tissue samples. Minimal invasive, high-throughput, spatially sensitive and single-shot QPM based on PTLS will enable wider penetration of QPM in life sciences and clinical applications.

Inverse scattering for reflection intensity phase microscopy

Reflection phase imaging provides label-free, high-resolution characterization of biological samples, typically using interferometric-based techniques. Here, we investigate reflection phase microscopy from intensity-only measurements under diverse illumination. We evaluate the forward and inverse scattering model based on the first Born approximation for imaging scattering objects above a glass slide. Under this design, the measured field combines linear forward-scattering and height-dependent nonlinear back-scattering from the object that complicates object phase recovery. Using only the forward-scattering, we derive a linear inverse scattering model and evaluate this model's validity range in simulation and experiment using a standard reflection microscope modified with a programmable light source. Our method provides enhanced contrast of thin, weakly scattering samples that complement transmission techniques. This model provides a promising development for creating simplified intensity-based reflection quantitative phase imaging systems easily adoptable for biological research.

Geometric-Phase Microscopy for Quantitative Phase Imaging of Isotropic, Birefringent and Space-Variant Polarization Samples

We present geometric-phase microscopy allowing a multipurpose quantitative phase imaging in which the ground-truth phase is restored by quantifying the phase retardance. The method uses broadband spatially incoherent light that is polarization sensitively controlled through the geometric (Pancharatnam-Berry) phase. The assessed retardance possibly originates either in dynamic or geometric phase and measurements are customized for quantitative mapping of isotropic and birefringent samples or multi-functional geometric-phase elements. The phase restoration is based on the self-interference of polarization distinguished waves carrying sample information and providing pure reference phase, while passing through an inherently stable common-path setup. The experimental configuration allows an instantaneous (single-shot) phase restoration with guaranteed subnanometer precision and excellent ground-truth accuracy (well below 5 nm). The optical performance is demonstrated in advanced yet routinely feasible noninvasive biophotonic imaging executed in the automated manner and predestined for supervised machine learning. The experiments demonstrate measurement of cell dry mass density, cell classification based on the morphological parameters and visualization of dynamic dry mass changes. The multipurpose use of the method was demonstrated by restoring variations in the dynamic phase originating from the electrically induced birefringence of liquid crystals and by mapping the geometric phase of a space-variant polarization directed lens.