Color-coded LED microscopy for multi-contrast and quantitative phase-gradient imaging

Noise correction in differential phase contrast for improving phase sensitivity

Differential phase contrast (DPC) imaging relies on computational analysis to extract quantitative phase information from phase gradient images. However, even modest noise level can introduce errors that propagate through the computational process, degrading the quality of the final phase result and further reducing phase sensitivity. Here, we introduce the noise-corrected DPC (ncDPC) to enhance phase sensitivity. This approach is based on a theoretical DPC model that effectively considers most relevant noise sources in the camera and non-uniform illumination in DPC. In particular, the dominating shot noise and readout noise variance can be jointly estimated using frequency analysis and further corrected by block-matching 3D (BM3D) method. Finally, the denoised images are used for phase retrieval based on the common Tikhonov inversion. Our results, based on both simulated and experimental data, demonstrate that ncDPC outperforms the traditional DPC (tDPC), enabling significant improvements in both phase reconstruction quality and phase sensitivity. Besides, we have demonstrated the broad applicability of ncDPC by showing its performance in various experimental datasets.

A commentary on the development and use of smartphone imaging devices

Current-age smartphones are known for their wide array of functionality and are now being utilized in the field of healthcare and medicine due to their proven capabilities as smartphone imaging devices (SIDs). Recent technical advancements enabled the integration of special add-on lenses with smartphones to transform them into SIDs. With the rising demand for efficient point-of-care (PoC) devices for better diagnostic applications, SIDs will be a one-stop solution. Additionally, portability, user-friendliness and low-cost make it accessible for all even at remote locations. Furthermore, improvements in resolution, magnification and field-of-view (FOV) have attracted the scientific community to use SIDs in various biomedical applications such as disease diagnosis, food quality control and pathogen detection. SIDs can be arranged in various combinational setups by using different illumination sources and optics to achieve suitable contrast and visibility of the specimen under study. This Commentary illustrates the various illumination sources used in SID and also spotlights their design and applications.

Contrast-enhanced, single-shot LED array microscopy based on Fourier ptychographic algorithm and deep learning

LED array microscopes have the advantages of miniaturisation and low cost. It has been demonstrated that LED array microscopes outperform Köhler illumination microscopes in some applications. A LED array allows for a large numerical aperture of illumination. The larger numerical aperture of illumination brings the higher spatial resolution, but the lower image contrast as well. Therefore, there is a tradeoff between resolution and contrast for LED array microscopes. The Fourier ptychographic algorithm can overcome this tradeoff by increasing image contrast without sacrificing spatial resolution. However, the Fourier ptychographic algorithm requires acquisition of multiple images, which is time-consuming and results in live sample imaging challenging. To solve this problem, we develop contrast-enhanced, single-shot LED array microscopy based on the Fourier ptychographic algorithm and deep learning. The sample to be imaged is under illumination by all LEDs of the array simultaneously. The image captured is fed to several trained convolutional neural networks to generate the same number of images that are required by the Fourier ptychographic algorithm. We experimentally present that the image contrast of the final reconstruction is remarkably improved in comparison with the image captured. The proposed method can also produce chromatic-aberration-free results, even when an objective without aberration correction is used. We believe the method might provide live sample imaging with a low-cost approach.

Single-shot refractive index slice imaging using spectrally multiplexed optical transfer function reshaping

The refractive index (RI) of cells and tissues is crucial in pathophysiology as a noninvasive and quantitative imaging contrast. Although its measurements have been demonstrated using three-dimensional quantitative phase imaging methods, these methods often require bulky interferometric setups or multiple measurements, which limits the measurement sensitivity and speed. Here, we present a single-shot RI imaging method that visualizes the RI of the in-focus region of a sample. By exploiting spectral multiplexing and optical transfer function engineering, three color-coded intensity images of a sample with three optimized illuminations were simultaneously obtained in a single-shot measurement. The measured intensity images were then deconvoluted to obtain the RI image of the in-focus slice of the sample. As a proof of concept, a setup was built using Fresnel lenses and a liquid-crystal display. For validation purposes, we measured microspheres of known RI and cross-validated the results with simulated results. Various static and highly dynamic biological cells were imaged to demonstrate that the proposed method can conduct single-shot RI slice imaging of biological samples with subcellular resolution.

Quantitative phase gradient metrology using diffraction phase microscopy and deep learning

In quantitative phase microscopy, measurement of the phase gradient is an important problem for biological cell morphological studies. In this paper, we propose a method based on a deep learning approach that is capable of direct estimation of the phase gradient without the requirement of phase unwrapping and numerical differentiation operations. We show the robustness of the proposed method using numerical simulations under severe noise conditions. Further, we demonstrate the method's utility for imaging different biological cells using diffraction phase microscopy setup.

Retinex-qDPC: Automatic background-rectified quantitative differential phase contrast imaging

BACKGROUND AND OBJECTIVE

The quality of quantitative differential phase contrast reconstruction (qDPC) can be severely degenerated by the mismatch of the background of two oblique illuminated images, yielding problematic phase recovery results. These background mismatches may result from illumination patterns, inhomogeneous media distribution, or other defocusing layers. In previous reports, the background is manually calibrated which is time-consuming, and unstable, since new calibrations are needed if any modification to the optical system was made. It is also impossible to calibrate the background from the defocusing layers, or for high dynamic observation as the background changes over time. The background mismatch reduces the experimental robustness of qDPC and largely limits its applications. To tackle the mismatch of background and increases the experimental robustness, we propose the Retinex-qDPC.

METHODS

In Retinex-qDPC, we replace the data fidelity term of the previous cost function for qDPC inverse problem, by the images' edge features yielding L₂-Retinex-qDPC and L₁-Retinex-qDPC for high background-robustness qDPC reconstruction. The split Bregman method is used to solve the L₁-Retinex DPC. We compare both Retinex-qDPC models against state-of-the-art DPC reconstruction algorithms including total-variation regularized qDPC, and isotropic-qDPC using both simulated and experimental data.

RESULTS

Retinex qDPC can significantly improve the phase recovery quality by suppressing the impact of mismatch background. Within, the L₁-Retinex-qDPC is better than L₂-Retinex and other state-of-the-art qDPC algorithms.

CONCLUSIONS

The Retinex-qDPC increases the experimental robustness against background illumination without any modification of the optical system, which will benefit all qDPC applications.

High-fidelity optical diffraction tomography of live organisms using iodixanol refractive index matching

Optical diffraction tomography (ODT) enables the three-dimensional (3D) refractive index (RI) reconstruction. However, when the RI difference between a sample and a medium increases, the effects of light scattering become significant, preventing the acquisition of high-quality and accurate RI reconstructions. Herein, we present a method for high-fidelity ODT by introducing non-toxic RI matching media. Optimally reducing the RI contrast enhances the fidelity and accuracy of 3D RI reconstruction, enabling visualization of the morphology and intra-organization of live biological samples without producing toxic effects. We validate our method using various biological organisms, including C. albicans and C. elegans.

Quantitative phase and refractive index imaging of 3D objects via optical transfer function reshaping

Deconvolution phase microscopy enables high-contrast visualization of transparent samples through reconstructions of their transmitted phases or refractive indexes. Herein, we propose a method to extend 2D deconvolution phase microscopy to thick 3D samples. The refractive index distribution of a sample can be obtained at a specific axial plane by measuring only four intensity images obtained under optimized illumination patterns. Also, the optical phase delay of a sample can be measured using different illumination patterns.

Optical module for single-shot quantitative phase imaging based on the transport of intensity equation with field of view multiplexing

We present a cost-effective, simple, and robust method that enables single-shot quantitative phase imaging (QPI) based on the transport of intensity equation (TIE) using an add-on optical module that can be assembled into the exit port of any regular microscope. The module integrates a beamsplitter (BS) cube (placed in a non-conventional way) for duplicating the output image onto the digital sensor (field of view - FOV - multiplexing), a Stokes lens (SL) for astigmatism compensation (introduced by the BS cube), and an optical quality glass plate over one of the FOV halves for defocusing generation (needed for single-shot TIE algorithm). Altogether, the system provides two laterally separated intensity images that are simultaneously recorded and slightly defocused one to each other, thus enabling accurate QPI by conventional TIE-based algorithms in a single snapshot. The proposed optical module is first calibrated for defining the configuration providing best QPI performance and, second, experimentally validated by using different phase samples (static and dynamic ones). The proposed configuration might be integrated in a compact three-dimensional (3D) printed module and coupled to any conventional microscope for QPI of dynamic transparent samples.

Pupil-modulation ghost phase imaging

Computational ghost imaging (CGI) allows us to reconstruct images under a low signal-to-noise-ratio condition. However, CGI cannot retrieve phase information; it is unsuitable for observation of transparent objects such as living cells. A phase imaging method with CGI architecture is proposed. The proposed method realizes phase imaging with a simple optical setup by introducing pupil modulation differential phase contrast (PMDPC) to CGI. In PMDPC, phase information can be obtained from intensity distributions, which have phase gradient information, and its optical setup is similar to that of CGI. Therefore, the two methods are highly compatible, and the introduction of PMDPC to CGI can be easily achieved. Numerical simulation and an optical experiment demonstrated the feasibility of the proposed method.

Polarization-sensitive differential phase-contrast microscopy

We present a novel, to the best of our knowledge, form of polarization microscopy capable of producing quantitative optic-axis and phase retardation maps of transparent and anisotropic materials. The proposed method operates on differential phase-contrast (DPC) microscopy that produces a phase image of a thin specimen using multi-axis intensity measurements. For polarization-sensitive imaging, patterned illumination light is circularly polarized to illuminate a specimen. The light transmitted through a specimen is split into two orthogonal polarization states and measured by an image sensor. Subsequent DPC computation based on the illumination patterns, acquired images, and the imaging model enables the retrieval of polarization-dependent quantitative phase images, which are utilized to reconstruct the orientation and retardation of the specimen. We demonstrate the validity of the proposed method by measuring the optic-axis and phase retardation maps of calibrated and various anisotropic samples.

Multiplane differential phase contrast imaging using asymmetric illumination in volume holographic microscopy

SIGNIFICANCE

Differential phase contrast (DPC) is a well-known imaging technique for phase imaging. However, simultaneously acquiring multidepth DPC images is a non-trivial task. We propose simultaneous multiplane DPC imaging using volume holographic microscopy (VHM).

AIM

To design and implement a new configuration of DPC-VHM for multiplane imaging.

APPROACH

The angularly multiplexed volume holographic gratings (AMVHGs) and the wavelength-coded volume holographic gratings (WC-VHGs) are used for this purpose. To obtain asymmetric illumination for DPC images, a dynamic illumination system is designed by modifying the regular Köhler illumination using a thin film transistor panel (TFT-panel).

RESULTS

Multidepth DPC images of standard resolution chart and biosamples were used to compare imaging performance with the corresponding bright-field images. An average contrast enhancement of around three times is observed for target resolution chart by DPC-VHM. Imaging performance of our system is studied by modulation transfer function analysis, which suggests that DPC-VHM not only suppresses the DC component but also enhances high-frequency information.

CONCLUSIONS

Proposed DPC-VHM can acquire multidepth-resolved DPC images without axial scanning. The illumination part of the system is adjustable so that the system can be adapted to bright-field mode, phase contrast mode, and DPC mode by controlling the pattern on the TFT-panel.

Acquisition of Multi-Modal Images of Structural Modifications in Glass with Programmable LED-Array-Based Illumination

Ultrashort laser pulses can induce structural modifications in bulk glass, leading to refractive index change and scattering damage. As bright-field, dark-field, and phase imaging each provide complementary information about laser-induced structures, it is often desired to use multiple observations simultaneously. As described herein, we present the acquisition of bright-field, dark-field, and differential phase-contrast images of structural modifications induced in glass by femtosecond laser pulses with an LED array microscope. The contrast of refractive index change can be enhanced by differential phase-contrast images. We also report on the simultaneous acquisition of bright-field and dark-field images of structural modifications in a glass with LED-array-based Rheinberg illumination. A single-shot color image is separated to obtain bright field and dark field images simultaneously. We provide an experimental demonstration on multi-modal imaging of structural modifications in a glass with an LED array microscope using temporally-coded illumination and color-coded illumination.

Quantitative differential phase contrast imaging at high resolution with radially asymmetric illumination

Half-circle illumination-based differential phase contrast (DPC) microscopy has been utilized to recover phase images through a pair of images along multiple axes. Recently, the half-circle based DPC using 12-axis measurements significantly provides a circularly symmetric phase transfer function to improve accuracy for more stable phase recovery. Instead of using half-circle-based DPC, we propose a new scheme of DPC under radially asymmetric illumination to achieve circularly symmetric phase transfer function and enhance the accuracy of phase recovery in a more stable and efficient fashion. We present the design, implementation, and experimental image data demonstrating the ability of our method to obtain quantitative phase images of microspheres, as well as live fibroblast cell samples.

Enhancing imaging contrast via weighted feedback for iterative multi-image phase retrieval

Iterative phase retrieval (IPR) has developed into a feasible and simple computational method to retrieve a complex-valued sample. Due to coherent illumination, the reconstructed image quality is degraded by speckle noise arising from a laser. Accordingly, partially coherent illumination has been introduced to alleviate this restriction. We apply weighted feedback modality into multidistance and multiwavelength phase retrieval to realize high-contrast and fast imaging. In simulation, it is proved that IPR based on weighted feedback accelerates the convergence in partially coherent illumination and speckle illumination. In experiment, the resolution chart and biological specimen are reconstructed in lensless and lens-based systems, which also demonstrate the performance of weighted feedback. This work provides a simple and high-contrast imaging modality for IPR. Also, it facilitates compact and flexible experimental implementation for label-free imaging.

Quantitative phase imaging by optimized asymmetric illumination

We have presented a simple approach for quantitative phase imaging by optimizing asymmetric illumination of a conventional microscope. With this illumination, the light intensity modulation accompanying refraction at the surface profile of phase objects occurs, and "phase-gradient information" can be derived by detecting it. Two images with phase-gradient information on different axes are converted into the two-dimensional phase distribution of the specimen by introducing the phase-gradient transfer function, which is the intensity change due to refraction by the phase-gradient of a specimen. We experimentally confirm accurate and repeatable performance of our method and demonstrate phase imaging of live cells.

Compact single-shot four-wavelength quantitative phase microscopy with polarization- and frequency-division demultiplexing

We present a novel single-shot four-wavelength quantitative phase microscopy (FW-QPM). Four lasers operating at different wavelengths are multiplexed with a pair of dichroic mirrors and a polarization beam splitter in a three-mirror quasi-common-path interferometer. After a single-shot interference pattern is obtained with a monochrome camera, four holograms of different wavelengths were demultiplexed from it in the frequency domain with polarization- and frequency-division multiplexing. Polarization-division demultiplexing scheme uses polarization dependent visibility changes in an interference pattern, and it plays a critical role in making only two interference patterns exist within a single quadrant in the frequency domain. We have used a single-mode optical fiber as a phase object sample and demonstrated that a measured single-shot interference pattern can be successfully demultiplexed into four different interferograms of different wavelengths with our proposed scheme.

Smartphone-based multi-contrast microscope using color-multiplexed illumination

We present a portable multi-contrast microscope capable of producing bright-field, dark-field, and differential phase contrast images of thin biological specimens on a smartphone platform. The microscopy method is based on an imaging scheme termed “color-coded light-emitting-diode (LED) microscopy (cLEDscope),” in which a specimen is illuminated with a color-coded LED array and light transmitted through the specimen is recorded by a color image sensor. Decomposition of the image into red, green, and blue colors and subsequent computation enable multi-contrast imaging in a single shot. In order to transform a smartphone into a multi-contrast imaging device, we developed an add-on module composed of a patterned color micro-LED array, specimen stage, and miniature objective. Simple installation of this module onto a smartphone enables multi-contrast imaging of transparent specimens. In addition, an Android-based app was implemented to acquire an image, perform the associated computation, and display the multi-contrast images in real time. Herein, the details of our smartphone module and experimental demonstrations with various biological specimens are presented.

Fourier ptychographic microscopy using wavelength multiplexing

Fourier ptychographic microscopy (FPM) is a recently developed technique stitching low-resolution images in Fourier domain to realize wide-field high-resolution imaging. However, the time-consuming process of image acquisition greatly narrows its applications in dynamic imaging. We report a wavelength multiplexing strategy to speed up the acquisition process of FPM several folds. A proof-of-concept system is built to verify its feasibility. Distinguished from many current multiplexing methods in Fourier domain, we explore the potential of high-speed FPM in spectral domain. Compatible with most existing FPM methods, our strategy provides an approach to high-speed gigapixel microscopy. Several experimental results are also presented to validate the strategy.

Single-exposure quantitative phase imaging in color-coded LED microscopy

We demonstrate single-shot quantitative phase imaging (QPI) in a platform of color-coded LED microscopy (cLEDscope). The light source in a conventional microscope is replaced by a circular LED pattern that is trisected into subregions with equal area, assigned to red, green, and blue colors. Image acquisition with a color image sensor and subsequent computation based on weak object transfer functions allow for the QPI of a transparent specimen. We also provide a correction method for color-leakage, which may be encountered in implementing our method with consumer-grade LEDs and image sensors. Most commercially available LEDs and image sensors do not provide spectrally isolated emissions and pixel responses, generating significant error in phase estimation in our method. We describe the correction scheme for this color-leakage issue, and demonstrate improved phase measurement accuracy. The computational model and single-exposure QPI capability of our method are presented by showing images of calibrated phase samples and cellular specimens.

Single-shot quantitative phase microscopy with color-multiplexed differential phase contrast (cDPC)

We present a new technique for quantitative phase and amplitude microscopy from a single color image with coded illumination. Our system consists of a commercial brightfield microscope with one hardware modification-an inexpensive 3D printed condenser insert. The method, color-multiplexed Differential Phase Contrast (cDPC), is a single-shot variant of Differential Phase Contrast (DPC), which recovers the phase of a sample from images with asymmetric illumination. We employ partially coherent illumination to achieve resolution corresponding to 2× the objective NA. Quantitative phase can then be used to synthesize DIC and phase contrast images or extract shape and density. We demonstrate amplitude and phase recovery at camera-limited frame rates (50 fps) for various in vitro cell samples and c. elegans in a micro-fluidic channel.

Quantitative phase imaging and complex field reconstruction by pupil modulation differential phase contrast

Differential phase contrast (DPC) is a non-interferometric quantitative phase imaging method achieved by using an asymmetric imaging procedure. We report a pupil modulation differential phase contrast (PMDPC) imaging method by filtering a sample's Fourier domain with half-circle pupils. A phase gradient image is captured with each half-circle pupil, and a quantitative high resolution phase image is obtained after a deconvolution process with a minimum of two phase gradient images. Here, we introduce PMDPC quantitative phase image reconstruction algorithm and realize it experimentally in a 4f system with an SLM placed at the pupil plane. In our current experimental setup with the numerical aperture of 0.36, we obtain a quantitative phase image with a resolution of 1.73μm after computationally removing system aberrations and refocusing. We also extend the depth of field digitally by 20 times to ±50μm with a resolution of 1.76μm.