Three-dimensional quantitative phase imaging via tomographic deconvolution phase microscopy

Fourier space aberration correction for high resolution refractive index imaging using incoherent light

An aberration correction method is introduced for 3D phase deconvolution microscopy. Our technique capitalizes on multiple illumination patterns to iteratively extract Fourier space aberrations, utilizing the overlapping information inherent in these patterns. By refining the point spread function based on the retrieved aberration data, we significantly improve the precision of refractive index deconvolution. We validate the effectiveness of our method on both synthetic and biological three-dimensional samples, achieving notable enhancements in resolution and measurement accuracy. The method's reliability in aberration retrieval is further confirmed through controlled experiments with intentionally induced spherical aberrations, underscoring its potential for wide-ranging applications in microscopy and biomedicine.

Roadmap on Label-Free Super-Resolution Imaging

Label-free super-resolution (LFSR) imaging relies on light-scattering processes in nanoscale objects without a need for fluorescent (FL) staining required in super-resolved FL microscopy. The objectives of this Roadmap are to present a comprehensive vision of the developments, the state-of-the-art in this field, and to discuss the resolution boundaries and hurdles which need to be overcome to break the classical diffraction limit of the LFSR imaging. The scope of this Roadmap spans from the advanced interference detection techniques, where the diffraction-limited lateral resolution is combined with unsurpassed axial and temporal resolution, to techniques with true lateral super-resolution capability which are based on understanding resolution as an information science problem, on using novel structured illumination, near-field scanning, and nonlinear optics approaches, and on designing superlenses based on nanoplasmonics, metamaterials, transformation optics, and microsphere-assisted approaches. To this end, this Roadmap brings under the same umbrella researchers from the physics and biomedical optics communities in which such studies have often been developing separately. The ultimate intent of this paper is to create a vision for the current and future developments of LFSR imaging based on its physical mechanisms and to create a great opening for the series of articles in this field.

Single-shot multispectral quantitative phase imaging of biological samples using deep learning

Multispectral quantitative phase imaging (MS-QPI) is a high-contrast label-free technique for morphological imaging of the specimens. The aim of the present study is to extract spectral dependent quantitative information in single-shot using a highly spatially sensitive digital holographic microscope assisted by a deep neural network. There are three different wavelengths used in our method: λ=532, 633, and 808 nm. The first step is to get the interferometric data for each wavelength. The acquired datasets are used to train a generative adversarial network to generate multispectral (MS) quantitative phase maps from a single input interferogram. The network was trained and validated on two different samples: the optical waveguide and MG63 osteosarcoma cells. Validation of the present approach is performed by comparing the predicted MS phase maps with numerically reconstructed (F T+T I E) phase maps and quantifying with different image quality assessment metrices.

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.

Parallel synthetic aperture transport-of-intensity diffraction tomography with annular illumination

Transport-of-intensity diffraction tomography (TIDT) is a recently developed label-free computational microscopy technique that retrieves high-resolution three-dimensional (3D) refractive index (RI) distribution of biological specimens from 3D intensity-only measurements. However, the non-interferometric synthetic aperture in TIDT is generally achieved sequentially through the acquisition of a large number of through-focus intensity stacks captured at different illumination angles, resulting in a very cumbersome and redundant data acquisition process. To this end, we present a parallel implementation of a synthetic aperture in TIDT (PSA-TIDT) with annular illumination. We found that the matched annular illumination provides a mirror-symmetric 3D optical transfer function, indicating the analyticity in the upper half-plane of the complex phase function, which allows for recovery of the 3D RI from a single intensity stack. We experimentally validated PSA-TIDT by conducting high-resolution tomographic imaging of various unlabeled biological samples, including human breast cancer cell lines (MCF-7), human hepatocyte carcinoma cell lines (HepG2), Henrietta Lacks (HeLa) cells, and red blood cells (RBCs).

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.

Nonparaxial optical transfer function for arbitrary illumination in partially coherent imaging systems and the oblique source application

Recent research in quantitative phase and refractive index microscopy showed promising results with methods using a partially coherent imaging setup, such as partially coherent optical diffraction tomography. For these methods, the phase optical transfer function (POTF), which describes the transmission of spatial frequencies by the imaging system, is crucial. Here, a one-dimensional integral representation of the POTF for imaging systems with arbitrary illumination is derived. It generalizes the existing expression, which is limited to axially symmetric setups. From the general integral form, an analytical solution is derived for the case of oblique homogeneous disk-shaped illumination. This demonstrates the potential of the general representation by offering an additional approach for illumination design in quantitative phase and refractive index microscopy.

Perspective: Emerging strategies for determining atomic-resolution structures of macromolecular complexes within cells

In principle, electron cryo-tomography (cryo-ET) of thin portions of cells provides high-resolution images of the three-dimensional spatial arrangement of all members of the proteome. In practice, however, radiation damage creates a tension between recording images at many different tilt angles, but at correspondingly reduced exposure levels, versus limiting the number of tilt angles in order to improve the signal-to-noise ratio (SNR). Either way, it is challenging to read the available information out at the level of atomic structure. Here, we first review work that explores the optimal strategy for data collection, which currently seems to favor the use of a limited angular range for tilting the sample or even the use of a single image to record the high-resolution information. Looking then to the future, we point to the alternative of so-called “deconvolution microscopy”, which may be applied to tilt-series or optically-sectioned, focal series data. Recording data as a focal series has the advantage that little or no translational alignment of frames might be needed, and a three-dimensional reconstruction might require only 2/3 the number of images as does standard tomography. We also point to the unexploited potential of phase plates to increase the contrast, and thus to reduce the electron exposure levels while retaining the ability align and merge the data. In turn, using much lower exposures per image could have the advantage that high-resolution information is retained throughout the full data-set, whether recorded as a tilt series or a focal series of images.

ADMM approach for efficient iterative tomographic deconvolution reconstruction of 3D quantitative phase images

Tomographic deconvolution phase microscopy (TDPM) is a promising approach for 3D quantitative imaging of phase objects such as biological cells and optical fibers. In the present work, the alternating direction method of multipliers (ADMM) is applied to TDPM to shorten its image acquisition and processing times while simultaneously improving its accuracy. ADMM-TDPM is used to optimize the image fidelity by minimizing Gaussian noise and by using total variation regularization with the constraints of nonnegativity and known zeros. ADMM-TDPM can reconstruct phase objects that are shift variant in three spatial dimensions. ADMM-TDPM achieves speedups of 5x in image acquisition time and greater than 10x in image processing time with accompanying higher accuracy compared to TDPM.

High-speed multifocus phase imaging in thick tissue

Phase microscopy is widely used to image unstained biological samples. However, most phase imaging techniques require transmission geometries, making them unsuited for thick sample applications. Moreover, when applied to volumetric imaging, phase imaging generally requires large numbers of measurements, often making it too slow to capture live biological processes with fast 3D index-of-refraction variations. By combining oblique back-illumination microscopy and a z-splitter prism, we perform phase imaging that is both epi-mode and multifocus, enabling high-speed 3D phase imaging in thick, scattering tissues with a single camera. We demonstrate here 3D qualitative phase imaging of blood flow in chick embryos over a field of view of 546 × 546 × 137 µm3 at speeds up to 47 Hz.

Real-time heart rate monitoring system for cardiotoxicity assessment of Daphnia magna using high-speed digital holographic microscopy

Machine vision techniques for monitoring heart rates in aquatic bioassays have been applied to cardiotoxicity assessment. However, the requisite large data sizes and long calculation times make long-term observations of heart rates difficult. In this study, we developed a real-time heart rate monitoring system for individual Daphnia magna in a water chamber mounter that immobilizes their movement in 100 mL media. Heart rates are calculated from real-time, time-resolved relative phase information from digital holograms acquired with a 200 fps camera and parallel computation using a graphics processing unit. With this system, we monitored the real-time changes in the heart rates of individual D. magna specimens exposed to H₂O₂ as a positive control for reactive oxygen species (ROS) levels in an aquatic environment for 10 h, a period long enough to observe dynamic heart rate responses to the mounting process and exposure and to establish heart rate trends. An additional group analysis was conducted to compare to conventional cardiotoxicity assessment, with results of both assessments showing that the heart rates reduced according to ROS level by H₂O₂ exposure concentration. Notably, the results of our real-time dynamic heart rate monitoring in aquatic conditions indicated that establishing a relaxation heart rate before measurements could improve the accuracy of toxicity assessment. It is believed that the system developed in this study, achieving the simultaneous measurement, analysis, and display of reconstructed results, will find wide application in other aquatic bioassays.

Common-path intrinsically achromatic optical diffraction tomography

In this work we propose an open-top like common-path intrinsically achromatic optical diffraction tomography system. It operates as a total-shear interferometer and employs Ronchi-type amplitude diffraction grating, positioned in between the camera and the tube lens without an additional 4f system, generating three-beam interferograms with achromatic second harmonic. Such configuration makes the proposed system low cost, compact and immune to vibrations. We present the results of the measurements of 3D-printed cell phantom using laser diode (coherent) and superluminescent diode (partially coherent) light sources. Broadband light sources can be naturally employed without the need for any cumbersome compensation because of the intrinsic achromaticity of the interferometric recording (holograms generated by -1st and +1st conjugated diffraction orders are not affected by the illumination wavelength). The results show that the decreased coherence offers much reduced coherent noise and higher fidelity tomographic reconstruction especially when applied nonnegativity constraint regularization procedure.

Spatial light interference microscopy: principle and applications to biomedicine

In this paper, we review spatial light interference microscopy (SLIM), a common-path, phase-shifting interferometer, built onto a phase-contrast microscope, with white-light illumination. As one of the most sensitive quantitative phase imaging (QPI) methods, SLIM allows for speckle-free phase reconstruction with sub-nanometer path-length stability. We first review image formation in QPI, scattering, and full-field methods. Then, we outline SLIM imaging from theory and instrumentation to diffraction tomography. Zernike's phase-contrast microscopy, phase retrieval in SLIM, and halo removal algorithms are discussed. Next, we discuss the requirements for operation, with a focus on software developed in-house for SLIM that enables high-throughput acquisition, whole slide scanning, mosaic tile registration, and imaging with a color camera. We introduce two methods for solving the inverse problem using SLIM, white-light tomography, and Wolf phase tomography. Lastly, we review the applications of SLIM in basic science and clinical studies. SLIM can study cell dynamics, cell growth and proliferation, cell migration, mass transport, etc. In clinical settings, SLIM can assist with cancer studies, reproductive technology, blood testing, etc. Finally, we review an emerging trend, where SLIM imaging in conjunction with artificial intelligence brings computational specificity and, in turn, offers new solutions to outstanding challenges in cell biology and pathology.

Analytical phase optical transfer function for Gaussian illumination and the optimized illumination profiles

The imaging performance of tomographic deconvolution phase microscopy can be described in terms of the phase optical transfer function (POTF) which, in turn, depends on the illumination profile. To facilitate the optimization of the illumination profile, an analytical calculation method based on polynomial fitting is developed to describe the POTF for general nonuniform axially symmetric illumination. This is then applied to Gaussian and related profiles. Compared to numerical integration methods that integrate over a series of annuli, the present analytical method is much faster and is equally accurate. Further, a "balanced distribution" criterion for the POTF and a least-squares minimization are presented to optimize the uniformity of the POTF. An optimum general profile is found analytically by relaxed optimal search, and an optimum Gaussian profile is found through a tree search. Numerical simulations confirm the performance of these optimum profiles and support the balanced distribution criterion introduced.

Optimizing illumination in three-dimensional deconvolution microscopy for accurate refractive index tomography

In light transmission microscopy, axial scanning does not directly provide tomographic reconstruction of specimen. Phase deconvolution microscopy can convert a raw intensity image stack into a refractive index tomogram, the intrinsic sample contrast which can be exploited for quantitative morphological analysis. However, this technique is limited by reconstruction artifacts due to unoptimized optical conditions, which leads to a sparse and non-uniform optical transfer function. Here, we propose an optimization method based on simulated annealing to systematically obtain optimal illumination schemes that enable artifact-free deconvolution. The proposed method showed precise tomographic reconstruction of unlabeled biological samples.

Three-dimensional phase optical transfer function in axially symmetric microscopic quantitative phase imaging

Three-dimensional quantitative phase imaging (3D QPI) is widely recognized as a potentially high-impact microscopic modality. Central to determining the resolution capability of 3D QPI is the phase optical transfer function (POTF). The magnitude of the POTF over its spatial frequency coverage (SFC) specifies the intensity of the response for each allowed spatial frequency. In this paper, a detailed analysis of the POTF for an axially symmetric optical configuration is presented. First, a useful geometric interpretation of the SFC, which enables its visualization, is presented. Second, a closed-form 1D integral expression is derived for the POTF in the general nonparaxial case, which enables rapid calculation of the POTF. Third, this formulation is applied to disk, annular, multi-annuli, and Gaussian illuminations as well as to an annular objective. Taken together, these contributions enable the visualization and simplified calculation of the 3D axially symmetric POTF and provide a basis for optimizing QPI in a wide range of applications.

Revealing architectural order with quantitative label-free imaging and deep learning

We report quantitative label-free imaging with phase and polarization (QLIPP) for simultaneous measurement of density, anisotropy, and orientation of structures in unlabeled live cells and tissue slices. We combine QLIPP with deep neural networks to predict fluorescence images of diverse cell and tissue structures. QLIPP images reveal anatomical regions and axon tract orientation in prenatal human brain tissue sections that are not visible using brightfield imaging. We report a variant of U-Net architecture, multi-channel 2.5D U-Net, for computationally efficient prediction of fluorescence images in three dimensions and over large fields of view. Further, we develop data normalization methods for accurate prediction of myelin distribution over large brain regions. We show that experimental defects in labeling the human tissue can be rescued with quantitative label-free imaging and neural network model. We anticipate that the proposed method will enable new studies of architectural order at spatial scales ranging from organelles to tissue.

Numerical simulations of partially coherent illumination for multi-scattering phase objects via a beam propagation method

Many studies have performed imaging under partially coherent illumination. However, to the best of our knowledge, there are no imaging methods for complicated objects such as cell colonies, which are large and diffract light multiple times. In this paper, we propose an image calculation method for the partially coherent illumination of a large-scale three-dimensional multi-diffractive object. The image is calculated via the summation of coherent images of each illumination angle using the beam propagation method. We apply this method to various microscopic observations, including phase contrast and differential interference contrast. Our method shows excellent agreement with experimental images of a bead and a photonic crystal fiber. As with a cell colony, our method reproduced the characteristics of the image through experimentation. Finally, we discuss the accuracy and the restriction conditions of our method.

Quantitative phase imaging of fiber Bragg gratings in multicore fibers

Fiber Bragg gratings (FBGs) and multi-core fibers (MCFs) have independently demonstrated high levels of performance in numerous diverse applications. When integrated together, the devices can offer enhanced performance as well as open more applications. In all of these cases, the refractive index (RI) characterization of the FBGs is crucial in monitoring and validating the fabricated devices. To accomplish this, quantitative phase imaging (QPI) is a promising RI characterization candidate satisfying all of the requirements: noninvasive measurement, quantitative characterization, sub-micrometer resolution, no a priori knowledge, and 3D reconstruction. In this paper, we propose a new QPI method for characterization of the RI distribution of multiple FBGs in a single MCF. We have identified the key challenges associated with this approach: the pixel integration effect, aliasing effect, numerical aperture requirement, and characteristic functions recovery. We have further identified approaches for overcoming each of these challenges that have previously impeded this direction of research. The proposed method is supported by simulations of 2D and 3D gratings.

Partially coherent illumination engineering for enhanced refractive index tomography

Optical diffraction tomography based on partially coherent illumination (PC-ODT) is a quantitative label-free imaging technique that allows reconstructing of the object's 3D refractive index from measured through-focus intensity images. PC illumination provides advantages such as speckle noise-free imaging and inherent compatibility with conventional wide-field microscopes. Here we experimentally demonstrate that a proper design of the PC illumination, different from the familiar bright-field one, and the use of more realistic optical transfer functions (OTFs) have crucial importance in PC-ODT to significantly increase the accuracy in 3D refractive index reconstruction. While realistic OTFs properly account for the real experimental illumination conditions, the proposed PC illumination design allows for gathering the object spatial-frequency content attenuated when bright-field illumination is used.

Three-dimensional tomographic microscopy technique with multi-frequency combination with partially coherent illuminations

We demonstrate a three-dimensional (3D) optical diffraction tomographic technique with multi-frequency combination (MFC-ODT) for the 3D quantitative phase imaging of unlabeled specimens. Three sets of through-focus intensity images are captured under an annular aperture and two circular apertures with different coherence parameters. The 3D phase optical transfer functions (POTF) corresponding to different illumination apertures are combined to obtain a synthesized frequency response, achieving high-quality, low-noise 3D reconstructions with imaging resolution up to the incoherent diffraction limit. Besides, the expression of 3D POTF for arbitrary illumination pupils is derived and analyzed, and the 3D imaging performance of annular illumination is explored. It is shown that the phase-contrast washout effect in high-NA circular apertures can be effectively addressed by introducing a complementary annular aperture, which strongly boosts the phase contrast and improves the imaging resolution. By incorporating high-NA illumination as well as high-NA detection, MFC-ODT can achieve a theoretical transverse resolution up to 200 nm and an axial resolution of 645 nm. To test the feasibility of the proposed MFC-ODT technique, the 3D refractive index reconstruction results are based on a simulated 3D resolution target and experimental investigations of micro polystyrene bead and unstained biological samples are presented. Due to its capability for high-resolution 3D phase imaging as well as the compatibility with a widely available commercial microscope, the MFC-ODT is expected to find versatile applications in biological and biomedical research.

High-throughput intensity diffraction tomography with a computational microscope

We demonstrate a motion-free intensity diffraction tomography technique that enables the direct inversion of 3D phase and absorption from intensity-only measurements for weakly scattering samples. We derive a novel linear forward model featuring slice-wise phase and absorption transfer functions using angled illumination. This new framework facilitates flexible and efficient data acquisition, enabling arbitrary sampling of the illumination angles. The reconstruction algorithm performs 3D synthetic aperture using a robust computation and memory efficient slice-wise deconvolution to achieve resolution up to the incoherent limit. We demonstrate our technique with thick biological samples having both sparse 3D structures and dense cell clusters. We further investigate the limitation of our technique when imaging strongly scattering samples. Imaging performance and the influence of multiple scattering is evaluated using a 3D sample consisting of stacked phase and absorption resolution targets. This computational microscopy system is directly built on a standard commercial microscope with a simple LED array source add-on, and promises broad applications by leveraging the ubiquitous microscopy platforms with minimal hardware modifications.

Iterative optimization in tomographic deconvolution phase microscopy

Tomographic deconvolution phase microscopy (TDPM) is a three-dimensional (3D) quantitative phase imaging (QPI) method using partially coherent light that can be implemented on a commercial microscope platform. However, the measurement procedure is relatively time-consuming because it requires many illumination angles. In the present work, an edge-preserving iterative optimization algorithm is presented and applied to TDPM, so that the required number of illumination angles is reduced from 15 to 3, while the measurement accuracy remains high. In addition, the iterative algorithm does not require matrix representation of operators, so the memory requirement is correspondingly reduced.

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.

Fast label-free microscopy technique for 3D dynamic quantitative imaging of living cells

The refractive index (RI) is an important optical characteristic that is often exploited in label-free microscopy for analysis of biological objects. A technique for 3D RI reconstruction of living cells has to be fast enough to capture the cell dynamics and preferably needs to be compatible with standard wide-field microscopes. To solve this challenging problem, we present a technique that provides fast measurement and processing of data required for real-time 3D visualization of the object RI. Specifically, the 3D RI is reconstructed from the measurement of bright-field intensity images, axially scanned by a high-speed focus tunable lens mounted in front of a sCMOS camera, by using a direct deconvolution approach designed for partially coherent light microscopy in the non-paraxial regime. Both the measurement system and the partially coherent illumination, that provides optical sectioning and speckle-noise suppression, enable compatibility with wide-field microscopes resulting in a competitive and affordable alternative to the current holographic laser microscopes. Our experimental demonstrations show video-rate 3D RI visualization of living bacteria both freely swimming and optically manipulated by using freestyle laser traps allowing for their trapping and transport along 3D trajectories. These results prove that is possible to conduct simultaneous 4D label-free quantitative imaging and optical manipulation of living cells, which is promising for the study of the cell biophysics and biology.

Clarification and unification of the obliquity factor in diffraction and scattering theories: discussion

Two-dimensional (2D) and three-dimensional (3D) diffraction theories form the underlying basis of quantitative phase imaging. This paper reviews how 2D and 3D diffraction theories are developed based on thin and thick object requirements. However, some previously reported work has mixed 2D and 3D theories. This discussion shows that it is possible to enable consistent mixed use of 2D and 3D theories by applying appropriate obliquity factor (OF) modifications. The discussion is concluded with an overall unifying representation for the usage of the OF modifications in 2D and 3D diffraction theories as applied to both thin and thick objects.

Label-free quantitative 3D tomographic imaging for partially coherent light microscopy

Crucial benefits provided by partially coherent light microscopy such as improved spatial resolution, optical sectioning and speckle-noise suppression are exploited here to achieve 3D quantitative imaging: reconstruction of the object refractive index (RI). We present a partially coherent optical diffraction tomography technique (PC-ODT) that can be easily implemented in commercially available bright-field microscopes. We show that the high numerical apertures of the objective and condenser lenses, together with optical refocusing, are main issues for achieving fast and successful 3D RI reconstruction of weak objects. In particular, the optical refocusing is performed by a high-speed focus tunable lens mounted in front of the digital camera enabling compatibility with commercial microscopes. The technique is experimentally demonstrated on different examples: diatom cells (biosilica shells), polystyrene micro-spheres and blood cells. The results confirm the straightforward 3D-RI reconstruction of the samples providing valuable quantitative information for their analysis. Thus, the PC-ODT can be considered as an efficient and affordable alternative to coherent ODT which requires specially designed holographic microscopes.

A Mismatch Detection Method Based on Affine Transformation for Stereo Light Microscopy Stereo Matching

For the light microscopy images that have the characteristics of shallow depth of field, serious distortion and poor resolution, mismatch is a ubiquitous phenomenon. The paper presents a mismatch detection method for the stereo light microscopy stereo matching. Affine transformation matrix and matching constraint condition are calibrated by the calibration board which has the precision solid dots and the motorized stage. Bias vector of affine transformation of each matching pair is taken as the criteria to apply mismatch detection. The experimental results show that the method can detect more mismatching pairs and preserve more matching pairs than the traditional RANSAC method and the epipolar rectification method.

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.

3D differential phase contrast microscopy

We demonstrate 3D phase and absorption recovery from partially coherent intensity images captured with a programmable LED array source. Images are captured through-focus with four different illumination patterns. Using first Born and weak object approximations (WOA), a linear 3D differential phase contrast (DPC) model is derived. The partially coherent transfer functions relate the sample's complex refractive index distribution to intensity measurements at varying defocus. Volumetric reconstruction is achieved by a global FFT-based method, without an intermediate 2D phase retrieval step. Because the illumination is spatially partially coherent, the transverse resolution of the reconstructed field achieves twice the NA of coherent systems and improved axial resolution.