Model-based wavefront shaping microscopy

Using high-resolution microscopy data to generate realistic structures for electromagnetic FDTD simulations from complex biological models

Finite-difference time-domain (FDTD) electromagnetic simulations are a computational method that has seen much success in the study of biological optics; however, such simulations are often hindered by the difficulty of faithfully replicating complex biological microstructures in the simulation space. Recently, we designed simulations to calculate the trajectory of electromagnetic light waves through realistically reconstructed retinal photoreceptors and found that cone photoreceptor mitochondria play a substantial role in shaping incoming light. In addition to vision research and ophthalmology, such simulations are broadly applicable to studies of the interaction of electromagnetic radiation with biological tissue. Here, we present our method for discretizing complex 3D models of cellular structures for use in FDTD simulations using MEEP, the MIT Electromagnetic Equation Propagation software, including subpixel smoothing at mesh boundaries. Such models can originate from experimental imaging or be constructed by hand. We also include sample code for use in MEEP. Implementation of this algorithm in new code requires understanding of 3D mathematics and may require several weeks of effort, whereas use of our sample code requires knowledge of MEEP and C++ and may take up to a few hours to prepare a model of interest for 3D FDTD simulation. In all cases, access to a facility supercomputer with parallel processing capabilities is recommended. This protocol offers a practical solution to a significant challenge in the field of computational electrodynamics and paves the way for future advancements in the study of light interaction with biological structures.

Single-shot digital optical fluorescence phase conjugation through forward multiple-scattering samples

Aberrations and multiple scattering in biological tissues critically distort light beams into highly complex speckle patterns. In this regard, digital optical phase conjugation (DOPC) is a promising technique enabling in-depth focusing. However, DOPC becomes challenging when using fluorescent guide stars for four main reasons: the low photon budget available, the large spectral bandwidth of the fluorescent signal, the Stokes shift between the emission and the excitation wavelength, and the absence of reference beam preventing holographic measurement. Here, we demonstrate the possibility to focus a laser beam through multiple-scattering samples by measuring speckle fields in a single acquisition step with a reference-free, high-resolution wavefront sensor. By taking advantage of the large spectral bandwidth of forward multiply scattering samples, digital fluorescence phase conjugation is achieved to focus a laser beam at the excitation wavelength while measuring the broadband speckle field arising from a micrometer-sized fluorescent bead.

Wavefront shaping improves the transparency of the scattering media: a review

Significance

Wavefront shaping (WFS) can compensate for distortions by optimizing the wavefront of the input light or reversing the transmission matrix of the media. It is a promising field of research. A thorough understanding of principles and developments of WFS is important for optical research.

Aim

To provide insight into WFS for researchers who deal with scattering in biomedicine, imaging, and optical communication, our study summarizes the basic principles and methods of WFS and reviews recent progress.

Approach

The basic principles, methods of WFS, and the latest applications of WFS in focusing, imaging, and multimode fiber (MMF) endoscopy are described. The practical challenges and prospects of future development are also discussed.

Results

Data-driven learning-based methods are opening up new possibilities for WFS. High-resolution imaging through MMFs can support small-diameter endoscopy in the future.

Conclusion

The rapid development of WFS over the past decade has shown that the best solution is not to avoid scattering but to find ways to correct it or even use it. WFS with faster speed, more optical modes, and more modulation degrees of freedom will continue to drive exciting developments in various fields.

Tracing multiple scattering trajectories for deep optical imaging in scattering media

Multiple light scattering hampers imaging objects in complex scattering media. Approaches used in real practices mainly aim to filter out multiple scattering obscuring the ballistic waves that travel straight through the scattering medium. Here, we propose a method that makes the deterministic use of multiple scattering for microscopic imaging of an object embedded deep within scattering media. The proposed method finds a stack of multiple complex phase plates that generate similar light trajectories as the original scattering medium. By implementing the inverse scattering using the identified phase plates, our method rectifies multiple scattering and amplifies ballistic waves by almost 600 times. This leads to a significant increase in imaging depth-more than three times the scattering mean free path-as well as the correction of image distortions. Our study marks an important milestone in solving the long-standing high-order inverse scattering problems.

NeuWS: Neural wavefront shaping for guidestar-free imaging through static and dynamic scattering media

Diffraction-limited optical imaging through scattering media has the potential to transform many applications such as airborne and space-based imaging (through the atmosphere), bioimaging (through skin and human tissue), and fiber-based imaging (through fiber bundles). Existing wavefront shaping methods can image through scattering media and other obscurants by optically correcting wavefront aberrations using high-resolution spatial light modulators-but these methods generally require (i) guidestars, (ii) controlled illumination, (iii) point scanning, and/or (iv) statics scenes and aberrations. We propose neural wavefront shaping (NeuWS), a scanning-free wavefront shaping technique that integrates maximum likelihood estimation, measurement modulation, and neural signal representations to reconstruct diffraction-limited images through strong static and dynamic scattering media without guidestars, sparse targets, controlled illumination, nor specialized image sensors. We experimentally demonstrate guidestar-free, wide field-of-view, high-resolution, diffraction-limited imaging of extended, nonsparse, and static/dynamic scenes captured through static/dynamic aberrations.

Numerical simulation of phase-optimized light beams in two-dimensional scattering media

Manipulating the incident wavefront in biomedical applications to enhance the penetration depth and energy delivery in scattering media such as biological tissue has gained a lot of attention in recent years. However, focusing inside scattering media and examining the electromagnetic field inside the medium still is an elaborate task. This is where electromagnetic field simulations that model the wavefront shaping process can help us understand how the focal near field evolves at different depths. Here we use a two-step beam synthesis method to simulate the scattering of complex incident wavefronts by well-characterized media. The approach uses plane wave electromagnetic near-field solutions in combination with an angular spectrum approach to model different light beams. We apply this approach to various two-dimensional scattering media and investigate the focus intensity over depth while scanning with and without phase optimization. We find that the scanned non-optimized beams have two regions characterized by exponential decays. The absolute progression of the focus intensity over depth for phase-optimized beams using all channels can be described by solutions of the radiative transfer theory. Furthermore, the average enhancement factor over depth of the phase-optimized focus intensity compared to that without optimization is investigated for different numerical apertures and scattering media. Our results show that, albeit the incident beam is diffusively scattered, the theoretical enhancement for a large number of optimization channels cannot be reached due to correlations between the channels. An increase in focus depth and an increase in the numerical aperture reduces the difference between the expected theoretical and simulated enhancement factors.

Wavefront shaping: A versatile tool to conquer multiple scattering in multidisciplinary fields

Optical techniques offer a wide variety of applications as light-matter interactions provide extremely sensitive mechanisms to probe or treat target media. Most of these implementations rely on the usage of ballistic or quasi-ballistic photons to achieve high spatial resolution. However, the inherent scattering nature of light in biological tissues or tissue-like scattering media constitutes a critical obstacle that has restricted the penetration depth of non-scattered photons and hence limited the implementation of most optical techniques for wider applications. In addition, the components of an optical system are usually designed and manufactured for a fixed function or performance. Recent advances in wavefront shaping have demonstrated that scattering- or component-induced phase distortions can be compensated by optimizing the wavefront of the input light pattern through iteration or by conjugating the transmission matrix of the scattering medium. This offers unprecedented opportunities in many applications to achieve controllable optical delivery or detection at depths or dynamically configurable functionalities by using scattering media to substitute conventional optical components. In this article, the recent progress of wavefront shaping in multidisciplinary fields is reviewed, from optical focusing and imaging with scattering media, functionalized devices, modulation of mode coupling, and nonlinearity in multimode fiber to multimode fiber-based applications. Apart from insights into the underlying principles and recent advances in wavefront shaping implementations, practical limitations and roadmap for future development are discussed in depth. Looking back and looking forward, it is believed that wavefront shaping holds a bright future that will open new avenues for noninvasive or minimally invasive optical interactions and arbitrary control inside deep tissues. The high degree of freedom with multiple scattering will also provide unprecedented opportunities to develop novel optical devices based on a single scattering medium (generic or customized) that can outperform traditional optical components.

Snapshot time-reversed ultrasonically encoded optical focusing guided by time-reversed photoacoustic wave

Deep-tissue optical imaging is a longstanding challenge limited by scattering. Both optical imaging and treatment can benefit from focusing light in deep tissue beyond one transport mean free path. Wavefront shaping based on time-reversed ultrasonically encoded (TRUE) optical focusing utilizes ultrasound focus, which is much less scattered than light in biological tissues as the 'guide star'. However, the traditional TRUE is limited by the ultrasound focusing area and pressure tagging efficiency, especially in acoustically heterogeneous medium. Even the improved version of iterative TRUE comes at a large time consumption, which limits the application of TRUE. To address this problem, we proposed a method called time-reversed photoacoustic wave guided time-reversed ultrasonically encoded (TRPA-TRUE) optical focusing by integrating accurate ultrasonic focusing through acoustically heterogeneous medium guided by time-reversing PA signals, and the ultrasound modulation of diffused coherent light with optical phase conjugation (OPC), achieving dynamic focusing of light into scattering medium. Simulation results show that the focusing accuracy of the proposed method has been significantly improved compared with conventional TRUE, which is more suitable for practical applications that suffers severe acoustic distortion, e.g. transcranial optical focusing.

Two-photon microscopy with enhanced resolution and signal-to-background ratio using hollow Gaussian beam excitation

Two-photon microscopy (TPM) offers deeper imaging depth inside the scattering medium, however, it suffers from limited resolution owing to the longer excitation wavelength. We demonstrate the use of a hollow Gaussian beam (HGB) at the therapeutic window to improve the resolution and signal-to-background ratio (SBR). The HGB was produced by omitting the azimuthal phase term from the vortex mode, and the excitation point spread function (PSF) can be readily tuned by the mode order. The performance of the TPM with HGB was evaluated by experimentally imaging 100 nm fluorescent beads to estimate the PSF. The HGB improved the lateral resolution of the TPM by 36% in contrast to the conventional TPM. The HGB also furnishes an improvement of SBR by eliminating the out-of-focus light owing to its ring shape. Furthermore, we have used a translating lens-based module for additional lateral resolution tuning and reduced the resolution further down to 44% with respect to conventional TPM. Finally, we have performed imaging with merely two-dimensional scanning of a 50 µm thick mouse brain slice (Thy-YFP H-line) using the developed TPM with HGB. Our compact, robust, and low-cost design of the HGB generation scheme can easily be integrated into the commercial TPM to accommodate the improvements.

Oxygen control: the often overlooked but essential piece to create better in vitro systems

Variations in oxygen levels play key roles in numerous physiological and pathological processes, but are often not properly controlled in in vitro models, introducing a significant bias in experimental outcomes. Recent developments in microfluidic technology have introduced a paradigm shift by providing new opportunities to better mimic physiological and pathological conditions, which is achieved by both regulating and monitoring oxygen levels at the micrometre scale in miniaturized devices. In this review, we first introduce the nature and relevance of oxygen-dependent pathways in both physiological and pathological contexts. Subsequently, we discuss strategies to control oxygen in microfluidic devices, distinguishing between engineering approaches that operate at the device level during its fabrication and chemical approaches that involve the active perfusion of fluids oxygenated at a precise level or supplemented with oxygen-producing or oxygen-scavenging materials. In addition, we discuss readout approaches for monitoring oxygen levels at the cellular and tissue levels, focusing on electrochemical and optical detection schemes for high-resolution measurements directly on-chip. An overview of different applications in which microfluidic devices have been utilized to answer biological research questions is then provided. In the final section, we provide our vision for further technological refinements of oxygen-controlling devices and discuss how these devices can be employed to generate new fundamental insights regarding key scientific problems that call for emulating oxygen levels as encountered in vivo. We conclude by making the case that ultimately emulating physiological or pathological oxygen levels should become a standard feature in all in vitro cell, tissue, and organ models.

Multiorgan-on-a-Chip: A Systemic Approach To Model and Decipher Inter-Organ Communication

Multiorgan-on-a-chip (multi-OoC) platforms have great potential to redefine the way in which human health research is conducted. After briefly reviewing the need for comprehensive multiorgan models with a systemic dimension, we highlight scenarios in which multiorgan models are advantageous. We next overview existing multi-OoC platforms, including integrated body-on-a-chip devices and modular approaches involving interconnected organ-specific modules. We highlight how multi-OoC models can provide unique information that is not accessible using single-OoC models. Finally, we discuss remaining challenges for the realization of multi-OoC platforms and their worldwide adoption. We anticipate that multi-OoC technology will metamorphose research in biology and medicine by providing holistic and personalized models for understanding and treating multisystem diseases.