Small near-infrared photochromic protein for photoacoustic multi-contrast imaging and detection of protein interactions in vivo

Challenges and advances in two-dimensional photoacoustic computed tomography: a review

Significance

Photoacoustic computed tomography (PACT), a hybrid imaging modality combining optical excitation with acoustic detection, has rapidly emerged as a prominent biomedical imaging technique.

Aim

We review the challenges and advances of PACT, including (1) limited view, (2) anisotropy resolution, (3) spatial aliasing, (4) acoustic heterogeneity (speed of sound mismatch), and (5) fluence correction of spectral unmixing.

Approach

We performed a comprehensive literature review to summarize the key challenges in PACT toward practical applications and discuss various solutions.

Results

There is a wide range of contributions from both industry and academic spaces. Various approaches, including emerging deep learning methods, are proposed to improve the performance of PACT further.

Conclusions

We outline contemporary technologies aimed at tackling the challenges in PACT applications.

Next-Generation Genetically Encoded Fluorescent Biosensors Illuminate Cell Signaling and Metabolism

Genetically encoded fluorescent biosensors have revolutionized the study of cell signaling and metabolism, as they allow for live-cell measurements with high spatiotemporal resolution. This success has spurred the development of tailor-made biosensors that enable the study of dynamic phenomena on different timescales and length scales. In this review, we discuss different approaches to enhancing and developing new biosensors. We summarize the technologies used to gain structural insights into biosensor design and comment on useful screening technologies. Furthermore, we give an overview of different applications where biosensors have led to key advances over recent years. Finally, we give our perspective on where future work is bound to make a large impact.

Photoacoustic Tomography with Temporal Encoding Reconstruction (PATTERN) for cross-modal individual analysis of the whole brain

Cross-modal analysis of the same whole brain is an ideal strategy to uncover brain function and dysfunction. However, it remains challenging due to the slow speed and destructiveness of traditional whole-brain optical imaging techniques. Here we develop a new platform, termed Photoacoustic Tomography with Temporal Encoding Reconstruction (PATTERN), for non-destructive, high-speed, 3D imaging of ex vivo rodent, ferret, and non-human primate brains. Using an optimally designed image acquisition scheme and an accompanying machine-learning algorithm, PATTERN extracts signals of genetically-encoded probes from photobleaching-based temporal modulation and enables reliable visualization of neural projection in the whole central nervous system with 3D isotropic resolution. Without structural and biological perturbation to the sample, PATTERN can be combined with other whole-brain imaging modalities to acquire the whole-brain image with both high resolution and morphological fidelity. Furthermore, cross-modal transcriptome analysis of an individual brain is achieved by PATTERN imaging. Together, PATTERN provides a compatible and versatile strategy for brain-wide cross-modal analysis at the individual level.

On the Importance of Low-Frequency Signals in Functional and Molecular Photoacoustic Computed Tomography

In photoacoustic computed tomography (PACT) with short-pulsed laser excitation, wideband acoustic signals are generated in biological tissues with frequencies related to the effective shapes and sizes of the optically absorbing targets. Low-frequency photoacoustic signal components correspond to slowly varying spatial features and are often omitted during imaging due to the limited detection bandwidth of the ultrasound transducer, or during image reconstruction as undesired background that degrades image contrast. Here we demonstrate that low-frequency photoacoustic signals, in fact, contain functional and molecular information, and can be used to enhance structural visibility, improve quantitative accuracy, and reduce spare-sampling artifacts. We provide an in-depth theoretical analysis of low-frequency signals in PACT, and experimentally evaluate their impact on several representative PACT applications, such as mapping temperature in photothermal treatment, measuring blood oxygenation in a hypoxia challenge, and detecting photoswitchable molecular probes in deep organs. Our results strongly suggest that low-frequency signals are important for functional and molecular PACT.

Current Trends of Bacterial and Fungal Optoproteins for Novel Optical Applications

Photoproteins, luminescent proteins or optoproteins are a kind of light-response protein responsible for the conversion of light into biochemical energy that is used by some bacteria or fungi to regulate specific biological processes. Within these specific proteins, there are groups such as the photoreceptors that respond to a given light wavelength and generate reactions susceptible to being used for the development of high-novel applications, such as the optocontrol of metabolic pathways. Photoswitchable proteins play important roles during the development of new materials due to their capacity to change their conformational structure by providing/eliminating a specific light stimulus. Additionally, there are bioluminescent proteins that produce light during a heatless chemical reaction and are useful to be employed as biomarkers in several fields such as imaging, cell biology, disease tracking and pollutant detection. The classification of these optoproteins from bacteria and fungi as photoreceptors or photoresponse elements according to the excitation-emission spectrum (UV-Vis-IR), as well as their potential use in novel applications, is addressed in this article by providing a structured scheme for this broad area of knowledge.

On the importance of low-frequency signals in functional and molecular photoacoustic computed tomography

In photoacoustic computed tomography (PACT) with short-pulsed laser excitation, wideband acoustic signals are generated in biological tissues with frequencies related to the effective shapes and sizes of the optically absorbing targets. Low-frequency photoacoustic signal components correspond to slowly varying spatial features and are often omitted during imaging due to the limited detection bandwidth of the ultrasound transducer, or during image reconstruction as undesired background that degrades image contrast. Here we demonstrate that low-frequency photoacoustic signals, in fact, contain functional and molecular information, and can be used to enhance structural visibility, improve quantitative accuracy, and reduce spare-sampling artifacts. We provide an in-depth theoretical analysis of low-frequency signals in PACT, and experimentally evaluate their impact on several representative PACT applications, such as mapping temperature in photothermal treatment, measuring blood oxygenation in a hypoxia challenge, and detecting photoswitchable molecular probes in deep organs. Our results strongly suggest that low-frequency signals are important for functional and molecular PACT.

Non-invasive Deep-Brain Imaging with 3D Integrated Photoacoustic Tomography and Ultrasound Localization Microscopy (3D-PAULM)

Photoacoustic computed tomography (PACT) is a proven technology for imaging hemodynamics in deep brain of small animal models. PACT is inherently compatible with ultrasound (US) imaging, providing complementary contrast mechanisms. While PACT can quantify the brain's oxygen saturation of hemoglobin (sO2), US imaging can probe the blood flow based on the Doppler effect. Further, by tracking gas-filled microbubbles, ultrasound localization microscopy (ULM) can map the blood flow velocity with sub-diffraction spatial resolution. In this work, we present a 3D deep-brain imaging system that seamlessly integrates PACT and ULM into a single device, 3D-PAULM. Using a low ultrasound frequency of 4 MHz, 3D-PAULM is capable of imaging the whole-brain hemodynamic functions with intact scalp and skull in a totally non-invasive manner. Using 3D-PAULM, we studied the mouse brain functions with ischemic stroke. Multi-spectral PACT, US B-mode imaging, microbubble-enhanced power Doppler (PD), and ULM were performed on the same mouse brain with intrinsic image co-registration. From the multi-modality measurements, we future quantified blood perfusion, sO2, vessel density, and flow velocity of the mouse brain, showing stroke-induced ischemia, hypoxia, and reduced blood flow. We expect that 3D-PAULM can find broad applications in studying deep brain functions on small animal models.

Nonadiabatic Coupling in Trajectory Surface Hopping: How Approximations Impact Excited-State Reaction Dynamics

Photochemical reactions are widely modeled using the popular trajectory surface hopping (TSH) method, an affordable mixed quantum-classical approximation to the full quantum dynamics of the system. TSH is able to account for nonadiabatic effects using an ensemble of trajectories, which are propagated on a single potential energy surface at a time and which can hop from one electronic state to another. The occurrences and locations of these hops are typically determined using the nonadiabatic coupling between electronic states, which can be assessed in a number of ways. In this work, we benchmark the impact of some approximations to the coupling term on the TSH dynamics for several typical isomerization and ring-opening reactions. We have identified that two of the schemes tested, the popular local diabatization scheme and a scheme based on biorthonormal wave function overlap implemented in the OpenMOLCAS code as part of this work, reproduce at a much reduced cost the dynamics obtained using the explicitly calculated nonadiabatic coupling vectors. The other two schemes tested can give different results, and in some cases, even entirely incorrect dynamics. Of these two, the scheme based on configuration interaction vectors gives unpredictable failures, while the other scheme based on the Baeck-An approximation systematically overestimates hopping to the ground state as compared to the reference approaches.

Application of photoacoustic computed tomography in biomedical imaging: A literature review

Photoacoustic computed tomography (PACT) is a hybrid imaging modality that combines optical excitation and acoustic detection techniques. It obtains high-resolution deep-tissue images based on the deep penetration of light, the anisotropy of light absorption in objects, and the photoacoustic effect. Hence, PACT shows great potential in biomedical sample imaging. Recently, due to its advantages of high sensitivity to optical absorption and wide scalability of spatial resolution with the desired imaging depth, PACT has received increasing attention in preclinical and clinical practice. To date, there has been a proliferation of PACT systems designed for specific biomedical imaging applications, from small animals to human organs, from ex vivo to in vivo real-time imaging, and from simple structural imaging to functional and molecular imaging with external contrast agents. Therefore, it is of great importance to summarize the previous applications of PACT systems in biomedical imaging and clinical practice. In this review, we searched for studies related to PACT imaging of biomedical tissues and samples over the past two decades; divided the studies into two categories, PACT imaging of preclinical animals and PACT imaging of human organs and body parts; and discussed the significance of the studies. Finally, we pointed out the future directions of PACT in biomedical applications. With the development of exogenous contrast agents and advances of imaging technique, in the future, PACT will enable biomedical imaging from organs to whole bodies, from superficial vasculature to internal organs, from anatomy to functions, and will play an increasingly important role in biomedical research and clinical practice.

In situ synthesized nanozyme for photoacoustic-imaging-guided photothermal therapy and tumor hypoxia relief

Nanozymes have attracted extensive research interest due to their ideal enzymatic catalytic performance; however, uncontrollable activities and nonspecific accumulation limit their further clinical application. To overcome these obstacles, we proposed in situ synthesized nanozyme, and realized the concept through an intelligent nanosystem (ISSzyme) based on Prussian blue (PB) precursor. PB nanozyme was synthesized at the tumor sites through the interaction of ISSzyme with glutathione, which was demonstrated by comparing with conventional PB nanozyme. ISSzyme is capable of tumor-specific photoacoustic imaging (PAI) and photothermal therapy (PTT), reducing the false-positive signals of PAI and the treatment side effects of PTT. ISSzyme has catalase-like activities, resulting in tumor hypoxia relief and metastasis inhibition. More importantly, the in situ synthesized PB nanozyme has the favorable property of minimal liver accumulation. Considering the above advantages, ISSzyme is expected to shed light on the design of the next-generation artificial enzymes, with many new biomedical applications.

Recent Advances in Contrast-Enhanced Photoacoustic Imaging: Overcoming the Physical and Practical Challenges

For decades now, photoacoustic imaging (PAI) has been investigated to realize its potential as a niche biomedical imaging modality. Despite its highly desirable optical contrast and ultrasonic spatiotemporal resolution, PAI is challenged by such physical limitations as a low signal-to-noise ratio (SNR), diminished image contrast due to strong optical attenuation, and a lower-bound on spatial resolution in deep tissue. In addition, contrast-enhanced PAI has faced practical limitations such as insufficient cell-specific targeting due to low delivery efficiency and difficulties in developing clinically translatable agents. Identifying these limitations is essential to the continuing expansion of the field, and substantial advances in developing contrast-enhancing agents, complemented by high-performance image acquisition systems, have synergistically dealt with the challenges of conventional PAI. This review covers the past four years of research on pushing the physical and practical challenges of PAI in terms of SNR/contrast, spatial resolution, targeted delivery, and clinical application. Promising strategies for dealing with each challenge are reviewed in detail, and future research directions for next generation contrast-enhanced PAI are discussed.

A photoacoustic patch for three-dimensional imaging of hemoglobin and core temperature

Electronic patches, based on various mechanisms, allow continuous and noninvasive monitoring of biomolecules on the skin surface. However, to date, such devices are unable to sense biomolecules in deep tissues, which have a stronger and faster correlation with the human physiological status than those on the skin surface. Here, we demonstrate a photoacoustic patch for three-dimensional (3D) mapping of hemoglobin in deep tissues. This photoacoustic patch integrates an array of ultrasonic transducers and vertical-cavity surface-emitting laser (VCSEL) diodes on a common soft substrate. The high-power VCSEL diodes can generate laser pulses that penetrate >2 cm into biological tissues and activate hemoglobin molecules to generate acoustic waves, which can be collected by the transducers for 3D imaging of the hemoglobin with a high spatial resolution. Additionally, the photoacoustic signal amplitude and temperature have a linear relationship, which allows 3D mapping of core temperatures with high accuracy and fast response. With access to biomolecules in deep tissues, this technology adds unprecedented capabilities to wearable electronics and thus holds significant implications for various applications in both basic research and clinical practice.

Fabry-Pérot resonant avalanche-mode silicon LEDs for tunable narrow-band emission

We report on the effect of Fabry-Pérot (FP) resonance on hot-carrier electroluminescence (EL) spectra and the optical power efficiencies of silicon (Si) avalanche-mode (AM) LEDs in the wavelength range from 500 nm to 950 nm. The LEDs, fabricated in a silicon-on-insulator photonics technology, consist of symmetric p-n junctions placed within a 0.21 µm thick Si micro-ring of varying width and radius. We show that the peak wavelength in the EL-spectra can be tuned within a range of 100 nm by varying the ring width from 0.16 µm to 0.30 µm, which is explained by FP resonance. The measured EL-spectra features relatively narrow bands (with a spectral width of ∼50 nm) with high intensities compared to conventional Si AMLEDs. By varying the ring radius and using a high doping level, we obtain a record high optical power efficiency of 3.2×10^-5. Our work is a breakthrough in engineering the EL spectrum of Si, foreseen to benefit the performance of Si-integrated optical interconnects and sensors.

Three-Dimensional Deep-Tissue Functional and Molecular Imaging by Integrated Photoacoustic, Ultrasound, and Angiographic Tomography (PAUSAT)

Non-invasive small-animal imaging technologies, such as optical imaging, magnetic resonance imaging and x -ray computed tomography, have enabled researchers to study normal biological phenomena or disease progression in their native conditions. However, existing small-animal imaging technologies often lack either the penetration capability for interrogating deep tissues (e.g., optical microscopy), or the functional and molecular sensitivity for tracking specific activities (e.g., magnetic resonance imaging). To achieve functional and molecular imaging in deep tissues, we have developed an integrated photoacoustic, ultrasound and acoustic angiographic tomography (PAUSAT) system by seamlessly combining light and ultrasound. PAUSAT can perform three imaging modes simultaneously with complementary contrast: high-frequency B-mode ultrasound imaging of tissue morphology, microbubble-enabled acoustic angiography of tissue vasculature, and multi-spectral photoacoustic imaging of molecular probes. PAUSAT can provide three-dimensional (3D) multi-contrast images that are co-registered, with high spatial resolutions at large depths. Using PAUSAT, we performed proof-of-concept in vivo experiments on various small animal models: monitoring longitudinal development of placenta and embryo during mouse pregnancy, tracking biodistribution and metabolism of near-infrared organic dye on the whole-body scale, and detecting breast tumor expressing genetically-encoded photoswitchable phytochromes. These results have collectively demonstrated that PAUSAT has broad applicability in biomedical research, providing comprehensive structural, functional, and molecular imaging of small animal models.

Multiscale photoacoustic tomography of neural activities with GCaMP calcium indicators

SIGNIFICANCE

Optical imaging of responses in fluorescently labeled neurons has progressed significantly in recent years. However, there is still a need to monitor neural activities at divergent spatial scales and at depths beyond the optical diffusion limit.

AIM

To meet these needs, we aim to develop multiscale photoacoustic tomography (PAT) to image neural activities across spatial scales with a genetically encoded calcium indicator GCaMP.

APPROACH

First, using photoacoustic microscopy, we show that depth-resolved GCaMP signals can be monitored in vivo from a fly brain in response to odor stimulation without depth scanning and even with the cuticle intact. In vivo monitoring of GCaMP signals was also demonstrated in mouse brains. Next, using photoacoustic computed tomography, we imaged neural responses of a mouse brain slice at depths beyond the optical diffusion limit.

RESULTS

We provide the first unambiguous demonstration that multiscale PAT can be used to record neural activities in transgenic flies and mice with select neurons expressing GCaMP.

CONCLUSIONS

Our results indicate that the combination of multiscale PAT and fluorescent neural activity indicators provides a methodology for imaging targeted neurons at various scales.

Application of Genetically Encoded Molecular Imaging Probes in Tumor Imaging

In recent years, imaging technology has made rapid progress to improve the sensitivity of tumor diagnostic. With the development of genetic engineering and synthetic biology, various genetically encoded molecular imaging probes have also been extensively developed. As a biomedical imaging method with excellent detectable sensitivity and spatial resolution, genetically encoded molecular imaging has great application potential in the visualization of cellular and molecular functions during tumor development. Compared to chemosynthetic dyes and nanoparticles with an imaging function, genetically encoded molecular imaging probes can more easily label specific cells or proteins of interest in tumor tissues and have higher stability and tissue contrast in vivo. Therefore, genetically encoded molecular imaging probes have attracted increasing attention from researchers in engineering and biomedicine. In this review, we aimed to introduce the genetically encoded molecular imaging probes and further explained their applications in tumor imaging.

Video-rate full-ring ultrasound and photoacoustic computed tomography with real-time sound speed optimization

Full-ring dual-modal ultrasound and photoacoustic imaging provide complementary contrasts, high spatial resolution, full view angle and are more desirable in pre-clinical and clinical applications. However, two long-standing challenges exist in achieving high-quality video-rate dual-modal imaging. One is the increased data processing burden from the dense acquisition. Another one is the object-dependent speed of sound variation, which may cause blurry, splitting artifacts, and low imaging contrast. Here, we develop a video-rate full-ring ultrasound and photoacoustic computed tomography (VF-USPACT) with real-time optimization of the speed of sound. We improve the imaging speed by selective and parallel image reconstruction. We determine the optimal sound speed via co-registered ultrasound imaging. Equipped with a 256-channel ultrasound array, the dual-modal system can optimize the sound speed and reconstruct dual-modal images at 10 Hz in real-time. The optimized sound speed can effectively enhance the imaging quality under various sample sizes, types, or physiological states. In animal and human imaging, the system shows co-registered dual contrasts, high spatial resolution (140 µm), single-pulse photoacoustic imaging (< 50 µs), deep penetration (> 20 mm), full view, and adaptive sound speed correction. We believe VF-USPACT can advance many real-time biomedical imaging applications, such as vascular disease diagnosing, cancer screening, or neuroimaging.

Looking deep inside tissue with photoacoustic molecular probes: a review

Significance

Deep tissue noninvasive high-resolution imaging with light is challenging due to the high degree of light absorption and scattering in biological tissue. Photoacoustic imaging (PAI) can overcome some of the challenges of pure optical or ultrasound imaging to provide high-resolution deep tissue imaging. However, label-free PAI signals from light absorbing chromophores within the tissue are nonspecific. The use of exogeneous contrast agents (probes) not only enhances the imaging contrast (and imaging depth) but also increases the specificity of PAI by binding only to targeted molecules and often providing signals distinct from the background.

Aim

We aim to review the current development and future progression of photoacoustic molecular probes/contrast agents.

Approach

First, PAI and the need for using contrast agents are briefly introduced. Then, the recent development of contrast agents in terms of materials used to construct them is discussed. Then, various probes are discussed based on targeting mechanisms, in vivo molecular imaging applications, multimodal uses, and use in theranostic applications.

Results

Material combinations are being used to develop highly specific contrast agents. In addition to passive accumulation, probes utilizing activation mechanisms show promise for greater controllability. Several probes also enable concurrent multimodal use with fluorescence, ultrasound, Raman, magnetic resonance imaging, and computed tomography. Finally, targeted probes are also shown to aid localized and molecularly specific photo-induced therapy.

Conclusions

The development of contrast agents provides a promising prospect for increased contrast, higher imaging depth, and molecularly specific information. Of note are agents that allow for controlled activation, explore other optical windows, and enable multimodal use to overcome some of the shortcomings of label-free PAI.

A red-green photochromic bacterial protein as a new contrast agent for improved photoacoustic imaging

The GAF3 domain of the cyanobacteriochrome Slr1393 from Synechocystis sp. PCC6803, binding phycocyanobilin as a chromophore, shows photochromicity between two stable, green- and red-absorbing states, characterized by relatively high photoconversion yields. Using nanosecond-pulsed excitation by red or green light, respectively, and suitable cw photoconversion beams, we demonstrate that the light-modulatable photoacoustic waveforms arising from GAF3 can be easily distinguished from background signals originating from non-modulatable competitive absorbers and scattering media. It is demonstrated that this effect can be exploited to identify the position of the photochromic molecule by using as a phantom a cylindrical capillary tube filled with either a GAF3 solution or with an E.coli suspension overexpressing GAF3. These properties identify the high potential of GAF3 to be included in the palette of genetically encoded photochromic probes for photoacoustic imaging.

Spectral crosstalk in photoacoustic computed tomography

Multispectral photoacoustic (PA) imaging faces two major challenges: the spectral coloring effect, which has been studied extensively as an optical inversion problem, and the spectral crosstalk, which is basically a result of non-ideal acoustic inversion. So far, there is no systematic work to analyze the spectral crosstalk because acoustic inversion and spectroscopic measurement are always treated as decoupled. In this work, we theorize and demonstrate through a series of simulations and experiments how imperfect acoustic inversion induces inaccurate PA spectrum measurement. We provide detailed analysis to elucidate how different factors, including limited bandwidth, limited view, light attenuation, out-of-plane signal, and image reconstruction schemes, conspire to render the measured PA spectrum inaccurate. We found that the model-based reconstruction outperforms universal back-projection in suppressing the spectral crosstalk in some cases.

High frame rate (∼3 Hz) circular photoacoustic tomography using single-element ultrasound transducer aided with deep learning

SIGNIFICANCE

In circular scanning photoacoustic tomography (PAT), it takes several minutes to generate an image of acceptable quality, especially with a single-element ultrasound transducer (UST). The imaging speed can be enhanced by faster scanning (with high repetition rate light sources) and using multiple-USTs. However, artifacts arising from the sparse signal acquisition and low signal-to-noise ratio at higher scanning speeds limit the imaging speed. Thus, there is a need to improve the imaging speed of the PAT systems without hampering the quality of the PAT image.

AIM

To improve the frame rate (or imaging speed) of the PAT system by using deep learning (DL).

APPROACH

For improving the frame rate (or imaging speed) of the PAT system, we propose a novel U-Net-based DL framework to reconstruct PAT images from fast scanning data.

RESULTS

The efficiency of the network was evaluated on both single- and multiple-UST-based PAT systems. Both phantom and in vivo imaging demonstrate that the network can improve the imaging frame rate by approximately sixfold in single-UST-based PAT systems and by approximately twofold in multi-UST-based PAT systems.

CONCLUSIONS

We proposed an innovative method to improve the frame rate (or imaging speed) by using DL and with this method, the fastest frame rate of ∼ 3    Hz imaging is achieved without hampering the quality of the reconstructed image.

Optogenetic manipulation and photoacoustic imaging using a near-infrared transgenic mouse model

Optogenetic manipulation and optical imaging in the near-infrared range allow non-invasive light-control and readout of cellular and organismal processes in deep tissues in vivo. Here, we exploit the advantages of Rhodopseudomonas palustris BphP1 bacterial phytochrome, which incorporates biliverdin chromophore and reversibly photoswitches between the ground (740-800 nm) and activated (620-680 nm) states, to generate a loxP-BphP1 transgenic mouse model. The mouse enables Cre-dependent temporal and spatial targeting of BphP1 expression in vivo. We validate the optogenetic performance of endogenous BphP1, which in the activated state binds its engineered protein partner QPAS1, to trigger gene transcription in primary cells and living mice. We demonstrate photoacoustic tomography of BphP1 expression in different organs, developing embryos, virus-infected tissues and regenerating livers, with the centimeter penetration depth. The transgenic mouse model provides opportunities for both near-infrared optogenetics and photoacoustic imaging in vivo and serves as a source of primary cells and tissues with genomically encoded BphP1.

A guide to designing photocontrol in proteins: methods, strategies and applications

Light is essential for various biochemical processes in all domains of life. In its presence certain proteins inside a cell are excited, which either stimulates or inhibits subsequent cellular processes. The artificial photocontrol of specifically proteins is of growing interest for the investigation of scientific questions on the organismal, cellular and molecular level as well as for the development of medicinal drugs or biocatalytic tools. For the targeted design of photocontrol in proteins, three major methods have been developed over the last decades, which employ either chemical engineering of small-molecule photosensitive effectors (photopharmacology), incorporation of photoactive non-canonical amino acids by genetic code expansion (photoxenoprotein engineering), or fusion with photoreactive biological modules (hybrid protein optogenetics). This review compares the different methods as well as their strategies and current applications for the light-regulation of proteins and provides background information useful for the implementation of each technique.

Video-Rate Dual-Modal Wide-Beam Harmonic Ultrasound and Photoacoustic Computed Tomography

Dual-modal ultrasound (US) and photoacoustic (PA) imaging has tremendous advantages in biomedical applications, such as pharmacokinetics, cancer screening, and imaging-guided therapy. Compared with ring-shaped arrays, a linear piezoelectric transducer array applies to more anatomical sites and has been widely used in US/PA imaging. However, the linear array may limit the imaging quality due to narrow bandwidth, partial detection view, or sparse spatial sampling. To meet clinic demand of high-quality US/PA imaging with the linear transducer, we develop dual-modal wide-beam harmonic ultrasound (WBHUS) and photoacoustic computed tomography at video rate. The harmonic US imaging employs pulse phase inversion to reduce clutters and improve spatial resolution. Wide-beam US transmission can shorten the scanning times by 267% and enables a 20-Hz imaging rate, which can minimize motion artifacts in in vivo imaging. The harmonic US imaging does not only provide accurate anatomical references for locating PA features but also reduces artifacts in PA images. The improved image quality allows us to acquire high-resolution anatomical structures in deep tissue without labeling. The fast-imaging speed enables visualizing interventional procedures and monitoring the pulsations of the thoracic aorta and radial artery in real-time. The video-rate dual-modal harmonic US and single-shot PA computed tomography use a clinical-grade linear-array transducer and thus can be readily implemented in clinical US imaging.

Alginate beads as a highly versatile test-sample for optoacoustic imaging

Test-samples are necessary for the development of emerging imaging approaches such as optoacoustics (OA); these can be used to benchmark new labeling agents and instrumentation, or to characterize image analysis algorithms or the inversion required to form the three-dimensional reconstructions. Alginate beads (AlBes) loaded with labeled mammalian or bacterial cells provide a method of creating defined structures of controllable size and photophysical characteristics and are well-suited for both in vitro and in vivo use. Here we describe a simple and rapid method for efficient and reproducible production of AlBes with specific characteristics and show three example applications with multispectral OA tomography imaging. We show the advantage of AlBes for studying and eventually improving photo-switching OA imaging approaches. As highly defined, homogeneous, quasi point-like signal sources, AlBes might hold similar advantages for studying other agents, light-fluence models, or the impact of detection geometries on correct image formation in the near future.

Background-suppressed tumor-targeted photoacoustic imaging using bacterial carriers

Photoacoustic (PA) imaging offers promise for biomedical applications due to its ability to image deep within biological tissues while providing detailed molecular information; however, its detection sensitivity is limited by high background signals that arise from endogenous chromophores. Genetic reporter proteins with photoswitchable properties enable the removal of background signals through the subtraction of PA images for each light-absorbing form. Unfortunately, the application of photoswitchable chromoproteins for tumor-targeted imaging has been hampered by the lack of an effective targeted delivery scheme; that is, photoswitchable probes must be delivered in vivo with high targeting efficiency and specificity. To overcome this limitation, we have developed a tumor-targeting delivery system in which tumor-homing bacteria (Escherichia coli) are exploited as carriers to affect the point-specific delivery of genetically encoded photochromic probes to the tumor area. To improve the efficiency of the desired background suppression, we engineered a phytochrome-based reporter protein (mDrBphP-PCMm/F469W) that displays higher photoswitching contrast than those in the current state of the art. Photoacoustic computed tomography was applied to achieve good depth and resolution in the context of in vivo (mice) imaging. The present system effectively integrates a genetically encoded phytochrome-based reporter protein, PA imaging, and synthetic biology (GPS), to achieve essentially background-suppressed tumor-targeted PA monitoring in deep-seated tissues. The ability to image tumors at substantial depths may enable target-specific cancer diagnoses to be made with greater sensitivity, fidelity, and specificity.

Genetically encoded photo-switchable molecular sensors for optoacoustic and super-resolution imaging

Reversibly photo-switchable proteins are essential for many super-resolution fluorescence microscopic and optoacoustic imaging methods. However, they have yet to be used as sensors that measure the distribution of specific analytes at the nanoscale or in the tissues of live animals. Here we constructed the prototype of a photo-switchable Ca²⁺ sensor based on GCaMP5G that can be switched with 405/488-nm light and describe its molecular mechanisms at the structural level, including the importance of the interaction of the core barrel structure of the fluorescent protein with the Ca²⁺ receptor moiety. We demonstrate super-resolution imaging of Ca²⁺ concentration in cultured cells and optoacoustic Ca²⁺ imaging in implanted tumor cells in mice under controlled Ca²⁺ conditions. Finally, we show the generalizability of the concept by constructing examples of photo-switching maltose and dopamine sensors based on periplasmatic binding protein and G-protein-coupled receptor-based sensors.

The Red Edge: Bilin-Binding Photoreceptors as Optogenetic Tools and Fluorescence Reporters

This review adds the bilin-binding phytochromes to the Chemical Reviews thematic issue "Optogenetics and Photopharmacology". The work is structured into two parts. We first outline the photochemistry of the covalently bound tetrapyrrole chromophore and summarize relevant spectroscopic, kinetic, biochemical, and physiological properties of the different families of phytochromes. Based on this knowledge, we then describe the engineering of phytochromes to further improve these chromoproteins as photoswitches and review their employment in an ever-growing number of different optogenetic applications. Most applications rely on the light-controlled complex formation between the plant photoreceptor PhyB and phytochrome-interacting factors (PIFs) or C-terminal light-regulated domains with enzymatic functions present in many bacterial and algal phytochromes. Phytochrome-based optogenetic tools are currently implemented in bacteria, yeast, plants, and animals to achieve light control of a wide range of biological activities. These cover the regulation of gene expression, protein transport into cell organelles, and the recruitment of phytochrome- or PIF-tagged proteins to membranes and other cellular compartments. This compilation illustrates the intrinsic advantages of phytochromes compared to other photoreceptor classes, e.g., their bidirectional dual-wavelength control enabling instant ON and OFF regulation. In particular, the long wavelength range of absorption and fluorescence within the "transparent window" makes phytochromes attractive for complex applications requiring deep tissue penetration or dual-wavelength control in combination with blue and UV light-sensing photoreceptors. In addition to the wide variability of applications employing natural and engineered phytochromes, we also discuss recent progress in the development of bilin-based fluorescent proteins.

A Deep Learning-Based Model That Reduces Speed of Sound Aberrations for Improved In Vivo Photoacoustic Imaging

Photoacoustic imaging (PAI) has attracted great attention as a medical imaging method. Typically, photoacoustic (PA) images are reconstructed via beamforming, but many factors still hinder the beamforming techniques in reconstructing optimal images in terms of image resolution, imaging depth, or processing speed. Here, we demonstrate a novel deep learning PAI that uses multiple speed of sound (SoS) inputs. With this novel method, we achieved SoS aberration mitigation, streak artifact removal, and temporal resolution improvement all at once in structural and functional in vivo PA images of healthy human limbs and melanoma patients. The presented method produces high-contrast PA images in vivo with reduced distortion, even in adverse conditions where the medium is heterogeneous and/or the data sampling is sparse. Thus, we believe that this new method can achieve high image quality with fast data acquisition and can contribute to the advance of clinical PAI.

Multimodal Contrast Agents for Optoacoustic Brain Imaging in Small Animals

Optoacoustic (photoacoustic) imaging has demonstrated versatile applications in biomedical research, visualizing the disease pathophysiology and monitoring the treatment effect in an animal model, as well as toward applications in the clinical setting. Given the complex disease mechanism, multimodal imaging provides important etiological insights with different molecular, structural, and functional readouts in vivo. Various multimodal optoacoustic molecular imaging approaches have been applied in preclinical brain imaging studies, including optoacoustic/fluorescence imaging, optoacoustic imaging/magnetic resonance imaging (MRI), optoacoustic imaging/MRI/Raman, optoacoustic imaging/positron emission tomography, and optoacoustic/computed tomography. There is a rapid development in molecular imaging contrast agents employing a multimodal imaging strategy for pathological targets involved in brain diseases. Many chemical dyes for optoacoustic imaging have fluorescence properties and have been applied in hybrid optoacoustic/fluorescence imaging. Nanoparticles are widely used as hybrid contrast agents for their capability to incorporate different imaging components, tunable spectrum, and photostability. In this review, we summarize contrast agents including chemical dyes and nanoparticles applied in multimodal optoacoustic brain imaging integrated with other modalities in small animals, and provide outlook for further research.

A practical guide to photoswitching optoacoustics tomography

Photochromic proteins and photoswitching optoacoustics (OA) are a promising combination, that allows OA imaging of even small numbers of cells in whole live animals and thus can facilitate a more wide-spread use of OA in life-science and preclinical research. The concept relies on exploiting the modulation achieved by the photoswitching to discriminate the agents' signal from the non-modulating background. Here we share our analysis approaches that can be readily used on data generated with commercial OA tomography imaging instrumentation allowing-depending on the used photoswitching agent and sample-routine visualizations of as little as several hundreds of transgene labeled cells per imaging volume in the live animal.

Recent Advances in Photoacoustic Tomography

Photoacoustic tomography (PAT) that integrates the molecular contrast of optical imaging with the high spatial resolution of ultrasound imaging in deep tissue has widespread applications in basic biological science, preclinical research, and clinical trials. Recently, tremendous progress has been made in PAT regarding technical innovations, preclinical applications, and clinical translations. Here, we selectively review the recent progresses and advances in PAT, including the development of advanced PAT systems for small-animal and human imaging, newly engineered optical probes for molecular imaging, broad-spectrum PAT for label-free imaging of biological tissues, high-throughput snapshot photoacoustic topography, and integration of machine learning for image reconstruction and processing. We envision that PAT will have further technical developments and more impactful applications in biomedicine.

Nonlinear mechanisms in photoacoustics-Powerful tools in photoacoustic imaging

Many nonlinear effects have been discovered and developed in photoacoustic imaging. These nonlinear mechanisms have been explored for different utilizations, such as enhancing imaging contrast, measuring tissue temperature, achieving super-resolution imaging, enabling functional imaging, and extracting important physical parameters. This review aims to introduce different nonlinear mechanisms in photoacoustics, underline the fundamental principles, highlight their representative applications, and outline the occurrence conditions and applicable range of each nonlinear mechanism. Furthermore, this review thoroughly discusses the nonlinearity rule concerning how the mathematical structure of the nonlinear dependence is correlated to its practical applications. This summarization is useful for identifying and guiding the potential applications of nonlinearity based on their mathematical expressions, and is helpful for new nonlinear mechanism discovery or implementation in the future, which facilitates further breakthroughs in nonlinear photoacoustics.

Nonlinear mechanisms in photoacoustics-Powerful tools in photoacoustic imaging

Many nonlinear effects have been discovered and developed in photoacoustic imaging. These nonlinear mechanisms have been explored for different utilizations, such as enhancing imaging contrast, measuring tissue temperature, achieving super-resolution imaging, enabling functional imaging, and extracting important physical parameters. This review aims to introduce different nonlinear mechanisms in photoacoustics, underline the fundamental principles, highlight their representative applications, and outline the occurrence conditions and applicable range of each nonlinear mechanism. Furthermore, this review thoroughly discusses the nonlinearity rule concerning how the mathematical structure of the nonlinear dependence is correlated to its practical applications. This summarization is useful for identifying and guiding the potential applications of nonlinearity based on their mathematical expressions, and is helpful for new nonlinear mechanism discovery or implementation in the future, which facilitates further breakthroughs in nonlinear photoacoustics.

Nanoparticles: A New Approach to Upgrade Cancer Diagnosis and Treatment

Traditional cancer therapeutics have been criticized due to various adverse effects and insufficient damage to targeted tumors. The breakthrough of nanoparticles provides a novel approach for upgrading traditional treatments and diagnosis. Actually, nanoparticles can not only solve the shortcomings of traditional cancer diagnosis and treatment, but also create brand-new perspectives and cutting-edge devices for tumor diagnosis and treatment. However, most of the research about nanoparticles stays in vivo and in vitro stage, and only few clinical researches about nanoparticles have been reported. In this review, we first summarize the current applications of nanoparticles in cancer diagnosis and treatment. After that, we propose the challenges that hinder the clinical applications of NPs and provide feasible solutions in combination with the updated literature in the last two years. At the end, we will provide our opinions on the future developments of NPs in tumor diagnosis and treatment.

Snapshot photoacoustic topography through an ergodic relay of optical absorption in vivo

Photoacoustic tomography (PAT) has demonstrated versatile biomedical applications, ranging from tracking single cells to monitoring whole-body dynamics of small animals and diagnosing human breast cancer. Currently, PAT has two major implementations: photoacoustic computed tomography (PACT) and photoacoustic microscopy (PAM). PACT uses a multi-element ultrasonic array for parallel detection, which is relatively complex and expensive. In contrast, PAM requires point-by-point scanning with a single-element detector, which has a limited imaging throughput. The trade-off between the system cost and throughput demands a new imaging method. To this end, we have developed photoacoustic topography through an ergodic relay (PATER). PATER can capture a wide-field image with only a single-element ultrasonic detector upon a single laser shot. This protocol describes the detailed procedures for PATER system construction, including component selection, equipment setup and system alignment. A step-by-step guide for in vivo imaging of a mouse brain is provided as an example application. Data acquisition, image reconstruction and troubleshooting procedures are also elaborated. It takes ~130 min to carry out this protocol, including ~60 min for both calibration and snapshot wide-field data acquisition using a laser with a 2-kHz pulse repetition rate. PATER offers low-cost snapshot wide-field imaging of fast dynamics, such as visualizing blood pulse wave propagation and tracking melanoma tumor cell circulation in mice in vivo. We envision that PATER will have wide biomedical applications and anticipate that the compact size of the setup will allow it to be further developed as a wearable device to monitor human vital signs.

Genetically encodable materials for non-invasive biological imaging

Many questions in basic biology and medicine require the ability to visualize the function of specific cells and molecules inside living organisms. In this context, technologies such as ultrasound, optoacoustics and magnetic resonance provide non-invasive imaging access to deep-tissue regions, as used in many laboratories and clinics to visualize anatomy and physiology. In addition, recent work has enabled these technologies to image the location and function of specific cells and molecules inside the body by coupling the physics of sound waves, nuclear spins and light absorption to unique protein-based materials. These materials, which include air-filled gas vesicles, capsid-like nanocompartments, pigment-producing enzymes and transmembrane transporters, enable new forms of biomolecular and cellular contrast. The ability of these protein-based contrast agents to be genetically encoded and produced by cells creates opportunities for unprecedented in vivo studies of cellular function, while their amenability to genetic engineering enables atomic-level design of their physical, chemical and biological properties.

Toward photoswitchable electronic pre-resonance stimulated Raman probes

Reversibly photoswitchable probes allow for a wide variety of optical imaging applications. In particular, photoswitchable fluorescent probes have significantly facilitated the development of super-resolution microscopy. Recently, stimulated Raman scattering (SRS) imaging, a sensitive and chemical-specific optical microscopy, has proven to be a powerful live-cell imaging strategy. Driven by the advances of newly developed Raman probes, in particular the pre-resonance enhanced narrow-band vibrational probes, electronic pre-resonance SRS (epr-SRS) has achieved super-multiplex imaging with sensitivity down to 250 nM and multiplexity up to 24 colors. However, despite the high demand, photoswitchable Raman probes have yet to be developed. Here, we propose a general strategy for devising photoswitchable epr-SRS probes. Toward this goal, we exploit the molecular electronic and vibrational coupling, in which we switch the electronic states of the molecules to four different states to turn their ground-state epr-SRS signals on and off. First, we showed that inducing transitions to both the electronic excited state and triplet state can effectively diminish the SRS peaks. Second, we revealed that the epr-SRS signals can be effectively switched off in red-absorbing organic molecules through light-facilitated transitions to a reduced state. Third, we identified that photoswitchable proteins with near-infrared photoswitchable absorbance, whose states are modulable with their electronic resonances detunable toward and away from the pump photon energy, can function as the photoswitchable epr-SRS probes with desirable sensitivity (<1 µM) and low photofatigue (>40 cycles). These photophysical characterizations and proof-of-concept demonstrations should advance the development of novel photoswitchable Raman probes and open up the unexplored Raman imaging capabilities.

In vivo liver thermoacoustic imaging and demonstration based on localization wire

PURPOSE

Liver disease causes significant morbidity and mortality worldwide. Liver imaging plays an essential role in the noninvasive liver disease evaluation because of the limitation of liver biopsy. This paper aims to image in vivo liver with thermoacoustic imaging (TAI) and demonstrate this liver imaging technique with a cross-validation method.

METHODS

The imaging system composed of a large aperture antenna and a flexible transducer array was used, and we performed the position calibration using the delay and sum algorithm. The localization wire was utilized in the cross-validation of in vivo liver TAI.

RESULTS

We successfully validated in vivo liver TAI. In vivo images of different liver lobes without labels were observed. The imaging depth reached about 4 cm.

CONCLUSIONS

TAI has the potential to image the liver and provide useful dielectric properties of the liver tissue. This study realized the first in vivo liver TAI, suggesting its prospect in detecting liver disease noninvasively.

Integration of Multitargeted Polymer-Based Contrast Agents with Photoacoustic Computed Tomography: An Imaging Technique to Visualize Breast Cancer Intratumor Heterogeneity

One of the primary challenges in breast cancer diagnosis and treatment is intratumor heterogeneity (ITH), i.e., the coexistence of different genetically and epigenetically distinct malignant cells within the same tumor. Thus, the identification of ITH is critical for designing better treatments and hence to increase patient survival rates. Herein, we report a noninvasive hybrid imaging technology that integrates multitargeted and multiplexed patchy polymeric photoacoustic contrast agents (MTMPPPCAs) with single-impulse panoramic photoacoustic computed tomography (SIP-PACT). The target specificity ability of MTMPPPCAs to distinguish estrogen and progesterone receptor-positive breast tumors was demonstrated through both fluorescence and photoacoustic measurements and validated by tissue pathology analysis. This work provides the proof-of-concept of the MTMPPPCAs/SIP-PACT system to identify ITH in nonmetastatic tumors, with both high molecular specificity and real-time detection capability.

Improved pentamethine cyanine nanosensors for optoacoustic imaging of pancreatic cancer

Optoacoustic imaging is a new biomedical imaging technology with clear benefits over traditional optical imaging and ultrasound. While the imaging technology has improved since its initial development, the creation of dedicated contrast agents for optoacoustic imaging has been stagnant. Current exploration of contrast agents has been limited to standard commercial dyes that have already been established in optical imaging applications. While some of these compounds have demonstrated utility in optoacoustic imaging, they are far from optimal and there is a need for contrast agents with tailored optoacoustic properties. The synthesis, encapsulation within tumor targeting silica nanoparticles and applications in in vivo tumor imaging of optoacoustic contrast agents are reported.

Multi-scale optoacoustic molecular imaging of brain diseases

The ability to non-invasively visualize endogenous chromophores and exogenous probes and sensors across the entire rodent brain with the high spatial and temporal resolution has empowered optoacoustic imaging modalities with unprecedented capacities for interrogating the brain under physiological and diseased conditions. This has rapidly transformed optoacoustic microscopy (OAM) and multi-spectral optoacoustic tomography (MSOT) into emerging research tools to study animal models of brain diseases. In this review, we describe the principles of optoacoustic imaging and showcase recent technical advances that enable high-resolution real-time brain observations in preclinical models. In addition, advanced molecular probe designs allow for efficient visualization of pathophysiological processes playing a central role in a variety of neurodegenerative diseases, brain tumors, and stroke. We describe outstanding challenges in optoacoustic imaging methodologies and propose a future outlook.

Real-Time Quantification of Cartilage Degeneration by GAG-Targeted Cationic Nanoparticles for Efficient Therapeutic Monitoring in Living Mice

One of the characterizations of degenerative cartilage disease is the progressive loss of glycosaminoglycans (GAGs). The real-time imaging method to quantify GAGs is of great significance for the biochemical analysis of cartilage and diagnosis and therapeutic monitoring of cartilage degeneration in vivo. To this end, a cationic photoacoustic (PA) contrast agent, poly-l-lysine melanin nanoparticles (PLL-MNPs), specifically targeting anionic GAGs was developed in this study to investigate whether it can image cartilage degeneration. PLL-MNP assessed GAG depletion by Chondroitinase ABC in vitro rat cartilage and intact ex vivo mouse knee joint. A papain-induced cartilage degenerative mice model was used for in vivo photoacoustic imaging (PAI). Oral cartilage supplement glucosamine sulfate was intragastrically administered for mice cartilage repair and the therapeutic efficacy was monitored by PLL-MNP-enhanced PAI. Histologic findings were used to further confirm PAI results. In vitro results revealed that the PLL-MNPs not only had a high binding ability with GAGs but also sensitively monitored GAG content changes by PAI. The PA signal was gradually weakened along with the depletion of GAGs in cartilage. Particularly, PLL-MNPs depicted the cartilage structure and the distribution of GAGs was demonstrated in PA images in ex vivo joints. Compared with the normal joint, a lower signal intensity was detected from degenerative joint at 3 weeks after papain injection, suggesting an early diagnosis of cartilage lesion by PLL-MNPs. Importantly, this PA-enhanced nanoprobe was suitable for monitoring in vivo efficacy of glucosamine sulfate, which effectively blocked cartilage degradation in a high dose manner. In vivo imaging findings correlated well with histological examinations. PLL-MNPs provided sensitive visualization of cartilage degeneration and promising monitoring of therapeutic response in living subjects.

Photoacoustic Tomography Opening New Paradigms in Biomedical Imaging

After the emergence of the ultrasound, X-ray CT, PET, and MRI, photoacoustic tomography (PAT) is now in the phase of its exponential growth, with its expected full maturation being another form of mainstream clinical imaging modality. By combining the high contrast benefit of optical imaging and the high-resolution deep imaging capability of ultrasound, PAT can provide unprecedented anatomical image contrasts at clinically relevant depths as well as enable the use of a variety of functional and molecular imaging information, which is not possible with conventional imaging modalities. With these strengths, PAT has achieved numerous breakthroughs in various biomedical applications and also provided new technical platforms that may be able to resolve unmet issues in clinics. In this chapter, we provide an overview of the development of PAT technology for several major biomedical applications and provide an approximate projection of the future of PAT.

Sound Out the Deep Colors: Photoacoustic Molecular Imaging at New Depths

Photoacoustic tomography (PAT) has become increasingly popular for molecular imaging due to its unique optical absorption contrast, high spatial resolution, deep imaging depth, and high imaging speed. Yet, the strong optical attenuation of biological tissues has traditionally prevented PAT from penetrating more than a few centimeters and limited its application for studying deeply seated targets. A variety of PAT technologies have been developed to extend the imaging depth, including employing deep-penetrating microwaves and X-ray photons as excitation sources, delivering the light to the inside of the organ, reshaping the light wavefront to better focus into scattering medium, as well as improving the sensitivity of ultrasonic transducers. At the same time, novel optical fluence mapping algorithms and image reconstruction methods have been developed to improve the quantitative accuracy of PAT, which is crucial to recover weak molecular signals at larger depths. The development of highly-absorbing near-infrared PA molecular probes has also flourished to provide high sensitivity and specificity in studying cellular processes. This review aims to introduce the recent developments in deep PA molecular imaging, including novel imaging systems, image processing methods and molecular probes, as well as their representative biomedical applications. Existing challenges and future directions are also discussed.

Towards non-contact photoacoustic imaging [review]

Photoacoustic imaging (PAI) takes advantage of both optical and ultrasound imaging properties to visualize optical absorption with high resolution and contrast. Photoacoustic microscopy (PAM) is usually categorized with all-optical microscopy techniques such as optical coherence tomography or confocal microscopes. Despite offering high sensitivity, novel imaging contrast, and high resolution, PAM is not generally an all-optical imaging method unlike the other microscopy techniques. One of the significant limitations of photoacoustic microscopes arises from their need to be in physical contact with the sample through a coupling media. This physical contact, coupling, or immersion of the sample is undesirable or impractical for many clinical and pre-clinical applications. This also limits the flexibility of photoacoustic techniques to be integrated with other all-optical imaging microscopes for providing complementary imaging contrast. To overcome these limitations, several non-contact photoacoustic signal detection approaches have been proposed. This paper presents a brief overview of current non-contact photoacoustic detection techniques with an emphasis on all-optical detection methods and their associated physical mechanisms.