Spectrometer-free vibrational imaging by retrieving stimulated Raman signal from highly scattered photons

Adjunctive Testing Using Biospectral Emission Sequencing: Bioregulatory Intelligence Technology in Parallel With the Goals of Artificial Intelligence in Medicine

The many advancements in medical technology of the last century have continually sought to improve the sensitivity of testing and the specificity of treatment of human maladies. Conventional physical and pharmaceutical treatment is largely an imprecise process, stimulating the impetus for the advancement of machine learning-enhanced artificial intelligence (AI) medical technologies. Biospectral Emission Sequencing (BES) is a bioregulatory intelligence (BI) technology already in use as an adjunct to conventional testing. Biospectral Emission Sequencing provides a functional system of dynamic real-time adjunctive testing and treatment selection. This paper discusses the parallel technologies of present and future AI and BI technologies in medicine.

Frequency-Domain Low-Wavenumber Hyperspectral Stimulated Raman Scattering Microscopy

In recent years, stimulated Raman scattering (SRS) microscopy has experienced rapid technological advancements and has found widespread applications in chemical analysis. Hyperspectral SRS (hSRS) microscopy further enhances the chemical selectivity in imaging by providing a Raman spectrum for each pixel. Time-domain hSRS techniques often require interferometry and ultrashort femtosecond laser pulses. They are especially suited to measuring low-wavenumber Raman transitions but are susceptible to scattering-induced distortions. Frequency-domain hSRS microscopy, on the other hand, offers a simpler optical configuration and demonstrates high tolerance to sample scattering but typically operates within the spectral range of 400-4000 cm-1. Conventional frequency-domain hSRS microscopy is widely employed in biological applications but falls short in detecting chemical bonds with a weaker vibrational energy. In this work, we extend the spectral coverage of picosecond spectral-focusing hSRS microscopy to below 100 cm-1. This frequency-domain low-wavenumber hSRS approach can measure the weaker vibrational energy from the sample and has a strong tolerance to sample scattering. By expanding spectral coverage to 100-4000 cm-1, this development enhances the capability of spectral-domain SRS microscopy for chemical imaging.

Fast Real-Time Brain Tumor Detection Based on Stimulated Raman Histology and Self-Supervised Deep Learning Model

In intraoperative brain cancer procedures, real-time diagnosis is essential for ensuring safe and effective care. The prevailing workflow, which relies on histological staining with hematoxylin and eosin (H&E) for tissue processing, is resource-intensive, time-consuming, and requires considerable labor. Recently, an innovative approach combining stimulated Raman histology (SRH) and deep convolutional neural networks (CNN) has emerged, creating a new avenue for real-time cancer diagnosis during surgery. While this approach exhibits potential, there exists an opportunity for refinement in the domain of feature extraction. In this study, we employ coherent Raman scattering imaging method and a self-supervised deep learning model (VQVAE2) to enhance the speed of SRH image acquisition and feature representation, thereby enhancing the capability of automated real-time bedside diagnosis. Specifically, we propose the VQSRS network, which integrates vector quantization with a proxy task based on patch annotation for analysis of brain tumor subtypes. Training on images collected from the SRS microscopy system, our VQSRS demonstrates a significant speed enhancement over traditional techniques (e.g., 20-30 min). Comparative studies in dimensionality reduction clustering confirm the diagnostic capacity of VQSRS rivals that of CNN. By learning a hierarchical structure of recognizable histological features, VQSRS classifies major tissue pathological categories in brain tumors. Additionally, an external semantic segmentation method is applied for identifying tumor-infiltrated regions in SRH images. Collectively, these findings indicate that this automated real-time prediction technique holds the potential to streamline intraoperative cancer diagnosis, providing assistance to pathologists in simplifying the process.

Determining topical product bioequivalence with stimulated Raman scattering microscopy

Generic drugs are essential for affordable medicine and improving accessibility to treatments. Bioequivalence (BE) is typically demonstrated by assessing a generic product's pharmacokinetics (PK) relative to a reference-listed drug (RLD). Accurately estimating cutaneous PK (cPK) at or near the site of action can be challenging for locally acting topical products. Certain cPK approaches are available for assessing local bioavailability (BA) in the skin. Stimulated Raman scattering (SRS) microscopy has unique capabilities enabling continuous, high spatial and temporal resolution and quantitative imaging of drugs within the skin. In this paper, we developed an approach based on SRS and a polymer-based standard reference for the evaluation of topical product BA and BE in human skin ex vivo. BE assessment of tazarotene-containing formulations was achieved using cPK parameters obtained within different skin microstructures. The establishment of BE between the RLD and an approved generic product was successfully demonstrated. Interestingly, within the constraints of the current study design the results suggest similar BA between the tested gel formulation and the reference cream formulation, despite the differences in the formulation/dosage form. Another formulation containing polyethylene glycol as the vehicle was demonstrated to be not bioequivalent to the RLD. Compared to using the SRS approach without a standard reference, the developed approach enabled more consistent and reproducible results, which is crucial in BE assessment. The abundant information from the developed approach can help to systematically identify key areas of study design that will enable a better comparison of topical products and support an assessment of BE.

Hyper spectral resolution stimulated Raman spectroscopy with amplified fs pulse bursts

We present a novel approach for Stimulated Raman Scattering (SRS) spectroscopy in which a hyper spectral resolution and high-speed spectral acquisition are achieved by employing amplified offset-phase controlled fs-pulse bursts. We investigate the method by solving the coupled non-linear Schrödinger equations and validate it by numerically characterizing SRS in molecular nitrogen as a model compound. The spectral resolution of the method is found to be determined by the inverse product of the number of pulses in the burst and the intraburst pulse separation. The SRS spectrum is obtained through a motion-free scanning of the offset phase that results in a sweep of the Raman-shift frequency. Due to high spectral resolution and fast motion-free scanning the technique is beneficial for a number SRS-based applications such as gas sensing and chemical analysis.

Quantitative analysis of drug tablet aging by fast hyper-spectral stimulated Raman scattering microscopy

Pharmaceutical development of solid-state formulations requires testing active pharmaceutical ingredients (API) and excipients for uniformity and stability. Solid-state properties such as component distribution and grain size are crucial factors that influence the dissolution profile, which greatly affect drug efficacy and toxicity, and can only be analyzed spatially by chemical imaging (CI) techniques. Current CI techniques such as near infrared microscopy and confocal Raman spectroscopy are capable of high chemical and spatial resolution but cannot achieve the measurement speeds necessary for integration into the pharmaceutical production and quality assurance processes. To fill this gap, we demonstrate fast chemical imaging by epi-detected sparse spectral sampling stimulated Raman scattering to quantify API and excipient degradation and distribution.

Fast Raman imaging through the combination of context-aware matrix completion and low spectral resolution

Raman hyperspectral imaging is an effective method for label-free imaging with chemical specificity, yet the weak signals and correspondingly long integration times have hindered its wide adoption as a routine analytical method. Recently, low resolution Raman imaging has been proposed to improve the spectral signal-to-noise ratio, which significantly improves the speed of Raman imaging. In this paper, low resolution Raman spectroscopy is combined with "context-aware" matrix completion, where regions of the sample that are not of interest are skipped, and the regions that are measured are under-sampled, then reconstructed with a low-rank constraint. Both simulations and experiment show that low-resolution Raman boosts the speed and image quality of the computationally-reconstructed Raman images, allowing deeper sub-sampling, reduced exposure time, and an overall >10-fold improvement in imaging speed, without sacrificing chemical specificity or spatial image quality. As the method utilizes traditional point-scan imaging, it retains full confocality and is "backwards-compatible" with pre-existing traditional Raman instruments, broadening the potential scope of Raman imaging applications.

Toward the Next Frontiers of Vibrational Bioimaging

Chemical imaging based on vibrational contrasts can extract molecular information entangled in complex biological systems. To this end, nonlinear Raman scattering microscopy, mid-infrared photothermal (MIP) microscopy, and atomic force microscopy (AFM)-based force-detected photothermal microscopies are emerging with better chemical sensitivity, molecular specificity, and spatial resolution than conventional vibrational methods. Their utilization in bioimaging applications has provided biological knowledge in unprecedented detail. This Perspective outlines key methodological developments, bioimaging applications, and recent technical innovations of the three techniques. Representative biological demonstrations are also highlighted to exemplify the unique advantages of obtaining vibrational contrasts. With years of effort, these three methods compose an expanding vibrational bioimaging toolbox to tackle specific bioimaging needs, benefiting many biological investigations with rich information in both label-free and labeling manners. Each technique will be discussed and compared in the outlook, leading to possible future directions to accommodate growing needs in vibrational bioimaging.

Ultrafast Spectral Tuning of a Fiber Laser for Time-Encoded Multiplex Coherent Raman Scattering Microscopy

Coherent Raman scattering microscopy utilizing bioorthogonal tagging approaches like isotope or alkyne labeling allows for a targeted monitoring of spatial distribution and dynamics of small molecules of interest in cells, tissues, and other complex biological matrices. To fully exploit this approach in terms of real-time monitoring of several Raman tags, e.g., to study drug uptake dynamics, extremely fast tunable lasers are needed. Here, we present a laser concept without moving parts and fully electronically controlled for the quasi-simultaneous acquisition of coherent anti-Stokes Raman scattering images at multiple Raman resonances. The laser concept is based on the combination of a low noise and spectrally narrow Fourier domain mode-locked laser seeding a compact four wave mixing-based high-power fiber-based optical parametric amplifier.

Simultaneous Dual-Band Hyperspectral Stimulated Raman Scattering Microscopy with Femtosecond Optical Parametric Oscillators

Stimulated Raman scattering (SRS) microscopy is a label-free quantitative optical technique for imaging molecular distributions in cells and tissues by probing their intrinsic vibrational frequencies. Despite its usefulness, existing SRS imaging techniques have limited spectral coverage due to either a wavelength tuning constraint or narrow spectral bandwidth. High-wavenumber SRS imaging is commonly used to map lipid and protein distribution in biological cells and visualize cell morphology. However, to detect small molecules or Raman tags, imaging in the fingerprint region or "silent" region, respectively, is often required. For many applications, it is desirable to collect SRS images in two Raman spectral regions simultaneously for visualizing the distribution of specific molecules in cellular compartments or providing accurate ratiometric analysis. In this work, we present an SRS microscopy system using three beams generated by a femtosecond oscillator to acquire hyperspectral SRS image stacks in two arbitrary vibrational frequency bands, between 650-3280 cm-1, simultaneously. We demonstrate potential biomedical applications of the system in investigating fatty acid metabolism, cellular drug uptake and accumulation, and lipid unsaturation level in tissues. We also show that the dual-band hyperspectral SRS imaging system can be adapted for the broadband fingerprint region hyperspectral imaging (1100-1800 cm-1) by simply adding a modulator.

Raman Spectroscopy as a Tool to Study the Pathophysiology of Brain Diseases

The Raman phenomenon is based on the spontaneous inelastic scattering of light, which depends on the molecular characteristics of the dispersant. Therefore, Raman spectroscopy and imaging allow us to obtain direct information, in a label-free manner, from the chemical composition of the sample. Since it is well established that the development of many brain diseases is associated with biochemical alterations of the affected tissue, Raman spectroscopy and imaging have emerged as promising tools for the diagnosis of ailments. A combination of Raman spectroscopy and/or imaging with tagged molecules could also help in drug delivery and tracing for treatment of brain diseases. In this review, we first describe the basics of the Raman phenomenon and spectroscopy. Then, we delve into the Raman spectroscopy and imaging modes and the Raman-compatible tags. Finally, we center on the application of Raman in the study, diagnosis, and treatment of brain diseases, by focusing on traumatic brain injury and ischemia, neurodegenerative disorders, and brain cancer.

Instant diagnosis of gastroscopic biopsy via deep-learned single-shot femtosecond stimulated Raman histology

Gastroscopic biopsy provides the only effective method for gastric cancer diagnosis, but the gold standard histopathology is time-consuming and incompatible with gastroscopy. Conventional stimulated Raman scattering (SRS) microscopy has shown promise in label-free diagnosis on human tissues, yet it requires the tuning of picosecond lasers to achieve chemical specificity at the cost of time and complexity. Here, we demonstrate that single-shot femtosecond SRS (femto-SRS) reaches the maximum speed and sensitivity with preserved chemical resolution by integrating with U-Net. Fresh gastroscopic biopsy is imaged in <60 s, revealing essential histoarchitectural hallmarks perfectly agreed with standard histopathology. Moreover, a diagnostic neural network (CNN) is constructed based on images from 279 patients that predicts gastric cancer with accuracy >96%. We further demonstrate semantic segmentation of intratumor heterogeneity and evaluation of resection margins of endoscopic submucosal dissection (ESD) tissues to simulate rapid and automated intraoperative diagnosis. Our method holds potential for synchronizing gastroscopy and histopathological diagnosis.

Diagnosis of gastric cancer currently requires gastroscopic biopsy, which requires time and expertize to perform. Here, the authors demonstrate a femto-SRS imaging method which showed high accuracy in diagnosing gastric cancer without the need for pathologistbased diagnosis.

Stimulated Raman scattering microscopy in chemistry and life science - Development, innovation, perspectives

In this review, we present a summary of the basics of the Stimulated Raman Scattering (SRS) phenomenon, methods of detecting the signal, and collection of the SRS images. We demonstrate the advantages of SRS imaging, and recent developments, but also the limitations, especially in image capture speeds and spatial resolution. We also compare the use of SRS microscopy in biological system studies with other techniques such as fluorescence microscopy, second-harmonic generation (SHG)-based microscopy, coherent anti-Stokes Raman scattering (CARS), and spontaneous Raman, and we show the compatibility of SRS-based systems with other discussed methods. The review is also focused on indicating innovations in SRS microscopy, on the background of which we present the layout and performance of our homemade setup built from commercially available elements enabling for imaging of the molecular structure of single cells over the spectral range of 800-3600 cm^-1. Methods of image analysis are discussed, including machine learning methods for obtaining images of the distribution of selected molecules and for the detection of pathological lesions in tissues or malignant cells in the context of clinical diagnosis of a wide range of diseases with the use of SRS microscopy. Finally, perspectives for the development of SRS microscopy are proposed.

Shot-noise limited tunable dual-vibrational frequency stimulated Raman scattering microscopy

We present a shot-noise limited SRS implementation providing a >200 mW per excitation wavelength that is optimized for addressing two molecular vibrations simultaneously. As the key to producing a 3 ps laser of different colors out of a single fs-laser (15 nm FWHM), we use ultra-steep angle-tunable optical filters to extract 2 narrow-band Stokes laser beams (1-2 nm & 1-2 ps), which are separated by 100 cm^-1. The center part of the fs-laser is frequency doubled to pump an optical parametric oscillator (OPO). The temporal width of the OPO's output (1 ps) is matched to the Stokes beams and can be tuned from 650-980 nm to address simultaneously two Raman shifts separated by 100 cm^-1 that are located between 500 cm^-1 and 5000 cm^-1. We demonstrate background-free SRS imaging of C-D labeled biological samples (bacteria and Drosophila). Furthermore, high quality virtual stimulated Raman histology imaging of a brain adenocarcinoma is shown for pixel dwell times of 16 µs.

A decade of alkyne-tag Raman imaging (ATRI): applications in biological systems

Alkyne functional groups have Raman signatures in a region (1800 cm-1 to 2800 cm-1) that is free from interference from cell components, known as the "silent region", and alkyne signals in this region were first utilized a decade ago to visualize the nuclear localization of a thymidine analogue EdU. Since then, the strategy of Raman imaging of biological samples by using alkyne functional groups, called alkyne-tag Raman imaging (ATRI), has become widely used. This article reviews the applications of ATRI in biological samples ranging from organelles to whole animal models, and briefly discusses the prospects for this technique.

Multi-window sparse spectral sampling stimulated Raman scattering microscopy

Stimulated Raman scattering (SRS) is a nondestructive and rapid technique for imaging of biological and clinical specimens with label-free chemical specificity. SRS spectral imaging is typically carried out either via broadband methods, or by tuning narrowband ultrafast light sources over narrow spectral ranges thus specifically targeting vibrational frequencies. We demonstrate a multi-window sparse spectral sampling SRS (S4RS) approach where a rapidly-tunable dual-output all-fiber optical parametric oscillator is tuned into specific vibrational modes across more than 1400 cm-1 during imaging. This approach is capable of collecting SRS hyperspectral images either by scanning a full spectrum or by rapidly tuning into select target frequencies, hands-free and automatically, across the fingerprint, silent, and high wavenumber windows of the Raman spectrum. We further apply computational techniques for spectral decomposition and feature selection to identify a sparse subset of Raman frequencies capable of sample discrimination. Here we have applied this novel method to monitor spatiotemporal dynamic changes of active pharmaceutical ingredients in skin, which has particular relevance to topical drug product delivery.

Super-multiplex imaging of cellular dynamics and heterogeneity by integrated stimulated Raman and fluorescence microscopy

Observing multiple molecular species simultaneously with high spatiotemporal resolution is crucial for comprehensive understanding of complex, dynamic, and heterogeneous biological systems. The recently reported super-multiplex optical imaging breaks the “color barrier” of fluorescence to achieve multiplexing number over six in living systems, while its temporal resolution is limited to several minutes mainly by slow color tuning. Herein, we report integrated stimulated Raman and fluorescence microscopy with simultaneous multimodal color tunability at high speed, enabling super-multiplex imaging covering diverse molecular contrasts with temporal resolution of seconds. We highlight this technique by demonstrating super-multiplex time-lapse imaging and image-based cytometry of live cells to investigate the dynamics and cellular heterogeneity of eight intracellular components simultaneously. Our technique provides a powerful tool to elucidate spatiotemporal organization and interactions in biological systems.

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Integrated SRS and fluorescence microscopy with fast tunability has been developed

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Eight-color live-cell imaging can be conducted with a temporal resolution of seconds

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Super-multiplex time-lapse imaging reveals complex organelle interactions

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Super-multiplex image-based cytometry accesses high-dimensional heterogeneity

Coherent Raman scattering microscopy for chemical imaging of biological systems

Coherent Raman scattering (CRS) processes, including both the coherent anti-Stokes Raman scattering and stimulated Raman scattering, have been utilized in state-of-the-art microscopy platforms for chemical imaging of biological samples. The key advantage of CRS microscopy over fluorescence microscopy is label-free, which is an attractive characteristic for modern biological and medical sciences. Besides, CRS has other advantages such as higher selectivity to metabolites, no photobleaching, and narrow peak width. These features have brought fast-growing attention to CRS microscopy in biological research. In this review article, we will first briefly introduce the history of CRS microscopy, and then explain the theoretical background of the CRS processes in detail using the classical approach. Next, we will cover major instrumentation techniques of CRS microscopy. Finally, we will enumerate examples of recent applications of CRS imaging in biological and medical sciences.

Microsecond fingerprint stimulated Raman spectroscopic imaging by ultrafast tuning and spatial-spectral learning

Label-free vibrational imaging by stimulated Raman scattering (SRS) provides unprecedented insight into real-time chemical distributions. Specifically, SRS in the fingerprint region (400-1800 cm-1) can resolve multiple chemicals in a complex bio-environment. However, due to the intrinsic weak Raman cross-sections and the lack of ultrafast spectral acquisition schemes with high spectral fidelity, SRS in the fingerprint region is not viable for studying living cells or large-scale tissue samples. Here, we report a fingerprint spectroscopic SRS platform that acquires a distortion-free SRS spectrum at 10 cm-1 spectral resolution within 20 µs using a polygon scanner. Meanwhile, we significantly improve the signal-to-noise ratio by employing a spatial-spectral residual learning network, reaching a level comparable to that with 100 times integration. Collectively, our system enables high-speed vibrational spectroscopic imaging of multiple biomolecules in samples ranging from a single live microbe to a tissue slice.

Advances in stimulated Raman scattering imaging for tissues and animals

Stimulated Raman scattering (SRS) microscopy has emerged in the last decade as a powerful optical imaging technology with high chemical selectivity, speed, and subcellular resolution. Since the invention of SRS microscopy, it has been extensively employed in life science to study composition, structure, metabolism, development, and disease in biological systems. Applications of SRS in research and the clinic have generated new insights in many fields including neurobiology, tumor biology, developmental biology, metabolomics, pharmacokinetics, and more. Herein we review the advances and applications of SRS microscopy imaging in tissues and animals, as well as envision future applications and development of SRS imaging in life science and medicine.

Hadamard-transform spectral acquisition with an acousto-optic tunable filter in a broadband stimulated Raman scattering microscope

We present a novel configuration for high spectral resolution multiplexing acquisition based on the Hadamard transform in stimulated Raman scattering (SRS) microscopy. The broadband tunable output of a dual-beam femtosecond laser is filtered by a fast, narrowband, and multi-channel acousto-optic tunable filter (AOTF). By turning on and off different subsets of its 8 independent channels, the AOTF generates the spectral masks given by the Hadamard matrix. We demonstrate a seamless and automated operation in the Raman fingerprint and CH-stretch regions. In the presence of additive noise, the spectral measurements using the multiplexed method show the same signal-to-noise ratio of conventional single-wavenumber acquisitions performed with 4 times longer integration time.

A Spectral Resolution study in Femtosecond Stimulated Raman Scattering Microscopy

The simultaneous mapping and the specificity of different chemical species are desirable in several biological and biomedical applications. The stimulated Raman Scattering technique is a proven and well-established label-free method to map the distributions of individual species in a multi-component-based system due to the linear dependence of signals on concentration and its chemical selectivity. In this framework, spectral resolution, i.e., the ability to distinguish closely lying resonances, plays a fundamental role. Here in this work, the cross-correlation of Ti:Sa & OPO femtosecond laser beams in a stimulated Raman scattering microscope is measured. The separation between protein and lipid bands in the C-H region is important for biochemical research and is successfully classified.

High-Speed Chemical Imaging by Dense-Net Learning of Femtosecond Stimulated Raman Scattering

Hyperspectral stimulated Raman scattering (SRS) by spectral focusing can generate label-free chemical images through temporal scanning of chirped femtosecond pulses. Yet, pulse chirping decreases the pulse peak power and temporal scanning increases the acquisition time, resulting in a much slower imaging speed compared to single-frame SRS using femtosecond pulses. In this paper, we present a deep learning algorithm to solve the inverse problem of getting a chemically labeled image from a single-frame femtosecond SRS image. Our DenseNet-based learning method, termed as DeepChem, achieves high-speed chemical imaging with a large signal level. Speed is improved by 2 orders of magnitude with four subcellular components (lipid droplet, endoplasmic reticulum, nuclei, cytoplasm) classified in MIA PaCa-2 cells and other cell types which were not used for training. Lipid droplet dynamics and cellular response to dithiothreitol in live MIA PaCa-2 cells are demonstrated using this computationally multiplex method.

Raman image-activated cell sorting

The advent of image-activated cell sorting and imaging-based cell picking has advanced our knowledge and exploitation of biological systems in the last decade. Unfortunately, they generally rely on fluorescent labeling for cellular phenotyping, an indirect measure of the molecular landscape in the cell, which has critical limitations. Here we demonstrate Raman image-activated cell sorting by directly probing chemically specific intracellular molecular vibrations via ultrafast multicolor stimulated Raman scattering (SRS) microscopy for cellular phenotyping. Specifically, the technology enables real-time SRS-image-based sorting of single live cells with a throughput of up to ~100 events per second without the need for fluorescent labeling. To show the broad utility of the technology, we show its applicability to diverse cell types and sizes. The technology is highly versatile and holds promise for numerous applications that are previously difficult or undesirable with fluorescence-based technologies.

Most current cell sorting methods are based on fluorescence detection with no imaging capability. Here the authors generate and use Raman image-activated cell sorting with a throughput of around 100 events per second, providing molecular images with no need for labeling.

Shot-Noise-Limited Two-Color Stimulated Raman Scattering Microscopy with a Balanced Detection Scheme

Stimulated Raman scattering (SRS) microscopy has been considered a useful technique for investigating chemical components by selectively targeting the vibration mode of chemical structures. Its practical application to the observation of molecular structures and dynamics in complicated biological environments requires broad spectral coverage with both high resolution and a high signal-to-noise ratio. Here, we demonstrate a two-color SRS microscopy employing a balanced detection scheme and a spectral focusing method. Two different SRS signals are generated with pump and Stokes laser pulse pairs in perpendicular polarization, where each of them acts as an intensity reference for the other, significantly reducing the background noise level close to the shot-noise limit even with a fiber-based femtosecond laser system. The high spectral resolution comparable to that of spontaneous Raman scattering spectroscopy is achieved with the spectral focusing method. The two-color SRS images are obtained for a mixture of polymer beads and for the distributions of lipids and proteins in U2OS cells.

Plasmon-enhanced stimulated Raman scattering microscopy with single-molecule detection sensitivity

Stimulated Raman scattering (SRS) microscopy allows for high-speed label-free chemical imaging of biomedical systems. The imaging sensitivity of SRS microscopy is limited to ~10 mM for endogenous biomolecules. Electronic pre-resonant SRS allows detection of sub-micromolar chromophores. However, label-free SRS detection of single biomolecules having extremely small Raman cross-sections (~10^-30 cm² sr^-1) remains unreachable. Here, we demonstrate plasmon-enhanced stimulated Raman scattering (PESRS) microscopy with single-molecule detection sensitivity. Incorporating pico-Joule laser excitation, background subtraction, and a denoising algorithm, we obtain robust single-pixel SRS spectra exhibiting single-molecule events, verified by using two isotopologues of adenine and further confirmed by digital blinking and bleaching in the temporal domain. To demonstrate the capability of PESRS for biological applications, we utilize PESRS to map adenine released from bacteria due to starvation stress. PESRS microscopy holds the promise for ultrasensitive detection and rapid mapping of molecular events in chemical and biomedical systems.

Fingerprint-to-CH stretch continuously tunable high spectral resolution stimulated Raman scattering microscope

Stimulated Raman scattering (SRS) microscopy is a label-free method generating images based on chemical contrast within samples, and has already shown its great potential for high-sensitivity and fast imaging of biological specimens. The capability of SRS to collect molecular vibrational signatures in bio-samples, coupled with the availability of powerful statistical analysis methods, allows quantitative chemical imaging of live cells with sub-cellular resolution. This application has substantially driven the development of new SRS microscopy platforms. Indeed, in recent years, there has been a constant effort on devising configurations able to rapidly collect Raman spectra from samples over a wide vibrational spectral range, as needed for quantitative analysis by using chemometric methods. In this paper, an SRS microscope which exploits spectral shaping by a narrowband and rapidly tunable acousto-optical tunable filter (AOTF) is presented. This microscope enables spectral scanning from the Raman fingerprint region to the Carbon-Hydrogen (CH)-stretch region without any modification of the optical setup. Moreover, it features also a high enough spectral resolution to allow resolving Raman peaks in the crowded fingerprint region. Finally, application of the developed SRS microscope to broadband hyperspectral imaging of biological samples over a large spectral range from 800 to 3600 cm^-1 , is demonstrated.

Biological imaging of chemical bonds by stimulated Raman scattering microscopy

All molecules consist of chemical bonds, and much can be learned from mapping the spatiotemporal dynamics of these bonds. Since its invention a decade ago, stimulated Raman scattering (SRS) microscopy has become a powerful modality for imaging chemical bonds with high sensitivity, resolution, speed and specificity. We introduce the fundamentals of SRS microscopy and review innovations in SRS microscopes and imaging probes. We highlight examples of exciting biological applications, and share our vision for potential future breakthroughs for this technology.

Label-free chemical imaging flow cytometry by high-speed multicolor stimulated Raman scattering

Imaging flow cytometry is a powerful tool for analyzing every single cell in a large heterogeneous population but relies on fluorescent labeling, which comes with cytotoxicity, nonspecific binding, and interference with natural cellular functions. This paper presents label-free multicolor chemical imaging flow cytometry based on stimulated Raman scattering (SRS), a highly sensitive method of molecular vibrational spectroscopy. With the help of deep learning, it demonstrates high-precision characterization and classification of microalgal cells and cancer cells without the need for fluorescent labeling.

Combining the strength of flow cytometry with fluorescence imaging and digital image analysis, imaging flow cytometry is a powerful tool in diverse fields including cancer biology, immunology, drug discovery, microbiology, and metabolic engineering. It enables measurements and statistical analyses of chemical, structural, and morphological phenotypes of numerous living cells to provide systematic insights into biological processes. However, its utility is constrained by its requirement of fluorescent labeling for phenotyping. Here we present label-free chemical imaging flow cytometry to overcome the issue. It builds on a pulse pair-resolved wavelength-switchable Stokes laser for the fastest-to-date multicolor stimulated Raman scattering (SRS) microscopy of fast-flowing cells on a 3D acoustic focusing microfluidic chip, enabling an unprecedented throughput of up to ∼140 cells/s. To show its broad utility, we use the SRS imaging flow cytometry with the aid of deep learning to study the metabolic heterogeneity of microalgal cells and perform marker-free cancer detection in blood.

Raman Imaging of Small Biomolecules

Imaging techniques greatly facilitate the comprehensive knowledge of biological systems. Although imaging methodology for biomacromolecules such as protein and nucleic acids has been long established, microscopic techniques and contrast mechanisms are relatively limited for small biomolecules, which are equally important participants in biological processes. Recent developments in Raman imaging, including both microscopy and tailored vibrational tags, have created exciting opportunities for noninvasive imaging of small biomolecules in living cells, tissues, and organisms. Here, we summarize the principle and workflow of small-biomolecule imaging by Raman microscopy. Then, we review recent efforts in imaging, for example, lipids, metabolites, and drugs. The unique advantage of Raman imaging has been manifested in a variety of applications that have provided novel biological insights.

Demonstration of wavelength-scan-free action spectroscopy in pump/probe measurement with supercontinuum pump light

We devise and introduce the principle of wavelength-scan-free spectroscopy for the pump light in pump/probe measurement (action spectroscopy) using supercontinuum light; we demonstrate its implementation by measuring transmission spectra. We use the supercontinuum light noise as a code in order to discriminate wavelength. We extract the stimulation at the desired wavelength by correlating the noise at that wavelength observed separately and the observed total stimulation carried by the probe light. The wavelength-scan-free spectroscopy is enabled with a simultaneous procedure for multiple wavelengths.

Real-Time Monitoring of Pharmacokinetics of Antibiotics in Biofilms with Raman-Tagged Hyperspectral Stimulated Raman Scattering Microscopy

Antibiotics resistance developed by biofilms has posed a clinical challenge in the effective treatment of bacterial infections. However, the resistance mechanisms have not been well understood due to a lack of suitable tools for dynamic observation of the interplay between antibiotics and biofilm. In this work, with the use of rapid hyperspectral stimulated Raman scattering microscopy associated with an aryl-alkyne-based Raman tag synthesized, we investigate dynamic interactions between vancomycin and Staphylococcus aureus (S. aureus) biofilm to gain new insights into the resistance mechanisms of the biofilm. Methods: We utilize spectral focusing hyperspectral stimulated Raman scattering microscopy ensued with multivariate curve resolution analysis to spectrally decompose S. aureus biofilm into its major components (i.e., bacteria and extracellular polymeric substances). Concurrently, vancomycin is conjugated with aryl-alkyne Raman tag (Raman peak at 2218 cm-1) for in vivo tracking of its uptake into biofilm without tissue interference. Results: We find that vancomycin penetration is a non-uniform diffusion process with penetration depths limited by the preferential affinity to the cell clusters. Semi-quantitative analysis shows that the majority of vancomycin binds to the bacteria, achieving intracellular concentrations of up to 4- to 10- fold higher than the administered dosage. The diffusion constant of ~3.16 µm2/min based on the diffusion and antibiotic binding equations is obtained that well accounts for the antibiotic penetration into the biofilm. SRS longitudinal monitoring of antibiotic effect on the growth of biofilms shows that the antibiotics can eradicate the upper layer of the biofilm exposed to sufficient dosages, while the lower layer of the biofilm at a sub-inhibitory dose remains viable, eventually re-growing to significant bio-volume. Conclusion: The Raman-tagged hyperspectral SRS microscopy developed is a powerful imaging tool for dynamic monitoring of inhibitory effects of antibiotics on the growing biofilm in vivo, which would facilitate the formulation of new antibiotics for more effective treatments of bacterial infections in near future.

In situ chemically specific mapping of agrochemical seed coatings using stimulated Raman scattering microscopy

Providing sufficient, healthy food for the increasing global population is putting a great deal of pressure on the agrochemical industry to maximize crop yields without sustaining environmental damage. The growth and yield of every plant with sexual reproduction, depends on germination and emergence of sown seeds, which is affected greatly by seed disease. This can be most effectively controlled by treating seeds with pesticides before they are sown. An effective seed coating treatment requires a high surface coverage and adhesion of active ingredients onto the seed surface and the addition of adhesive agents in coating formulations plays a key role in achieving this. Although adhesive agents are known to enhance seed germination, little is understood about how they affect surface distribution of actives and how formulations can be manipulated to rationally engineer seed coating preparations with optimized coverage and efficacy. We show, for the first time, that stimulated Raman scattering microscopy can be used to map the seed surface with microscopic spatial resolution and with chemical specificity to identify formulation components distributed on the seed surface. This represents a major advance in our capability to rationally engineer seed coating formulations with enhanced efficacy.

Dual-focus stimulated Raman scattering microscopy: a concept for multi-focus scaling

High-speed imaging is of the utmost importance for video-rate live cell investigations or to study extended sample areas at sufficient spatial resolution within reasonable time scales. Improving the speed of single-focus stimulated Raman scattering (SRS) microscopy is ultimately restricted by the sample's damage threshold and the shot noise of the demodulated laser source. To overcome this limitation, we present a dual-focus SRS approach modulating the pump laser for each focus at a distinct frequency. The corresponding probe beams are detected each by a photodiode and demodulated individually by two separate lock-in units to avoid inter-focal cross-talk. Two laterally or axially displaced images as well as hyperspectral SRS images can be obtained simultaneously within the field of view of the objective lens. The modular implementation presented here can be extended to multiple foci by using multi-channel acousto-optics modulators in combination with multi-channel lock-in amplifiers.

Simultaneous dual-channel stimulated Raman scattering microscopy demultiplexed at distinct modulation frequencies

To increase the information per pixel in stimulated Raman scattering (SRS) microscopy as well as to correct from artifacts, it is valuable to acquire images at two different Raman shifts. We present a three-color SRS approach acquiring two perfectly registered SRS images where both pump beams are modulated at distinct frequencies while demodulating the Stokes beam. Our implementation uses two optical parametric oscillators that can be tuned to an almost arbitrary energy difference of Raman shifts, allowing investigation of fingerprint resonances simultaneously to CH-stretch vibrations.

Histological coherent Raman imaging: a prognostic review

Histopathology plays a central role in diagnosis of many diseases including solid cancers. Efforts are underway to transform this subjective art to an objective and quantitative science. Coherent Raman imaging (CRI), a label-free imaging modality with sub-cellular spatial resolution and molecule-specific contrast possesses characteristics which could support the qualitative-to-quantitative transition of histopathology. In this work we briefly survey major themes related to modernization of histopathology, review applications of CRI to histopathology and, finally, discuss potential roles for CRI in the transformation of histopathology that is already underway.

Fast hyperspectral phase and amplitude imaging in scattering tissue

Hyperspectral imaging in scattering tissue generally suffers from low light collection efficiency. In this Letter, we propose a microscope based on Fourier transform spectroscopy and oblique back-illumination microscopy that provides hyperspectral phase and amplitude images of thick, scattering samples with high throughput. Images can be acquired at >0.1  Hz rates with spectral resolution better than 200  cm-1, over a wide spectral range of 450-1700 nm. Proof-of-principle demonstrations are presented with chorioallantoic membrane of a chick embryo, illustrating the possibility of high-resolution hemodynamics imaging in thick tissue, based on transmission contrast.

Challenges and opportunities in clinical translation of biomedical optical spectroscopy and imaging

Medical devices face many hurdles before they enter routine clinical practice to address unmet clinical needs. This is also the case for biomedical optical spectroscopy and imaging systems that are used here to illustrate the opportunities and challenges involved. Following initial concept, stages in clinical translation include instrument development, preclinical testing, clinical prototyping, clinical trials, prototype-to-product conversion, regulatory approval, commercialization, and finally clinical adoption and dissemination, all in the face of potentially competing technologies. Optical technologies face additional challenges from their being extremely diverse, often targeting entirely different diseases and having orders-of-magnitude differences in resolution and tissue penetration. However, these technologies can potentially address a wide variety of unmet clinical needs since they provide rich intrinsic biochemical and structural information, have high sensitivity and specificity for disease detection and localization, and are practical, safe (minimally invasive, nonionizing), and relatively affordable.

New insights of Raman spectroscopy for oral clinical applications

Oral injuries are currently diagnosed by histopathological analysis of biopsy, which is an invasive procedure and does not give immediate results.

Spectroscopic stimulated Raman scattering imaging of highly dynamic specimens through matrix completion

Spectroscopic stimulated Raman scattering (SRS) imaging generates chemical maps of intrinsic molecules, with no need for prior knowledge. Despite great advances in instrumentation, the acquisition speed for a spectroscopic SRS image stack is fundamentally bounded by the pixel integration time. In this work, we report three-dimensional sparsely sampled spectroscopic SRS imaging that measures ~20% of pixels throughout the stack. In conjunction with related work in low-rank matrix completion (e.g., the Netflix Prize), we develop a regularized non-negative matrix factorization algorithm to decompose the sub-sampled image stack into spectral signatures and concentration maps. This design enables an acquisition speed of 0.8 s per image stack, with 50 frames in the spectral domain and 40,000 pixels in the spatial domain, which is faster than the conventional raster laser-scanning scheme by one order of magnitude. Such speed allows real-time metabolic imaging of living fungi suspended in a growth medium while effectively maintaining the spatial and spectral resolutions. This work is expected to promote broad application of matrix completion in spectroscopic laser-scanning imaging.

Spectral focusing dual-comb coherent anti-Stokes Raman spectroscopic imaging

Coherent Raman microscopy provides label-free imaging by interrogating the intrinsic vibration of molecules. Here, we present a concept in a 100 MHz dual-comb scheme to facilitate high-speed and broadband coherent anti-Stokes Raman spectroscopic imaging based on down-converted, automatically varying delay-time in spectral focusing excitation. A rapid measurement of vibrational microspectroscopy on submicrosecond scale over a spectral span ∼700  cm^-1 with a refresh rate of 1.2 kHz provides access to well-resolved molecular signatures within the fingerprint region. We demonstrate hyperspectral images of a mixture of spatially inhomogeneous distributions of chemical substances.

Imaging chemistry inside living cells by stimulated Raman scattering microscopy

Stimulated Raman scattering (SRS) microscopy is a vibrational imaging platform developed to visualize chemical content of a biological sample based on molecular vibrational fingerprints. With high-speed, high-sensitivity, and three-dimensional sectioning capability, SRS microscopy has been used to study chemical distribution, molecular transport, and metabolic conversion in living cells in a label-free manner. Moreover, aided with bio-orthogonal small-volume Raman probes, SRS microscopy allows direct imaging of metabolic activities of small molecules in living cells.

A machine learning framework to analyze hyperspectral stimulated Raman scattering microscopy images of expressed human meibum

We develop and discuss a methodology for batch-level analysis of hyperspectral stimulated Raman scattering (hsSRS) data sets of human meibum in the CH-stretching vibrational range. The analysis consists of two steps. The first step uses a training set (n=19) to determine chemically meaningful reference spectra that jointly constitute a basis set for the sample. This procedure makes use of batch-level vertex component analysis (VCA), followed by unsupervised k-means clustering to express the data set in terms of spectra that represent lipid and protein mixtures in changing proportions. The second step uses a random forest classifier to rapidly classify hsSRS stacks in terms of the pre-determined basis set. The overall procedure allows a rapid quantitative analysis of large hsSRS data sets, enabling a direct comparison among samples using a single set of reference spectra. We apply this procedure to assess 50 specimens of expressed human meibum, rich in both protein and lipid, and show that the batch-level analysis reveals marked variation among samples that potentially correlate with meibum health quality.

Label-free pathology by spectrally sliced femtosecond stimulated Raman scattering (SRS) microscopy

Optical “virtual biopsy” is an attractive way to improve disease diagnosis and surgical guidance. Many optical microscopy techniques have been developed to provide diagnostic information without the need for tissue sectioning or staining. Among these techniques, label-free chemical imaging is the most desirable. Recently, it has been shown that narrowband, picosecond stimulated Raman scattering (SRS) can achieve comparable morphological contrast to hematoxylin and eosin staining (H&E staining), the ‘gold standard’ of pathology. However, to translate the technique from the bench to the bedside, optimal laser sources and parameters have yet to be identified. Here we describe an improvement to the narrowband SRS microscopy techniques for label-free tissue imaging. Through spectral slicing of broadband, femtosecond pulses, we are able to maintain the same protein/lipid contrast as narrowband SRS while achieving a higher signal-to-noise ratio (SNR). Our method draws upon the benefits of femtosecond pulses (e.g. higher peak power) while preserving those of picosecond pulses (e.g. adequate spectral resolution). We demonstrate this achievement through protein/lipid signal and contrast quantification of mouse brain tissue as a function of bandwidth, and comparison with numerical simulations. Further method validation is provided through imaging of additional mouse tissues: liver, kidney, and skin.

Programmable single-pixel-based broadband stimulated Raman scattering

We report a simple add-on for broadband stimulated Raman scattering (SRS) microscopes to enable fast and programmable spectroscopy acquisition. It comprises a conventional dispersive spectrometer layout incorporating a fast digital micromirror device (DMD). The approach is validated by acquiring SRS spectra of standard chemicals. We demonstrate a DMD's advantage in broadband SRS by showing higher signal-to-noise ratio using a multiplexed Hadamard spectral basis and compressive sensing detection. Our results apply to a variety of frequency-domain pump-probe spectroscopy.