Label-free Chemically Specific Imaging in Planta with Stimulated Raman Scattering Microscopy

Biomedical applications, perspectives and tag design concepts in the cell - silent Raman window

Spectroscopic studies increasingly employ Raman tags exhibiting a signal in the cell - silent region of the Raman spectrum (1800-2800 cm-1), where bands arising from biological molecules are inherently absent. Raman tags bearing functional groups which contain a triple bond, such as alkyne and nitrile or a carbon-deuterium bond, have a distinct vibrational frequency in this region. Due to the lack of spectral background and cell-associated bands in the specific area, the implementation of those tags can help overcome the inherently poor signal-to-noise ratio and presence of overlapping Raman bands in measurements of biological samples. The cell - silent Raman tags allow for bioorthogonal imaging of biomolecules with improved chemical contrast and they have found application in analyte detection and monitoring, biomarker profiling and live cell imaging. This review focuses on the potential of the cell - silent Raman region, reporting on the tags employed for biomedical applications using variants of Raman spectroscopy.

3D (x-y-t) Raman imaging of tomato fruit cuticle: Microchemistry during development

The cuticle is a protective extracellular matrix that covers the above-ground epidermis of land plants. Here, we studied the cuticle of tomato (Solanum lycopersicum L.) fruits in situ using confocal Raman microscopy. Microsections from cuticles isolated at different developmental stages were scanned to visualize cuticle components with a spatial resolution of 342 nm by univariate and multivariate data analysis. Three main components, cutin, polysaccharides, and aromatics, were identified, with the latter exhibiting the strongest Raman scattering intensity. Phenolic acids and flavonoids were differentiated within the cuticle, and three schematic cuticle models were identified during development. Phenolic acids were found across the entire cuticle at the earliest stage of development, i.e. during the formation of the procuticle layer. Based on a mixture analysis with reference component spectra, the phenolic acids were identified as mainly esterified p-coumaric acid together with free p-hydroxybenzoic acid. During the cell expansion period of growth, phenolic acids accumulated in an outermost layer of the cuticle and in the middle region of the pegs. In these stages of development, cellulose and pectin were detected next to the inner cuticle region, close to the epidermal cell where flavonoid impregnation started during ripening. In the first ripening stage, chalconaringenin was observed, while methoxylated chalcones were chosen by the algorithm to fit the mature cuticle spectra. The colocation of carbohydrates, esterified p-coumaric acid, and methoxylated chalconaringenin suggests that the latter two link polysaccharide and cutin domains. Elucidating the different distribution of aromatics within the cuticle, suggests important functions: (1) overall impregnation conferring mechanical and thermal functions (2) the outermost phenolic acid layer displaying UV-B protection of the plant tissue.

Miniaturized Chemical Tags for Optical Imaging

Recent advances in optical bioimaging have prompted the need for minimal chemical reporters that can retain the molecular recognition properties and activity profiles of biomolecules. As a result, several methodologies to reduce the size of fluorescent and Raman labels to a few atoms (e.g., single aryl fluorophores, Raman‐active triple bonds and isotopes) and embed them into building blocks (e.g., amino acids, nucleobases, sugars) to construct native‐like supramolecular structures have been described. The integration of small optical reporters into biomolecules has also led to smart molecular entities that were previously inaccessible in an expedite manner. In this article, we review recent chemical approaches to synthesize miniaturized optical tags as well as some of their multiple applications in biological imaging.

Imaging plant tissues: advances and promising clearing practices

The study of the organ structure of plants and understanding their physiological complexity requires 3D imaging with subcellular resolution. Most plant organs are highly opaque to light, and their study under optical sectioning microscopes is therefore difficult. In animals, many protocols have been developed to make organs transparent to light using clearing protocols (CPs). By contrast, clearing plant tissues is challenging because of the presence of fibers and pigments. We describe progress in the development of plant CPs over the past 20 years through a modified taxonomy of CPs based on their physical and optical parameters that affect tissue properties. We also discuss successful approaches that combine CPs with new microscopy methods and their future applications in plant science research.

Stimulated Raman scattering microscopy with spectral phasor analysis: applications in assessing drug-cell interactions

Statins have displayed significant, although heterogeneous, anti-tumour activity in breast cancer disease progression and recurrence. They offer promise as a class of drugs, normally used for cardiovascular disease control, that could have a significant impact on the treatment of cancer. Understanding their mode of action and accurately assessing their efficacy on live cancer cells is an important and significant challenge. Stimulated Raman scattering (SRS) microscopy is a powerful, label-free imaging technique that can rapidly characterise the biochemical responses of live cell populations following drug treatment. Here, we demonstrate multi-wavelength SRS imaging together with spectral phasor analysis to characterise a panel of breast cancer cell lines (MCF-7, SK-BR-3 and MDA-MB-231 cells) treated with two clinically relevant statins, atorvastatin and rosuvastatin. Label-free SRS imaging within the high wavenumber region of the Raman spectrum (2800–3050 cm⁻¹) revealed the lipid droplet distribution throughout populations of live breast cancer cells using biocompatible imaging conditions. A spectral phasor analysis of the hyperspectral dataset enables rapid differentiation of discrete cellular compartments based on their intrinsic SRS characteristics. Applying the spectral phasor method to studying statin treated cells identified a lipid accumulating phenotype in cell populations which displayed the lowest sensitivity to statin treatment, whilst a weaker lipid accumulating phenotype was associated with a potent reduction in cell viability. This study provides an insight into potential resistance mechanisms of specific cancer cells towards treatment with statins. Label-free SRS imaging provides a novel and innovative technique for phenotypic assessment of drug-induced effects across different cellular populations and enables effective analysis of drug–cell interactions at the subcellular scale.

Stimulated Raman scattering microscopy with spectral phasor analysis provides a label-free approach for phenotypic evaluation of drug-induced effects.

Characterization of Labeled Gold Nanoparticles for Surface-Enhanced Raman Scattering

Noble metal nanoparticles (NP) such as gold (AuNPs) and silver nanoparticles (AgNPs) can produce ultrasensitive surface-enhanced Raman scattering (SERS) signals owing to their plasmonic properties. AuNPs have been widely investigated for their biocompatibility and potential to be used in clinical diagnostics and therapeutics or combined for theranostics. In this work, labeled AuNPs in suspension were characterized in terms of size dependency of their localized surface plasmon resonance (LSPR), dynamic light scattering (DLS), and SERS activity. The study was conducted using a set of four Raman labels or reporters, i.e., small molecules with large scattering cross-section and a thiol moiety for chemisorption on the AuNP, namely 4-mercaptobenzoic acid (4-MBA), 2-naphthalenethiol (2-NT), 4-acetamidothiophenol (4-AATP), and biphenyl-4-thiol (BPT), to investigate their viability for SERS tagging of spherical AuNPs of different size in the range 5 nm to 100 nm. The results showed that, when using 785 nm laser excitation, the SERS signal increases with the increasing size of AuNP up to 60 or 80 nm. The signal is highest for BPT labelled 80 nm AuNPs followed by 4-AATP labeled 60 nm AuNPs, making BPT and 4-AATP the preferred candidates for Raman labelling of spherical gold within the range of 5 nm to 100 nm in diameter.

Lipids-Fluorophores Interactions Probed by Combined Nonlinear Polarized Microscopy

Studying the structural dynamics of lipid membranes requires methods that can address both microscopic and macroscopic characteristics. Fluorescence imaging is part of the most used techniques to study membrane properties in various systems from artificial membranes to cells: It benefits from a high sensitivity to local properties such as polarity and molecular orientational order, with a high spatial resolution down to the single-molecule level. The influence of embedded fluorescent lipid probes on the lipid membrane molecules is however poorly known and relies most often on molecular dynamics simulations, due to the challenges faced by experimental approaches to address the molecular-scale dimension of this question. In this work we develop an optical microscopy imaging method to probe the effect of fluorophores embedded in the membrane as lipid probes, on their lipid environment, with a lateral resolution of a few hundreds of nanometers. We combine polarized-nonlinear microscopy contrasts that can independently address the lipid probe, by polarized two-photon fluorescence, and the membrane lipids, by polarized coherent Raman scattering. Using trimethylamino derivative 1-(4-trimethylammonium-phenyl)-6-phenyl-1,3,5-hexatriene (TMA-DPH) and di-8-butyl-amino-naphthyl-ethylene-pyridinium-propyl-sulfonate (di-8-ANEPPS) as model probes, we show that both probes tend to induce an orientational disorder of their surrounding lipid CH-bonds in 1,2-dipalmitoylphosphatidylcholine (DPPC) lipids environments, while there is no noticeable effect in more disordered 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) lipid membranes.

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.

A Palette of Minimally Tagged Sucrose Analogues for Real-Time Raman Imaging of Intracellular Plant Metabolism

Sucrose is the main saccharide used for long-distance transport in plants and plays an essential role in energy metabolism; however, there are no analogues for real-time imaging in live cells. We have optimised a synthetic approach to prepare sucrose analogues including very small (≈50 Da or less) Raman tags in the fructose moiety. Spectroscopic analysis identified the alkyne-tagged compound 6 as a sucrose analogue recognised by endogenous transporters in live cells and with higher Raman intensity than other sucrose derivatives. Herein, we demonstrate the application of compound 6 as the first optical probe to visualise real-time uptake and intracellular localisation of sucrose in live plant cells using Raman microscopy.

A Palette of Minimally Tagged Sucrose Analogues for Real-Time Raman Imaging of Intracellular Plant Metabolism

Sucrose is the main saccharide used for long-distance transport in plants and plays an essential role in energy metabolism; however, there are no analogues for real-time imaging in live cells. We have optimised a synthetic approach to prepare sucrose analogues including very small (≈50 Da or less) Raman tags in the fructose moiety. Spectroscopic analysis identified the alkyne-tagged compound 6 as a sucrose analogue recognised by endogenous transporters in live cells and with higher Raman intensity than other sucrose derivatives. Herein, we demonstrate the application of compound 6 as the first optical probe to visualise real-time uptake and intracellular localisation of sucrose in live plant cells using Raman microscopy.

Multicolour chemical imaging of plant tissues with hyperspectral stimulated Raman scattering microscopy

Recent development of stimulated Raman scattering (SRS) microscopy allows for label-free biological imaging with chemical specificity based on molecular-vibrational signatures. In particular, hyperspectral SRS imaging can acquire a molecular-vibrational spectrum at each pixel, allowing us not only to investigate the spectral difference of various biological molecules but also to discriminate different constituents based on their spectral difference. However, the number of constituents discriminated in previous label-free SRS imaging was limited to four because of the subtleness of spectral difference. Here, we report hyperspectral SRS imaging of plant tissues including leaves of Camellia japonica, roots of Arabidopsis thaliana, and thalli of a liverwort Marchantia polymorpha L. We show that SRS can discriminate as many as six components in Marchantia polymorpha L. without labeling. Our results demonstrate the effectiveness of hyperspectral SRS imaging as a tool for label-free multicolour imaging analysis of various biomolecules in plant tissues.

Review of Stimulated Raman Scattering Microscopy Techniques and Applications in the Biosciences

Stimulated Raman scattering (SRS) microscopy is a nonlinear optical imaging method for visualizing chemical content based on molecular vibrational bonds. Featuring high speed, high resolution, high sensitivity, high accuracy, and 3D sectioning, SRS microscopy has made tremendous progress toward biochemical information acquisition, cellular function investigation, and label-free medical diagnosis in the biosciences. In this review, the principle of SRS, system design, and data analysis are introduced, and the current innovations of the SRS system are reviewed. In particular, combined with various bio-orthogonal Raman tags, the applications of SRS microscopy in cell metabolism, tumor diagnosis, neuroscience, drug tracking, and microbial detection are briefly examined. The future prospects for SRS microscopy are also shared.

Surface Plasmon Localization-Based Super-resolved Raman Microscopy

We investigate label-free measurement of molecular distribution by super-resolved Raman microscopy using surface plasmon (SP) localization. Localized SP was formed with plasmonic nanopost arrays (PNAs) for measurement of the molecular distribution in HeLa cells. Compared with conventional Raman microscopy on gold thin films, PNAs induce a localized near-field, which allows for the enhancement of the peak signal-to-noise ratio by as much as 4.5 dB in the Raman shifts. Super-resolved distributions of aromatic amino acids and lipids (C-C stretching and C-H₂ twist mode) as targets in HeLa cells were obtained after image reconstruction. Results show almost 4-fold improvement on average in the lateral precision over conventional diffraction-limited Raman microscopy images. Combined with axial imaging in an evanescent field, the results suggest an improvement in optical resolution due to superlocalized light volume by more than an order of magnitude over that of conventional diffraction-limited Raman microscopy.

Simultaneous stimulated Raman gain and loss detection (SRGAL)

The fidelity of stimulated Raman scattering (SRS) microscopy images is impaired by artifacts such as thermal lensing, cross-phase modulation and multi-photon absorption. These artifacts affect differently the stimulated Raman loss (SRL) and stimulated Raman gain (SRG) channels making SRL and SRG image comparisons attractive to identify and correct SRS image artifacts. To provide answer to the question: "Can I trust my SRS images?", we designed a novel, but straightforward SRS scheme that enables the dectection of the stimulated Raman gain and loss (SRGAL) simultaneously at the same pixel level. As an advantage over the conventional SRS imaging scheme, SRGAL doubles the SRS signal by acquiring both SRL as well as SRG and allows for the identification of SRS artifacts and their reduction via a balanced summation of the SRL and SRG images.

Background-suppressed SRS fingerprint imaging with a fully integrated system using a single optical parametric oscillator

Stimulated Raman Scattering (SRS) imaging can be hampered by non-resonant parasitic signals that lead to imaging artifacts and eventually overwhelm the Raman signal of interest. Stimulated Raman gain opposite loss detection (SRGOLD) is a three-beam excitation scheme capable of suppressing this nonlinear background while enhancing the resonant Raman signal. We present here a compact electro-optical system for SRGOLD excitation which conveniently exploits the idler beam generated by an optical parametric oscillator (OPO). We demonstrate its successful application for background suppressed SRS imaging in the fingerprint region. This system constitutes a simple and valuable add-on for standard coherent Raman laser sources since it enables flexible excitation and background suppression in SRS imaging.

Liver changes induced by cadmium poisoning distinguished by confocal Raman imaging

Heavy metal pollution has become an important issue threatening human health and the liver is a very important metabolic organ. Here, we use label-free Raman confocal imaging to study the alterations of the liver tissue after cadmium pollution. Raman imaging has been performed on 100μmx100μm liver tissues to study the distribution of important macromolecules and the average Raman spectrum of the entire region has been used to characterize and quantize the change of biochemical compositions in liver tissue. The poisoned livers displayed a significant decrease in the intensity of 748 cm^-1, 1128 cm^-1 and 1585 cm^-1 bands of cytochrome C, in comparison to the control. The collagen peak at 1082 cm^-1 is significantly higher than that of control, suggesting the increasing fibrosis of Cd liver tissues. To confirm the results, we selected a 30μmx15μm liver cell area for high-resolution Raman imaging. We observed a substantial increase of lipids and proteins at specific points of hepatocytes. The confocal Raman imaging of liver tissues provided a unique tool to better understand disease-induced changes in the biochemical phenotype of primary liver tissues. Our study provides valuable references as in vitro models for studying Cd accumulation and toxicity in human liver.

Time-resolved Assessment of Drying Plants by Brillouin and Raman Spectroscopies

Raman and Brillouin spectroscopy enable non-invasive assessment of chemical and elastic properties of biomaterials, respectively. In this report, Brillouin micro-spectroscopy was used for the time-resolved analysis of elastic properties of Populus and Geranium leaves, while Raman micro-spectroscopy was employed for the assessment of their chemical variation during drying. Spectroscopic assessment of elastic and chemical properties can improve our understanding of mechano-chemical changes of plants in response to environmental stress and pathogens at the microscopic cellular level. This report demonstrates the potential of multimodal optical sensing and imaging of plants as an emerging technique for the quantitative assessment of agricultural crops.

Optical imaging spectroscopy for plant research: more than a colorful picture

Optical imaging is a routine and indispensable tool in plant research. Here we review different emerging spectrally resolved optical imaging approaches and the wealth of information they can be used to obtain pertaining to the underlying chemistry, structure and mechanics of plants.

A Low-Cost Beam-Scanning Second Harmonic Generation Microscope with Application for Agrochemical Development and Testing

A low-cost second harmonic generation (SHG) microscope was constructed, and, for the first time, SHG microscopy was used for imaging agrochemical materials directly on the surface of common commercial crop leaves. The microscope uses a chromatically fixed (1560 nm) femtosecond fiber laser, a commercial 2D galvanometer mirror system, and a PCIe digital oscilloscope card, which together kept total instrument costs under $40 000 (USD), a significant decrease in cost and complexity from common systems (commercial and home-built) using tunable lasers and faster beam-scanning architectures. The figures of merit of the low-cost system still enabled a variety of measurements of agrochemical materials. Following confirmation of largely background-free SHG imaging of common crop leaves (soybean, maize, wheatgrass), SHG microscopy was used to image active ingredient crystallization after solution-phase deposition directly on the leaf surface, including at industrially relevant active ingredient concentrations (<0.05% w/w). Crystallization was also followed in real-time, with differences in crystallization time observed for different application procedures (spraying vs single droplet deposition). A strong dependency of active ingredient crystallization on the substrate was found, with an increased crystallization tendency observed on leaves vs on glass slides. Different crystal habits for the same active ingredient were also observed on different plant species. Finally, a model extended-release formulation was prepared, with a decrease in active ingredient crystallinity observed vs solution-phase deposition. These collective results demonstrate the need for making diagnostic measurements directly on the leaf surface and could help inform the next generation of pesticide products that ensure optimized agricultural output for a growing world population.

Advances in Imaging Plant Cell Walls

Understanding of cell wall architecture, including the crosslinking of cell wall polymers, provides crucial information for elucidating the relationship between cell wall structure and cell function. Moreover, examination of the cell wall informs efforts to improve biomass breakdown in bioreactor conditions. Over the past decades, imaging techniques have been used extensively to reveal the structural organization and chemical composition of cell walls, but detailed imaging of the native composition and architecture of the cell wall remains challenging. Here, we review progress in the development of cell wall imaging techniques. In particular, we focus on several advanced, label-free techniques for imaging cell walls and their potential applications in investigation of the biological functions of plant cell walls.

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 visualization of lignin deposition in loquats using complementary stimulated and spontaneous Raman microscopy

The lignification triggered by biotic or abiotic stresses hardens fruits and vegetables and eventually influences their consumer appeal. Extensive prior efforts have been made to unveil the underlying mechanism of flesh lignification, primarily focused on its physicochemical and molecular biological properties. Nevertheless, most of these studies used destroyed and homogenized bulk tissues as analytes; as a result, potentially valuable spatial information was lost. In this study, the deposition of lignin in loquat flesh during lignification was visualized from the tissue level to the single-cell level by combining the advantages of stimulated Raman scattering (SRS) and spontaneous Raman microscopy using label-free in situ molecular imaging. SRS has the advantages of being fast and providing large-area chemical imaging to reveal the spatial heterogeneity of lignin and cell wall polysaccharide distribution in loquat flesh. After 2 days of storage at 0 °C, increased lignins were observed by large-area SRS imaging. In addition, microscopic SRS images of the flesh cells indicated that the increased lignins were trapped in the cell corner (CC) and middle lamella (ML). Furthermore, the compositional and structural features of lignified cells (LCs), CC and ML of loquat flesh were investigated by spontaneous Raman microscopy, and the results showed that the LCs were a combination of lignin, cellulose, and hemicellulose, whereas CC and ML showed only deposited lignin and pectin without cross-linked cellulose and hemicellulose. This result further suggests that the lignins in the CC and ML regions of loquats were later synthesized alone during postharvest storage. This innovative combination of SRS and spontaneous Raman microscopy allows the label-free macroscale and fine chemical imaging of plant cell walls and will enhance our fundamental understanding of the structures and functions of the plant cell wall.

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.

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.

Hyperspectral volumetric coherent anti-Stokes Raman scattering microscopy: quantitative volume determination and NaCl as non-resonant standard

In this work, we demonstrate quantitative volume determination of chemical components in three dimensions using hyperspectral coherent anti-Stokes Raman scattering microscopy, phase-corrected Kramers-Kronig retrieval of the coherent anti-Stokes Raman scattering susceptibility and factorization into concentration of chemical components. We investigate the influence of the refractive index contrast between water and polymer beads (polystyrene and polymethylmethacrylate), showing that it leads mainly to concentration errors, while the spectral error is less affected. The volume of polystyrene beads of sizes from 200 nm to 3 μm is determined with 10% relative error and 1% absolute error in the region of interest. We furthermore establish the use of sodium chloride as non-resonant reference material free of Raman-active vibrational resonances.

Poplar-Root Knot Nematode Interaction: A Model for Perennial Woody Species

Plant root-knot nematode (RKN) interaction studies are performed on several host plant models. Though RKN interact with trees, no perennial woody model has been explored so far. Here, we show that poplar (Populus tremula × P. alba) grown in vitro is susceptible to Meloidogyne incognita, allowing this nematode to penetrate, to induce feeding sites, and to successfully complete its life cycle. Quantitative reverse transcription-polymerase chain reaction analysis was performed to study changes in poplar gene expression in galls compared with noninfected roots. Three genes (expansin A, histone 3.1, and asparagine synthase), selected as gall development marker genes, followed, during poplar-nematode interaction, a similar expression pattern to what was described for other plant hosts. Downregulation of four genes implicated in the monolignol biosynthesis pathway was evidenced in galls, suggesting a shift in the phenolic profile within galls developed on poplar roots. Raman microspectroscopy demonstrated that cell walls of giant cells were not lignified but mainly composed of pectin and cellulose. The data presented here suggest that RKN exercise conserved strategies to reproduce and to invade perennial plant species and that poplar is a suitable model host to study specific traits of tree-nematode interactions.

In Situ and In Vivo Molecular Analysis by Coherent Raman Scattering Microscopy

Coherent Raman scattering (CRS) microscopy is a high-speed vibrational imaging platform with the ability to visualize the chemical content of a living specimen by using molecular vibrational fingerprints. We review technical advances and biological applications of CRS microscopy. The basic theory of CRS and the state-of-the-art instrumentation of a CRS microscope are presented. We further summarize and compare the algorithms that are used to separate the Raman signal from the nonresonant background, to denoise a CRS image, and to decompose a hyperspectral CRS image into concentration maps of principal components. Important applications of single-frequency and hyperspectral CRS microscopy are highlighted. Potential directions of CRS microscopy are discussed.

Deciphering single cell metabolism by coherent Raman scattering microscopy

Metabolism is highly dynamic and intrinsically heterogeneous at the cellular level. Although fluorescence microscopy has been commonly used for single cell analysis, bulky fluorescent probes often perturb the biological activities of small biomolecules such as metabolites. Such challenge can be overcome by a vibrational imaging technique known as coherent Raman scattering microscopy, which is capable of chemically selective, highly sensitive, and high-speed imaging of biomolecules with submicron resolution. Such capability has enabled quantitative assessments of metabolic activities of biomolecules (e.g. lipids, proteins, nucleic acids) in single live cells in vitro and in vivo. These investigations provide new insights into the role of cell metabolism in maintenance of homeostasis and pathogenesis of diseases.

Making microscopy count: quantitative light microscopy of dynamic processes in living plants

Cell theory has officially reached 350 years of age as the first use of the word 'cell' in a biological context can be traced to a description of plant material by Robert Hooke in his historic publication 'Micrographia: or some physiological definitions of minute bodies'. The 2015 Royal Microscopical Society Botanical Microscopy meeting was a celebration of the streams of investigation initiated by Hooke to understand at the subcellular scale how plant cell function and form arises. Much of the work presented, and Honorary Fellowships awarded, reflected the advanced application of bioimaging informatics to extract quantitative data from micrographs that reveal dynamic molecular processes driving cell growth and physiology. The field has progressed from collecting many pixels in multiple modes to associating these measurements with objects or features that are meaningful biologically. The additional complexity involves object identification that draws on a different type of expertise from computer science and statistics that is often impenetrable to biologists. There are many useful tools and approaches being developed, but we now need more interdisciplinary exchange to use them effectively. In this review we show how this quiet revolution has provided tools available to any personal computer user. We also discuss the oft-neglected issue of quantifying algorithm robustness and the exciting possibilities offered through the integration of physiological information generated by biosensors with object detection and tracking.

Generation of synchronized picosecond pulses by a 1.06-µm gain-switched laser diode for stimulated Raman scattering microscopy

We propose that a gain-switched laser diode (GS-LD) can be used as a picosecond laser source for stimulated Raman scattering (SRS) microscopy. We employed a 1.06-µm GS-LD to generate ~13-ps pulses at a repetition rate of 38 MHz and amplified them to >100 mW with Yb-doped fiber amplifiers. The GS-LD was driven by 200-ps electrical pulses, which were triggered through a toggle flip-flop (T-FF) so that the GS-LD pulses were synchronized to Ti:sapphire laser (TSL) pulses at a repetition rate of 76 MHz. We found the timing jitter of GS-LD pulses to be approximately 2.7 ps in a jitter bandwidth of 7 MHz. We also show that the delay of electrical pulses can be less sensitive to the optical power of TSL pulses by controlling the threshold voltage of the T-FF. We demonstrate the SRS imaging of polymer beads and of HeLa cells with GS-LD pulses and TSL pulses, proving that GS-LD is readily applicable to SRS microscopy as a compact and stable pulse source.

Stimulated Raman scattering microscopy: an emerging tool for drug discovery

Optical microscopy techniques have emerged as a cornerstone of biomedical research, capable of probing the cellular functions of a vast range of substrates, whilst being minimally invasive to the cells or tissues of interest. Incorporating biological imaging into the early stages of the drug discovery process can provide invaluable information about drug activity within complex disease models. Spontaneous Raman spectroscopy has been widely used as a platform for the study of cells and their components based on chemical composition; but slow acquisition rates, poor resolution and a lack of sensitivity have hampered further development. A new generation of stimulated Raman techniques is emerging which allows the imaging of cells, tissues and organisms at faster acquisition speeds, and with greater resolution and sensitivity than previously possible. This review focuses on the development of stimulated Raman scattering (SRS), and covers the use of bioorthogonal tags to enhance sample detection, and recent applications of both spontaneous Raman and SRS as novel imaging platforms to facilitate the drug discovery process.

Using Raman spectroscopy to characterize biological materials

Raman spectroscopy can be used to measure the chemical composition of a sample, which can in turn be used to extract biological information. Many materials have characteristic Raman spectra, which means that Raman spectroscopy has proven to be an effective analytical approach in geology, semiconductor, materials and polymer science fields. The application of Raman spectroscopy and microscopy within biology is rapidly increasing because it can provide chemical and compositional information, but it does not typically suffer from interference from water molecules. Analysis does not conventionally require extensive sample preparation; biochemical and structural information can usually be obtained without labeling. In this protocol, we aim to standardize and bring together multiple experimental approaches from key leaders in the field for obtaining Raman spectra using a microspectrometer. As examples of the range of biological samples that can be analyzed, we provide instructions for acquiring Raman spectra, maps and images for fresh plant tissue, formalin-fixed and fresh frozen mammalian tissue, fixed cells and biofluids. We explore a robust approach for sample preparation, instrumentation, acquisition parameters and data processing. By using this approach, we expect that a typical Raman experiment can be performed by a nonspecialist user to generate high-quality data for biological materials analysis.

Vibrational spectroscopic imaging of living systems: An emerging platform for biology and medicine

Vibrational spectroscopy has been extensively applied to the study of molecules in gas phase, in condensed phase, and at interfaces. The transition from spectroscopy to spectroscopic imaging of living systems, which allows the spectrum of biomolecules to act as natural contrast, is opening new opportunities to reveal cellular machinery and to enable molecule-based diagnosis. Such a transition, however, involves more than a simple combination of spectrometry and microscopy. We review recent efforts that have pushed the boundary of the vibrational spectroscopic imaging field in terms of spectral acquisition speed, detection sensitivity, spatial resolution, and imaging depth. We further highlight recent applications in functional analysis of single cells and in label-free detection of diseases.

Molecular diffusion in the human nail measured by stimulated Raman scattering microscopy

The effective treatment of diseases of the nail remains an important unmet medical need, primarily because of poor drug delivery. To address this challenge, the diffusion, in real time, of topically applied chemicals into the human nail has been visualized and characterized using stimulated Raman scattering (SRS) microscopy. Deuterated water (D2O), propylene glycol (PG-d8), and dimethyl sulphoxide (DMSO-d6) were separately applied to the dorsal surface of human nail samples. SRS microscopy was used to image D2O, PG-d8/DMSO-d6, and the nail through the O-D, -CD2, and -CH2 bond stretching Raman signals, respectively. Signal intensities obtained were measured as functions of time and of depth into the nail. It was observed that the diffusion of D2O was more than an order of magnitude faster than that of PG-d8 and DMSO-d6. Normalization of the Raman signals, to correct in part for scattering and absorption, permitted semiquantitative analysis of the permeation profiles and strongly suggested that solvent diffusion diverged from classical behavior and that derived diffusivities may be concentration dependent. It appeared that the uptake of solvent progressively undermined the integrity of the nail. This previously unreported application of SRS has permitted, therefore, direct visualization and semiquantitation of solvent penetration into the human nail. The kinetics of uptake of the three chemicals studied demonstrated that each altered its own diffusion in the nail in an apparently concentration-dependent fashion. The scale of the unexpected behavior observed may prove beneficial in the design and optimization of drug formulations to treat recalcitrant nail disease.

On-line visualization of multicolor chemical images with stimulated Raman scattering spectral microscopy

On-line visualization of multicolor chemical images with stimulated Raman scattering spectral microscopy.

Fast vibrational imaging of single cells and tissues by stimulated Raman scattering microscopy

Traditionally, molecules are analyzed in a test tube. Taking biochemistry as an example, the majority of our knowledge about cellular content comes from analysis of fixed cells or tissue homogenates using tools such as immunoblotting and liquid chromatography-mass spectrometry. These tools can indicate the presence of molecules but do not provide information on their location or interaction with each other in real time, restricting our understanding of the functions of the molecule under study. For real-time imaging of labeled molecules in live cells, fluorescence microscopy is the tool of choice. Fluorescent labels, however, are too bulky for small molecules such as fatty acids, amino acids, and cholesterol. These challenges highlight a critical need for development of chemical imaging platforms that allow in situ or in vivo analysis of molecules. Vibrational spectroscopy based on spontaneous Raman scattering is widely used for label-free analysis of chemical content in cells and tissues. However, the Raman process is a weak effect, limiting its application for fast chemical imaging of a living system. With high imaging speed and 3D spatial resolution, coherent Raman scattering microscopy is enabling a new approach for real-time vibrational imaging of single cells in a living system. In most experiments, coherent Raman processes involve two excitation fields denoted as pump at ωp and Stokes at ωs. When the beating frequency between the pump and Stokes fields (ωp - ωs) is resonant with a Raman-active molecular vibration, four major coherent Raman scattering processes occur simultaneously, namely, coherent anti-Stokes Raman scattering (CARS) at (ωp - ωs) + ωp, coherent Stokes Raman scattering (CSRS) at ωs - (ωp - ωs), stimulated Raman gain (SRG) at ωs, and stimulated Raman loss (SRL) at ωp. In SRG, the Stokes beam experiences a gain in intensity, whereas in SRL, the pump beam experiences a loss. Both SRG and SRL belong to stimulated Raman scattering (SRS), in which the energy difference between the pump and Stokes fields is transferred to the molecule for vibrational excitation. The SRS signal appears at the same wavelengths as the excitation fields and is commonly extracted through a phase-sensitive detection scheme. The detected intensity change because of a Raman transition is proportional to Im[χ(3)]IpIs, where χ(3) represents the third-order nonlinear susceptibility, Ip and Is stand for the intensity of the pump and Stokes fields. In this Account, we discuss the most recent advances in the technical development and enabling applications of SRS microscopy. Compared to CARS, the SRS contrast is free of nonresonant background. Moreover, the SRS intensity is linearly proportional to the density of target molecules in focus. For single-frequency imaging, an SRS microscope offers a speed that is ∼1000 times faster than a line-scan Raman microscope and 10,000 times faster than a point-scan Raman microscope. It is important to emphasize that SRS and spontaneous Raman scattering are complementary to each other. Spontaneous Raman spectroscopy covers the entire window of molecular vibrations, which allows extraction of subtleties via multivariate analysis. SRS offers the speed advantage by focusing on either a single Raman band or a defined spectral window of target molecules. Integrating single-frequency SRS imaging and spontaneous Raman spectroscopy on a single platform allows quantitative compositional analysis of objects inside single live cells.

An update: improvements in imaging perfluorocarbon-mounted plant leaves with implications for studies of plant pathology, physiology, development and cell biology

Plant leaves are optically complex, which makes them difficult to image by light microscopy. Careful sample preparation is therefore required to enable researchers to maximize the information gained from advances in fluorescent protein labeling, cell dyes and innovations in microscope technologies and techniques. We have previously shown that mounting leaves in the non-toxic, non-fluorescent perfluorocarbon (PFC), perfluorodecalin (PFD) enhances the optical properties of the leaf with minimal impact on physiology. Here, we assess the use of the PFCs, PFD, and perfluoroperhydrophenanthrene (PP11) for in vivo plant leaf imaging using four advanced modes of microscopy: laser scanning confocal microscopy (LSCM), two-photon fluorescence microscopy, second harmonic generation microscopy, and stimulated Raman scattering (SRS) microscopy. For every mode of imaging tested, we observed an improved signal when leaves were mounted in PFD or in PP11, compared to mounting the samples in water. Using an image analysis technique based on autocorrelation to quantitatively assess LSCM image deterioration with depth, we show that PP11 outperformed PFD as a mounting medium by enabling the acquisition of clearer images deeper into the tissue. In addition, we show that SRS microscopy can be used to image PFCs directly in the mesophyll and thereby easily delimit the "negative space" within a leaf, which may have important implications for studies of leaf development. Direct comparison of on and off resonance SRS micrographs show that PFCs do not to form intracellular aggregates in live plants. We conclude that the application of PFCs as mounting media substantially increases advanced microscopy image quality of living mesophyll and leaf vascular bundle cells.

Label-free quantitative imaging of cholesterol in intact tissues by hyperspectral stimulated Raman scattering microscopy

A finger on the pulse: Current molecular analysis of cells and tissues routinely relies on separation, enrichment, and subsequent measurements by various assays. Now, a platform of hyperspectral stimulated Raman scattering microscopy has been developed for the fast, quantitative, and label-free imaging of biomolecules in intact tissues using spectroscopic fingerprints as the contrast mechanism.