Unsupervised hyperspectral stimulated Raman microscopy image enhancement: denoising and segmentation via one-shot deep learning.

Hyperspectral stimulated Raman scattering (SRS) microscopy is a label-free technique for biomedical and mineralogical imaging which can suffer from low signal-to-noise ratios. Here we demonstrate the use of an unsupervised deep learning neural network for rapid and automatic denoising of SRS images: UHRED (Unsupervised Hyperspectral Resolution Enhancement and Denoising). UHRED is capable of "one-shot" learning; only one hyperspectral image is needed, with no requirements for training on previously labelled datasets or images. Furthermore, by applying a k-means clustering algorithm to the processed data, we demonstrate automatic, unsupervised image segmentation, yielding, without prior knowledge of the sample, intuitive chemical species maps, as shown here for a lithium ore sample.

Oblique angle transient-reflectivity laser-scanning microscopy for mineral imaging in natural ores.

The microscopic arrangement of different minerals in ores is of high interest for mine planning, mineral processing and extractive metallurgy. Many economically important, naturally occurring minerals are highly absorbing semiconductors. To characterize these materials, we have implemented pump-probe laser scanning microscopy (LSM) in a two-lens reflective configuration that offers efficient collection of signal light by using a combination of galvanometer and sample stage scanning. We show that the short-time (∼10 ps) pump-probe response of a material allows us to distinguish economically important sulfide minerals.

All normal dispersion nonlinear fibre supercontinuum source characterization and application in hyperspectral stimulated Raman scattering microscopy.

Hyperspectral stimulated Raman scattering (SRS) microscopy is a powerful label-free, chemical-specific technique for biomedical and mineralogical imaging. Usually, broad and rapid spectral scanning across Raman bands is required for species identification. In many implementations, however, the Raman spectral scan speed is limited by the need to tune source laser wavelengths. Alternatively, a broadband supercontinuum source can be considered. In SRS microscopy, however, source noise is critically important, precluding many spectral broadening schemes. Here we show that a supercontinuum light source based on all normal dispersion (ANDi) fibres provides a stable broadband output with very low incremental source noise. We characterized the noise power spectral density of the ANDi fibre output and demonstrated its use in hyperspectral SRS microscopy applications. This confirms the viability and ease of implementation of ANDi fibre sources for broadband SRS imaging.

Amplitude and polarization modulated hyperspectral Stimulated Raman Scattering Microscopy.

We present a simple hyperspectral Stimulated Raman Scattering (SRS) microscopy method based on spectral focusing of chirped femtosecond pulses, combined with amplitude (AM) and polarization (PM) modulation. This approach permits the imaging of low concentration components with reduced background signals, combined with good hyperspectral resolution and rapid spectral scanning. We demonstrate, using PM-SRS in a Raman loss configuration, the spectrally resolved detection of deuterated dimethyl sulfoxide (DMSO-d6) at concentrations as low as 0.039 % (5.5 mM). In general, background signals due to cross-phase modulation (XPM), two-photon absorption (TPA) and thermal lensing (TL) can reduce the contrast in SRS microscopy. We show that the nonresonant background signal contributing to the SRS signal is, in our case, largely due to XPM. Polarization modulation of the Stokes beam eliminates the nonresonant XPM background, yielding high quality hyperspectral scans at low analyte concentration. The flexibility of our combined AM-PM approach, together with the use of variable modulation frequency and lock-in phase, should allow for optimization of SRS imaging in more complex samples.

Real-time measurement of free Ca2+ changes in CNS myelin by two-photon microscopy.

Here we describe a technique for measuring changes in Ca2+ in the cytosolic domain of mature compact myelin of live axons in the central nervous system (CNS). We label the myelin sheath of optic nerve and dorsal column axons by using the Ca2+ indicator X-rhod-1 coupled with DiOC6(3) to produce bright myelin counterstaining, thereby providing unambiguous identification of the myelin sheath for analysis of two-photon excited fluorescence. We present evidence for localization of the Ca2+ reporter to the cytosolic domain of myelin, obtained by using fluorescence lifetime, spectral measurements and Mn2+ quenching. Chemical ischemia increased myelinic X-rhod-1 fluorescence (approximately 50% after 30 min) in a manner dependent on extracellular Ca2+. Inhibiting Na+-dependent glutamate transporters (with TBOA) or glycine transporters (with sarcosine and ALX-1393) reduced the ischemia-induced increase in Ca2+. We show that myelinic N-methyl-D-aspartate (NMDA) receptors are activated by the two conventional coagonists glutamate and glycine, which are released by specific transporters under conditions of cellular Na+ loading and depolarization in injured white matter. This new technique facilitates detailed studies of living myelin, a vital component of the mammalian CNS.

Spatial-spectral coupling in coherent anti-Stokes Raman scattering microscopy.

Coherent anti-Stokes Raman scattering (CARS) microscopy is a third-order nonlinear optical technique which permits label-free, molecule-specific hyperspectral imaging. The interference between coherent resonant and non-resonant terms leads to well known distortions in the vibrational spectrum, requiring the use of retrieval algorithms. It also leads to spatial imaging distortions, largely due to the Gouy phase, when objects are smaller than the Rayleigh range. Here we consider that the focal position and spectral contributions to the nonlinear image formation are intrinsically coupled and cannot be corrected by conventional retrieval methods.

Dynamics of lipid droplets induced by the hepatitis C virus core protein.

The hepatitis C virus (HCV) is a global health problem, with limited treatment options and no vaccine available. HCV uses components of the host cell to proliferate, including lipid droplets (LD) onto which HCV core proteins bind and facilitate viral particle assembly. We have measured the dynamics of HCV core protein-mediated changes in LDs and rates of LD movement on microtubules using a combination of coherent anti-Stokes Raman scattering (CARS), two-photon fluorescence (TPF), and differential interference contrast (DIC) microscopies. Results show that the HCV core protein induces rapid increases in LD size. Particle tracking experiments show that HCV core protein slowly affects LD localization by controlling the directionality of LD movement on microtubules. These dynamic processes ultimately aid HCV in propagating and the molecules and interactions involved represent novel targets for potential therapeutic intervention.

Single laser source for multimodal coherent anti-Stokes Raman scattering microscopy.

Short laser pulse technology has significantly contributed to biomedical research, especially via nonlinear optical microscopy. Coherent anti-Stokes Raman scattering (CARS) microscopy is a label-free, chemical-selective method that is growing in importance as improved methods and light sources develop. Here we discuss different approaches to laser source development for CARS microscopy and highlight the advantages of a multimodal CARS microscope, illustrated by selected applications in biomedical research.

Optimally chirped multimodal CARS microscopy based on a single Ti:sapphire oscillator.

We demonstrate high performance coherent anti-Stokes Raman scattering (CARS) microscopy of live cells and tissues with user-variable spectral resolution and broad Raman tunability (2500 - 4100 cm(-1)), using a femtosecond Ti:Sapphire pump and photonic crystal fiber output for the broadband synchronized Stokes pulse. Spectral chirp of the fs laser pulses was a user-variable parameter for optimization in a spectral focusing implementation of multimodal CARS microscopy. High signal-to-noise, high contrast multimodal imaging of live cells and tissues was achieved with pixel dwell times of 2-8 micros and low laser powers (< 30 mW total).

All-fiber CARS microscopy of live cells.

Using an all-fiber laser system consisting of a femtosecond Er/Yb fiber oscillator as the pump and an ultra-highly nonlinear fiber for Stokes generation, we demonstrate multimodal (TPF+SHG+CARS) non-linear optical microscopy of both tissue samples and live cells. Multimodal imaging was successfully performed with pixel dwell times as short as 4 micros at low laser powers (< 40 mW total).

Cholesterol is required for efficient endoplasmic reticulum-to-Golgi transport of secretory membrane proteins.

Although cholesterol is synthesized in the endoplasmic reticulum (ER), compared with other cellular membranes, ER membrane has low cholesterol (3-6%). Most of the molecular machinery that regulates cellular cholesterol homeostasis also resides in the ER. Little is known about how cholesterol itself affects the ER membrane. Here, we demonstrate that acute cholesterol depletion in ER membranes impairs ER-to-Golgi transport of secretory membrane proteins. Cholesterol depletion is achieved by a brief inhibition of cholesterol synthesis with statins in cells grown in cholesterol-depleted medium. We provide evidence that secretory membrane proteins vesicular stomatitis virus glycoprotein and scavenger receptor A failed to be efficiently transported from the ER upon cholesterol depletion. Fluorescence photobleaching recovery experiments indicated that cholesterol depletion by statins leads to a severe loss of lateral mobility on the ER membrane of these transmembrane proteins, but not loss of mobility of proteins in the ER lumen. This impaired lateral mobility is correlated with impaired ER-to-Golgi transport. These results provide evidence for the first time that cholesterol is required in the ER membrane to maintain mobility of membrane proteins and thus protein secretion.

Pre-Clinical Translation of Second Harmonic Microscopy of Meniscal and Articular Cartilage Using a Prototype Nonlinear Microendoscope.

Previous studies using nonlinear microscopy have demonstrated that osteoarthritis (OA) is characterized by the gradual replacement of Type II collagen with Type I collagen. The objective of this study was to develop a prototype nonlinear laser scanning microendoscope capable of resolving the structural differences of collagen in various orthopaedically relevant cartilaginous surfaces. The current prototype developed a miniaturized femtosecond laser scanning instrument, mounted on an articulated positioning system, capable of both conventional arthroscopy and second-harmonic laser-scanning microscopy. Its optical system includes a multi-resolution optical system using a gradient index objective lens and a customized multi-purpose fiber optic sheath to maximize the collection of backscattered photons or provide joint capsule illumination. The stability and suitability of the prototype arthroscope to approach and image cartilage were evaluated through preliminary testing on fresh, minimally processed, and partially intact porcine knee joints. Image quality was sufficient to distinguish between hyaline cartilage and fibrocartilage through unique Type I and Type II collagen-specific characteristics. Imaging the meniscus revealed that the system was able to visualize differences in the collagen arrangement between the superficial and lamellar layers. Such detailed in vivo imaging of the cartilage surfaces could obviate the need to perform biopsies for ex vivo histological analysis in the future, and provide an alternative to conventional external imaging to characterize and diagnose progressive and degenerative cartilage diseases such as OA. Moreover, this system is readily customizable and may provide a suitable and modular platform for developing additional tools utilizing femtosecond lasers for tissue cutting within the familiar confines of two or three portal arthroscopy techniques.

Direct mineralogical imaging of economic ore and rock samples with multi-modal nonlinear optical microscopy.

Multi-modal nonlinear optical (NLO) microscopy, including stimulated Raman scattering (SRS) and second harmonic generation (SHG), was used to directly image mineralogical features of economic ore and rock samples. In SRS/SHG imaging, ore samples generally require minimal preparation and may be rapidly imaged, even in their wet state. 3D structural details, at submicron resolution, are revealed tens of microns deep within samples. Standard mineral imaging based on scanning electron microscopy (SEM), with elemental analysis via energy dispersive X-Ray spectroscopy, was used to independently validate the mineral composition of the samples. Spatially-resolved SRS from dominant Raman-resonant bands precisely maps the locations of specific minerals contained within the samples. SHG imaging reveals locally non-centrosymmetric structures, such as quartz grains. Competing absorption and nonlinear scattering processes, however, can reduce contrast in SRS imaging. Importantly, the correlation between standard electron microscopy and multi-modal NLO optical microscopy shows that the latter offers rapid image contrast based on the mineral content of the sample.

Coherent anti-Stokes Raman scattering microscopy using photonic crystal fiber with two closely lying zero dispersion wavelengths.

We demonstrate coherent anti-Stokes Raman scattering (CARS) microscopy of lipid-rich structures using a single unamplified femtosecond Ti:sapphire laser and a photonic crystal fiber (PCF) with two closely lying zero dispersion wavelengths (ZDW) for the Stokes source. The primary enabling factor for the fast data acquisition (84 micros per pixel) in the proof-of-principle CARS images, is the low noise supercontinuum (SC) generated in this type of PCF, in contrast to SC generated in a PCF with one ZDW. The dependence of the Stokes pulse on average input power, pump wavelength, pulse duration and polarization is experimentally characterized. We show that it is possible to control the spectral shape of the SC by tuning the pump wavelength of the input pulse and the consequence for CARS microscopy is discussed.

Hyperspectral multimodal CARS microscopy in the fingerprint region.

A simple scheme for multimodal coherent anti-Stokes Raman scattering (CARS) microscopy is based on the spectral focusing of ultrafast-oscillator-derived pump/probe light and synchronous photonic crystal fiber (PCF) fiber-generated broadband Stokes light. To date, such schemes allowed rapid hyperspectral imaging throughout the CH/OH high frequency region (2700-4000 cm(-1) ). Here we extend this approach to the middle (1640-3300 cm(-1) ) and fingerprint regions (850-1800 cm(-1) ) of the Raman spectrum. Our simple integrated approach to rapid hyperspectral CARS microscopy in the fingerprint region is demonstrated by applications to label-free multimodal imaging of cellulose and bulk bone, including use of the phosphate resonance at 960 cm(-1) .

Label-free hyperspectral nonlinear optical microscopy of the biofuel micro-algae Haematococcus Pluvialis.

We consider multi-modal four-wave mixing microscopies to be ideal tools for the in vivo study of carotenoid distributions within the important biofuel microalgae Haematococcus pluvialis. We show that hyperspectral coherent anti-Stokes Raman scattering (CARS) microscopy generates non-invasive, quantitative real-time concentrations maps of intracellular carotenoid distributions in live algae.

Stearoyl-CoA desaturase inhibition blocks formation of hepatitis C virus-induced specialized membranes.

Hepatitis C virus (HCV) replication is dependent on the formation of specialized membrane structures; however, the host factor requirements for the formation of these HCV complexes remain unclear. Herein, we demonstrate that inhibition of stearoyl-CoA desaturase 1 (SCD-1) halts the biosynthesis of unsaturated fatty acids, such as oleic acid, and negatively modulates HCV replication. Unsaturated fatty acids play key roles in membrane curvature and fluidity. Mechanistically, we demonstrate that SCD-1 inhibition disrupts the integrity of membranous HCV replication complexes and renders HCV RNA susceptible to nuclease-mediated degradation. Our work establishes a novel function for unsaturated fatty acids in HCV replication.

Fluorescence lifetime imaging of alterations to cellular metabolism by domain 2 of the hepatitis C virus core protein.

Hepatitis C virus (HCV) co-opts hepatic lipid pathways to facilitate its pathogenesis. The virus alters cellular lipid biosynthesis and trafficking, and causes an accumulation of lipid droplets (LDs) that gives rise to hepatic steatosis. Little is known about how these changes are controlled at the molecular level, and how they are related to the underlying metabolic states of the infected cell. The HCV core protein has previously been shown to independently induce alterations in hepatic lipid homeostasis. Herein, we demonstrate, using coherent anti-Stokes Raman scattering (CARS) microscopy, that expression of domain 2 of the HCV core protein (D2) fused to GFP is sufficient to induce an accumulation of larger lipid droplets (LDs) in the perinuclear region. Additionally, we performed fluorescence lifetime imaging of endogenous reduced nicotinamide adenine dinucleotides [NAD(P)H], a key coenzyme in cellular metabolic processes, to monitor changes in the cofactor's abundance and conformational state in D2-GFP transfected cells. When expressed in Huh-7 human hepatoma cells, we observed that the D2-GFP induced accumulation of LDs correlated with an increase in total NAD(P)H fluorescence and an increase in the ratio of free to bound NAD(P)H. This is consistent with an approximate 10 fold increase in cellular NAD(P)H levels. Furthermore, the lifetimes of bound and free NAD(P)H were both significantly reduced--indicating viral protein-induced alterations in the cofactors' binding and microenvironment. Interestingly, the D2-expressing cells showed a more diffuse localization of NAD(P)H fluorescence signal, consistent with an accumulation of the co-factor outside the mitochondria. These observations suggest that HCV causes a shift of metabolic control away from the use of the coenzyme in mitochondrial electron transport and towards glycolysis, lipid biosynthesis, and building of new biomass. Overall, our findings demonstrate that HCV induced alterations in hepatic metabolism is tightly linked to alterations in NAD(P)H functional states.

Nonlinear optical microscopy in decoding arterial diseases.

Pathological understanding of arterial diseases is mainly attributable to histological observations based on conventional tissue staining protocols. The emerging development of nonlinear optical microscopy (NLOM), particularly in second-harmonic generation, two-photon excited fluorescence and coherent Raman scattering, provides a new venue to visualize pathological changes in the extracellular matrix caused by atherosclerosis progression. These techniques in general require minimal tissue preparation and offer rapid three-dimensional imaging. The capability of label-free microscopic imaging enables disease impact to be studied directly on the bulk artery tissue, thus minimally perturbing the sample. In this review, we look at recent progress in applications related to arterial disease imaging using various forms of NLOM.

Forward-collected simultaneous fluorescence lifetime imaging and coherent anti-Stokes Raman scattering microscopy.

We demonstrate the simultaneous collection and separation of femtosecond-laser-based forward-collected coherent anti-Stokes Raman scattering (F-CARS) and two-photon-excitation-induced fluorescence lifetime images (FLIM) using time-correlated single photon counting (TCSPC). We achieve this in a nondescanned geometry using a single multimode fiber without significant loss of light, field of view, and most importantly, TCSPC timing fidelity. In addition to showing the ability to separate CARS images from FLIM images using time gating, we also demonstrate composite multimodal epicollected FLIM imaging with fiber-collected F-CARS imaging in live cells.