A white light confocal microscope for spectrally resolved multidimensional imaging

Hyperspectral confocal microscopy in the short-wave infrared range

We demonstrate hyperspectral confocal microscopy in the short-wave infrared (SWIR) range of 1100-1600 nm using a wavelength-scanning laser in tandem with laser scanning confocal microscopy. Confocal microscopy in the SWIR range allows for high-resolution inspection of an integrated circuit (IC) chip, while hyperspectral imaging, together with a chemometric analysis, enables us to identify functional circuit block groups in the acquired image. With the extended capability, the developed instrument can be potentially used for inline inspection and non-invasive failure analysis of IC chips.

Compact and ultracompact spectral imagers: technology and applications in biomedical imaging

Significance

Spectral imaging, which includes hyperspectral and multispectral imaging, can provide images in numerous wavelength bands within and beyond the visible light spectrum. Emerging technologies that enable compact, portable spectral imaging cameras can facilitate new applications in biomedical imaging.

Aim

With this review paper, researchers will (1) understand the technological trends of upcoming spectral cameras, (2) understand new specific applications that portable spectral imaging unlocked, and (3) evaluate proper spectral imaging systems for their specific applications.

Approach

We performed a comprehensive literature review in three databases (Scopus, PubMed, and Web of Science). We included only fully realized systems with definable dimensions. To best accommodate many different definitions of "compact," we included a table of dimensions and weights for systems that met our definition.

Results

There is a wide variety of contributions from industry, academic, and hobbyist spaces. A variety of new engineering approaches, such as Fabry-Perot interferometers, spectrally resolved detector array (mosaic array), microelectro-mechanical systems, 3D printing, light-emitting diodes, and smartphones, were used in the construction of compact spectral imaging cameras. In bioimaging applications, these compact devices were used for in vivo and ex vivo diagnosis and surgical settings.

Conclusions

Compact and ultracompact spectral imagers are the future of spectral imaging systems. Researchers in the bioimaging fields are building systems that are low-cost, fast in acquisition time, and mobile enough to be handheld.

Super-multiplexing excitation spectral microscopy with multiple fluorescence bands

Fluorescence microscopy, with high molecular specificity and selectivity, is a valuable tool for studying complex biological systems and processes. However, the ability to distinguish a large number of distinct subcellular structures in a single sample is impeded by the broad spectra of molecular fluorescence. We have recently shown that excitation spectral microscopy provides a powerful means to unmix up to six fluorophores in a single fluorescence band. Here, by working with multiple fluorescence bands, we extend this approach to the simultaneous imaging of up to ten targets, with the potential for further expansions. By covering the excitation/emission bandwidth across the full visible range, an ultra-broad 24-wavelength excitation scheme is established through frame-synchronized scanning of the excitation wavelength from a white lamp via an acousto-optic tunable filter (AOTF), so that full-frame excitation-spectral images are obtained every 24 camera frames, offering superior spectral information and multiplexing capability. With numerical simulations, we validate the concurrent imaging of 10 fluorophores spanning the visible range to achieve exceptionally low (∼0.5%) crosstalks. For cell imaging experiments, we demonstrate unambiguous identification of up to eight different intracellular structures labeled by common fluorophores of substantial spectral overlap with minimal color crosstalks. We thus showcase an easy-to-implement, cost-effective microscopy system for visualizing complex cellular components with more colors and lower crosstalks.

A method for the fast and photon-efficient analysis of time-domain fluorescence lifetime image data over large dynamic ranges

Fluorescence lifetime imaging (FLIM) allows the quantification of sub‐cellular processes in situ, in living cells. A number of approaches have been developed to extract the lifetime from time‐domain FLIM data, but they are often limited in terms of speed, photon efficiency, precision or the dynamic range of lifetimes they can measure. Here, we focus on one of the best performing methods in the field, the centre‐of‐mass method (CMM), that conveys advantages in terms of speed and photon efficiency over others. In this paper, however, we identify a loss of photon efficiency of CMM for short lifetimes when background noise is present. We subsequently present a new development and generalization of CMM that provides for the rapid and accurate extraction of fluorescence lifetime over a large lifetime dynamic range. We provide software tools to simulate, validate and analyse FLIM data sets and compare the performance of our approach against the standard CMM and the commonly employed least‐square minimization (LSM) methods. Our method features a better photon efficiency than standard CMM and LSM and is robust in the presence of background noise. The algorithm is applicable to any time‐domain FLIM data set.

Edge-Enhanced Microwell Immunoassay for Highly Sensitive Protein Detection

Highly sensitive biosensors that can detect low concentrations of protein biomarkers at the early stages of diseases or proteins secreted from single cells are of importance for disease diagnosis and treatment assessment. This work reports a new signal amplification mechanism, that is, edge enhancement based on the vertical sidewalls of microwells for ultra-sensitive protein detection. The fluorescence emission at the edge of the microwells is highly amplified due to the microscopic axial resolution (depth of field) and demonstrates a microring effect. The enhanced fluorescence intensity from microrings is calibrated for bovine serum albumin detection, which shows a 6-fold sensitivity enhancement and a lower limit of detection at the microwell edge, compared to those obtained on a flat surface. The microwell chip is used to separate single cells, and the wall of each microwell is used to detect interferon-γ secretion from T cells stimulated with a peptide and whole cancer cells. Given its edge-enhancement ability, the microwell technique can be a highly sensitive biosensing platform for disease diagnosis at an early stage and for assessing potential treatments at the single-cell level.

Excitation spectral microscopy for highly multiplexed fluorescence imaging and quantitative biosensing

The multiplexing capability of fluorescence microscopy is severely limited by the broad fluorescence spectral width. Spectral imaging offers potential solutions, yet typical approaches to disperse the local emission spectra notably impede the attainable throughput. Here we show that using a single, fixed fluorescence emission detection band, through frame-synchronized fast scanning of the excitation wavelength from a white lamp via an acousto-optic tunable filter, up to six subcellular targets, labeled by common fluorophores of substantial spectral overlap, can be simultaneously imaged in live cells with low (~1%) crosstalks and high temporal resolutions (down to ~10 ms). The demonstrated capability to quantify the abundances of different fluorophores in the same sample through unmixing the excitation spectra next enables us to devise novel, quantitative imaging schemes for both bi-state and Förster resonance energy transfer fluorescent biosensors in live cells. We thus achieve high sensitivities and spatiotemporal resolutions in quantifying the mitochondrial matrix pH and intracellular macromolecular crowding, and further demonstrate, for the first time, the multiplexing of absolute pH imaging with three additional target organelles/proteins to elucidate the complex, Parkin-mediated mitophagy pathway. Together, excitation spectral microscopy provides exceptional opportunities for highly multiplexed fluorescence imaging. The prospect of acquiring fast spectral images without the need for fluorescence dispersion or care for the spectral response of the detector offers tremendous potential.

Effects of two weak continuous-wave triggers on picosecond pulse pumped supercontinuum generation

The promising advancement of supercontinuum generation in optical fibers has initiated significant interest in recent research studies and several continuing applications. We numerically corroborate the effects of picosecond pulse pumped supercontinuum (SC) by using two weak continuous-wave (CW) triggers with 1% pump intensity. Compared with SC with one CW trigger, adding two CW triggers (1% pump power), both near the modulation instability peaks, can achieve wider spectra for a picosecond pulse pumped SC. Furthermore, good coherence properties may be achieved in the wavelength range from 1300-2000 nm when one CW trigger is near the pump center wavelength and the other CW trigger is distant from the pump. In our simulations, putting two CW triggers on the same side (concerning the pump wavelength) or putting them on different sides have similar effects on SC spectral and temporal coherence properties. Therefore, by engineering the wavelengths of two CW triggers to offer better bandwidth or coherence, we envision that the proposed technique could play a significant role in the generation of SC.

High-throughput, multi-parametric, and correlative fluorescence lifetime imaging

In this review, we discuss methods and advancements in fluorescence lifetime imaging microscopy that permit measurements to be performed at faster speed and higher resolution than previously possible. We review fast single-photon timing technologies and the use of parallelized detection schemes to enable high-throughput and high content imaging applications. We appraise different technological implementations of fluorescence lifetime imaging, primarily in the time-domain. We also review combinations of fluorescence lifetime with other imaging modalities to capture multi-dimensional and correlative information from a single sample. Throughout the review, we focus on applications in biomedical research. We conclude with a critical outlook on current challenges and future opportunities in this rapidly developing field.

Differences in the Structural Chemical Composition of the Primary Xylem of Cactaceae: A Topochemical Perspective

The xylem of Cactaceae is a complex system with different types of cells whose main function is to conduct and store water, mostly during the development of primary xylem, which has vessel elements and wide-band tracheids. The anatomy of primary xylem of Cactaceae has been widely studied, but little is known about its chemical composition. The aim of this study was to determine the structural chemical composition of the primary xylem of Cactaceae and to compare it with the anatomy in the group. Seeds from eight cacti species were used, representing the Pereskioideae, Opuntioideae, and Cactoideae subfamilies. Seeds were germinated and grown for 8 months. Subsequently, only the stem of the seedling was selected, dried, milled, and processed following the TAPPI T-222 om-02 norm; lignin was quantified using the Klason method and cellulose with the Kurshner-Höffer method. Using Fourier transform infrared spectroscopy, the percentage of syringyl and guaiacyl in lignin was calculated. Seedlings of each species were fixed, sectioned, and stained for their anatomical description and fluorescence microscopy analysis for the topochemistry of the primary xylem. The results showed that there were significant differences between species (p < 0.05), except in the hemicelluloses. Through a principal component analysis, it was found that the amount of extractive-free stem and hot water-soluble extractives were the variables that separated the species, followed by cellulose and hemicelluloses since the seedlings developed mainly parenchyma cells and the conductive tissue showed vessel elements and wide-band tracheids, both with annular and helical thickenings in secondary walls. The type of lignin with the highest percentage was guaiacyl-type, which is accumulated mainly in the vessels, providing rigidity. Whereas in the wide-band tracheids from metaxylem, syringyl lignin accumulated in the secondary walls S2 and S3, which permits an efficient flow of water and gives the plant the ability to endure difficult conditions during seedling development. Only one species can be considered to have paedomorphosis since the conductive elements had a similar chemistry in primary and secondary xylem.

Single particle trajectories reveal active endoplasmic reticulum luminal flow

The Endoplasmic Reticulum (ER), a network of membranous sheets and pipes, supports functions encompassing biogenesis of secretory proteins and delivery of functional solutes throughout the cell1,2. Molecular mobility through the ER network enables these functionalities, but diffusion alone is not sufficient to explain luminal transport across supramicron distances. Understanding the ER structure-function relationship is critical in light of mutations in ER morphology regulating proteins that give rise to neurodegenerative disorders3,4. Here, super-resolution microscopy and analysis of single particle trajectories of ER luminal proteins revealed that the topological organization of the ER correlates with distinct trafficking modes of its luminal content: with a dominant diffusive component in tubular junctions and a fast flow component in tubules. Particle trajectory orientations resolved over time revealed an alternating current of the ER contents, whilst fast ER super-resolution identified energy-dependent tubule contraction events at specific points as a plausible mechanism for generating active ER luminal flow. The discovery of active flow in the ER has implications for timely ER content distribution throughout the cell, particularly important for cells with extensive ER-containing projections such as neurons.

Imaging and Spectroscopy of Natural Fluorophores in Pine Needles

Many plant tissues fluoresce due to the natural fluorophores present in cell walls or within the cell protoplast or lumen. While lignin and chlorophyll are well-known fluorophores, other components are less well characterized. Confocal fluorescence microscopy of fresh or fixed vibratome-cut sections of radiata pine needles revealed the presence of suberin, lignin, ferulate, and flavonoids associated with cell walls as well as several different extractive components and chlorophyll within tissues. Comparison of needles in different physiological states demonstrated the loss of chlorophyll in both chlorotic and necrotic needles. Necrotic needles showed a dramatic change in the fluorescence of extractives within mesophyll cells from ultraviolet (UV) excited weak blue fluorescence to blue excited strong green fluorescence associated with tissue browning. Comparisons were made among fluorophores in terms of optimal excitation, relative brightness compared to lignin, and the effect of pH of mounting medium. Fluorophores in cell walls and extractives in lumens were associated with blue or green emission, compared to the red emission of chlorophyll. Autofluorescence is, therefore, a useful method for comparing the histology of healthy and diseased needles without the need for multiple staining techniques, potentially aiding visual screening of host resistance and disease progression in needle tissue.

Spectroscopic identification of individual fluorophores using photoluminescence excitation spectra

The identity of a fluorophore can be ambiguous if other fluorophores or nonspecific fluorescent impurities have overlapping emission spectra. The presence of overlapping spectra makes it difficult to differentiate fluorescent species using discrete detection channels and unmixing of spectra. The unique absorption and emission signatures of fluorophores provide an opportunity for spectroscopic identification. However, absorption spectroscopy may be affected by scattering, whereas fluorescence emission spectroscopy suffers from signal loss by gratings or other dispersive optics. Photoluminescence excitation spectra, where excitation is varied and emission is detected at a fixed wavelength, allows hyperspectral imaging with a single emission filter for high signal-to-background ratio without any moving optics on the emission side. We report a high throughput method for measuring the photoluminescence excitation spectra of individual fluorophores using a tunable supercontinuum laser and prism-type total internal reflection fluorescence microscope. We used the system to measure and sort the photoluminescence excitation spectra of individual Alexa dyes, fluorescent nanodiamonds (FNDs), and fluorescent polystyrene beads. We used a Gaussian mixture model with maximum likelihood estimation to objectively separate the spectra. Finally, we spectroscopically identified different species of fluorescent nanodiamonds with overlapping spectra and characterized the heterogeneity of fluorescent nanodiamonds of varying size.

White-Light Supercontinuum Laser-Based Multiple Wavelength Excitation for TCSPC-FLIM of Cutaneous Nanocarrier Uptake

We report here on a custom-built time-correlated single photon-counting (TCSPC)-based fluorescence lifetime imaging microscopy (FLIM) setup with a continuously tunable white-light supercontinuum laser combined with acousto-optical tunable filters (AOTF) as an excitation source for simultaneous excitation of multiple spectrally separated fluorophores. We characterized the wavelength dependence of the white-light supercontinuum laser pulse properties and demonstrated the performance of the FLIM setup, aiming to show the experimental setup in depth together with a biomedical application. We herein summarize the physical-technical parameters as well as our approach to map the skin uptake of nanocarriers using FLIM with a resolution compared to spectroscopy. As an example, we focus on the penetration study of indocarbocyanine-labeled dendritic core-multishell nanocarriers (CMS-ICC) into reconstructed human epidermis. Unique fluorescence lifetime signatures of indocarbocyanine-labeled nanocarriers indicate nanocarrier-tissue interactions within reconstructed human epidermis, bringing FLIM close to spectroscopic analysis.

TriPer, an optical probe tuned to the endoplasmic reticulum tracks changes in luminal H2O2

Background

The fate of hydrogen peroxide (H₂O₂) in the endoplasmic reticulum (ER) has been inferred indirectly from the activity of ER-localized thiol oxidases and peroxiredoxins, in vitro, and the consequences of their genetic manipulation, in vivo. Over the years hints have suggested that glutathione, puzzlingly abundant in the ER lumen, might have a role in reducing the heavy burden of H₂O₂ produced by the luminal enzymatic machinery for disulfide bond formation. However, limitations in existing organelle-targeted H₂O₂ probes have rendered them inert in the thiol-oxidizing ER, precluding experimental follow-up of glutathione’s role in ER H₂O₂ metabolism.

Results

Here we report on the development of TriPer, a vital optical probe sensitive to changes in the concentration of H₂O₂ in the thiol-oxidizing environment of the ER. Consistent with the hypothesized contribution of oxidative protein folding to H₂O₂ production, ER-localized TriPer detected an increase in the luminal H₂O₂ signal upon induction of pro-insulin (a disulfide-bonded protein of pancreatic β-cells), which was attenuated by the ectopic expression of catalase in the ER lumen. Interfering with glutathione production in the cytosol by buthionine sulfoximine (BSO) or enhancing its localized destruction by expression of the glutathione-degrading enzyme ChaC1 in the lumen of the ER further enhanced the luminal H₂O₂ signal and eroded β-cell viability.

Conclusions

A tri-cysteine system with a single peroxidatic thiol enables H₂O₂ detection in oxidizing milieux such as that of the ER. Tracking ER H₂O₂ in live pancreatic β-cells points to a role for glutathione in H₂O₂ turnover.

Electronic supplementary material

The online version of this article (doi:10.1186/s12915-017-0367-5) contains supplementary material, which is available to authorized users.

Lenslet array tunable snapshot imaging spectrometer (LATIS) for hyperspectral fluorescence microscopy

Snapshot hyperspectral imaging augments pixel dwell time and acquisition speeds over existing scanning systems, making it a powerful tool for fluorescence microscopy. While most snapshot systems contain fixed datacube parameters (x,y,λ), our novel snapshot system, called the lenslet array tunable snapshot imaging spectrometer (LATIS), demonstrates tuning its average spectral resolution from 22.66 nm (80x80x22) to 13.94 nm (88x88x46) over 485 to 660 nm. We also describe a fixed LATIS with a datacube of 200x200x27 for larger field-of-view (FOV) imaging. We report <1 sec exposure times and high resolution fluorescence imaging with minimal artifacts.

Fluorescence Self-Quenching from Reporter Dyes Informs on the Structural Properties of Amyloid Clusters Formed in Vitro and in Cells

The characterization of the aggregation kinetics of protein amyloids and the structural properties of the ensuing aggregates are vital in the study of the pathogenesis of many neurodegenerative diseases and the discovery of therapeutic targets. In this article, we show that the fluorescence lifetime of synthetic dyes covalently attached to amyloid proteins informs on the structural properties of amyloid clusters formed both in vitro and in cells. We demonstrate that the mechanism behind such a "lifetime sensor" of protein aggregation is based on fluorescence self-quenching and that it offers a good dynamic range to report on various stages of aggregation without significantly perturbing the process under investigation. We show that the sensor informs on the structural density of amyloid clusters in a high-throughput and quantitative manner and in these aspects the sensor outperforms super-resolution imaging techniques. We demonstrate the power and speed of the method, offering capabilities, for example, in therapeutic screenings that monitor biological self-assembly. We investigate the mechanism and advantages of the lifetime sensor in studies of the K18 protein fragment of the Alzheimer's disease related protein tau and its amyloid aggregates formed in vitro. Finally, we demonstrate the sensor in the study of aggregates of polyglutamine protein, a model used in studies related to Huntington's disease, by performing correlative fluorescence lifetime imaging microscopy and structured-illumination microscopy experiments in cells.

Optical Super-Resolution Imaging of β-Amyloid Aggregation In Vitro and In Vivo: Method and Techniques

Super-resolution microscopy has emerged as a powerful and non-invasive tool for the study of molecular processes both in vitro and in live cells. In particular, super-resolution microscopy has proven valuable for research studies in protein aggregation. In this chapter we present details of recent advances in this method and the specific techniques, enabling the study of amyloid beta aggregation optically, both in vitro and in cells. First, we show that variants of optical super-resolution microscopy provide a capability to visualize oligomeric and fibrillar structures directly, providing detailed information on species morphology in vitro and even in situ, in the cellular environment. We focus on direct Stochastic Optical Reconstruction Microscopy, dSTORM, which provides morphological detail on spatial scales below 20 nm, and provide detailed protocols for its implementation in the context of amyloid beta research. Secondly, we present a range of optical techniques that offer super-resolution indirectly, which we call multi-parametric microscopy. The latter offers molecular scale information on self-assembly reactions via changes in protein or fluorophore spectral signatures. These techniques are empowered by our recent discovery that disease related amyloid proteins adopt intrinsic energy states upon fibrilisation. We show that fluorescence lifetime imaging provides a particularly sensitive readout to report on the aggregation state, which is robustly quantifiable for experiments performed either in vitro or in vivo.

Dual-color three-dimensional STED microscopy with a single high-repetition-rate laser

We describe a dual-color three-dimensional stimulated emission depletion (3D-STED) microscopy employing a single laser source with a repetition rate of 80 MHz. Multiple excitation pulses synchronized with a STED pulse were generated by a photonic crystal fiber, and the desired wavelengths were selected by an acousto-optic tunable filter with high spectral purity. Selective excitation at different wavelengths permits simultaneous imaging of two fluorescent markers at a nanoscale resolution in three dimensions.

Optical properties of Ce(3+)-Nd(3+) co-doped YAG nanoparticles for visual and near-infrared biological imaging

Ce(3+)-Nd(3+) co-doped Y3Al5O12 (YAG) nanoparticles, an average size of 20-30 nm clusters aggregated by 8-10 nm YAG nanoparticles, were synthesized by a solvothermal method. When excited by blue irradiation source, strong and broad yellow luminescence (centered at 526 nm) from Ce(3+) as well as near-infrared (NIR) luminescence (890, 1066 and 1335 nm) of Nd(3+) was observed simultaneously. It occurred by the effective dipole-dipole energy transfer from Ce(3+) to Nd(3+). Energy transfer efficiency from Ce(3+) to Nd(3+) was also calculated to be 50%. The optical property suggests that Ce(3+)-Nd(3+) co-doped YAG nanoparticles can be used as an efficient fluorescence imaging agent for not only visual but also near-infrared imaging.

Retarded PDI diffusion and a reductive shift in poise of the calcium depleted endoplasmic reticulum

Background

Endoplasmic reticulum (ER) lumenal protein thiol redox balance resists dramatic variation in unfolded protein load imposed by diverse physiological challenges including compromise in the key upstream oxidases. Lumenal calcium depletion, incurred during normal cell signaling, stands out as a notable exception to this resilience, promoting a rapid and reversible shift towards a more reducing poise. Calcium depletion induced ER redox alterations are relevant to physiological conditions associated with calcium signaling, such as the response of pancreatic cells to secretagogues and neuronal activity. The core components of the ER redox machinery are well characterized; however, the molecular basis for the calcium-depletion induced shift in redox balance is presently obscure.

Results

In vitro, the core machinery for generating disulfides, consisting of ERO1 and the oxidizing protein disulfide isomerase, PDI1A, was indifferent to variation in calcium concentration within the physiological range. However, ER calcium depletion in vivo led to a selective 2.5-fold decline in PDI1A mobility, whereas the mobility of the reducing PDI family member, ERdj5 was unaffected. In vivo, fluorescence resonance energy transfer measurements revealed that declining PDI1A mobility correlated with formation of a complex with the abundant ER chaperone calreticulin, whose mobility was also inhibited by calcium depletion and the calcium depletion-mediated reductive shift was attenuated in cells lacking calreticulin. Measurements with purified proteins confirmed that the PDI1A-calreticulin complex dissociated as Ca²⁺ concentrations approached those normally found in the ER lumen ([Ca²⁺]K_0.5max = 190 μM).

Conclusions

Our findings suggest that selective sequestration of PDI1A in a calcium depletion-mediated complex with the abundant chaperone calreticulin attenuates the effective concentration of this major lumenal thiol oxidant, providing a plausible and simple mechanism for the observed shift in ER lumenal redox poise upon physiological calcium depletion.

Electronic supplementary material

The online version of this article (doi:10.1186/s12915-014-0112-2) contains supplementary material, which is available to authorized users.

Spectral radiance source based on supercontinuum laser and wavelength tunable bandpass filter: the spectrally tunable absolute irradiance and radiance source

A new spectrally tunable source for calibration of radiometric detectors in radiance, irradiance, or power mode has been developed and characterized. It is termed the spectrally tunable absolute irradiance and radiance source (STAIRS). It consists of a supercontinuum laser, wavelength tunable bandpass filter, power stabilization feedback control scheme, and output coupling optics. It has the advantages of relative portability and a collimated beam (low étendue), and is an alternative to conventional sources such as tungsten lamps, blackbodies, or tunable lasers. The supercontinuum laser is a commercial Fianium SC400-6-02, which has a wavelength range between 400 and 2500 nm and a total power of 6 W. The wavelength tunable bandpass filter, a PhotonEtc laser line tunable filter (LLTF), is tunable between 400 and 1000 nm and has a bandwidth of 1 or 2 nm depending on the wavelength selected. The collimated laser beam from the LLTF filter is converted to an appropriate spatial and angular distribution for the application considered (i.e., for radiance, irradiance, or power mode calibration of a radiometric sensor) with the output coupling optics, for example, an integrating sphere, and the spectral radiance/irradiance/power of the source is measured using a calibration optical sensor. A power stabilization feedback control scheme has been incorporated that stabilizes the source to better than 0.01% for averaging times longer than 100 s. The out-of-band transmission of the LLTF filter is estimated to be < -65 dB (0.00003%), and is sufficiently low for many end-user applications, for example the spectral radiance calibration of earth observation imaging radiometers and the stray light characterization of array spectrometers (the end-user optical sensor). We have made initial measurements of two end-user instruments with the STAIRS source, an array spectrometer and ocean color radiometer.

Multimodal fluorescence imaging spectroscopy

Multimodal fluorescence imaging is a versatile method that has a wide application range from biological studies to materials science. Typical observables in multimodal fluorescence imaging are intensity, lifetime, excitation, and emission spectra which are recorded at chosen locations at the sample. This chapter describes how to build instrumentation that allows for multimodal fluorescence imaging and explains data analysis procedures for the observables.

Extracellular monomeric tau protein is sufficient to initiate the spread of tau protein pathology

Understanding the formation and propagation of aggregates of the Alzheimer disease-associated Tau protein in vivo is vital for the development of therapeutics for this devastating disorder. Using our recently developed live-cell aggregation sensor in neuron-like cells, we demonstrate that different variants of exogenous monomeric Tau, namely full-length Tau (hTau40) and the Tau-derived construct K18 comprising the repeat domain, initially accumulate in endosomal compartments, where they form fibrillar seeds that subsequently induce the aggregation of endogenous Tau. Using superresolution imaging, we confirm that fibrils consisting of endogenous and exogenous Tau are released from cells and demonstrate their potential to spread Tau pathology. Our data indicate a greater pathological risk and potential toxicity than hitherto suspected for extracellular soluble Tau.

Lifetime imaging of a fluorescent protein sensor reveals surprising stability of ER thiol redox

Interfering with disulfide bond formation impedes protein folding and promotes endoplasmic reticulum (ER) stress. Due to limitations in measurement techniques, the relationships of altered thiol redox and ER stress have been difficult to assess. We report that fluorescent lifetime measurements circumvented the crippling dimness of an ER-tuned fluorescent redox-responsive probe (roGFPiE), faithfully tracking the activity of the major ER-localized protein disulfide isomerase, PDI. In vivo lifetime imaging by time-correlated single-photon counting (TCSPC) recorded subtle changes in ER redox poise induced by exposure of mammalian cells to a reducing environment but revealed an unanticipated stability of redox to fluctuations in unfolded protein load. By contrast, TCSPC of roGFPiE uncovered a hitherto unsuspected reductive shift in the mammalian ER upon loss of luminal calcium, whether induced by pharmacological inhibition of calcium reuptake into the ER or by physiological activation of release channels. These findings recommend fluorescent lifetime imaging as a sensitive method to track ER redox homeostasis in mammalian cells.

Mid-infrared supercontinuum generation in As2S3-silica "nano-spike" step-index waveguide

Efficient generation of a broad-band mid-infrared supercontinuum spectrum is reported in an arsenic trisulphide waveguide embedded in silica. A chalcogenide "nano-spike", designed to transform the incident light adiabatically into the fundamental mode of a 2-mm-long uniform section 1 µm in diameter, is used to achieve high launch efficiencies. The nano-spike is fully encapsulated in a fused silica cladding, protecting it from the environment. Nano-spikes provide a convenient means of launching light into sub-wavelength scale waveguides. Ultrashort (65 fs, repetition rate 100 MHz) pulses at wavelength 2 µm, delivered from a Tm-doped fiber laser, are launched with an efficiency ~12% into the sub-wavelength chalcogenide waveguide. Soliton fission and dispersive wave generation along the uniform section result in spectral broadening out to almost 4 µm for launched energies of only 18 pJ. The spectrum generated will have immediate uses in metrology and infrared spectroscopy.

A label-free, quantitative assay of amyloid fibril growth based on intrinsic fluorescence

Kinetic assay of seeded growth: The graph shows the variation in intrinsic fluorescence intensity of amyloid fibrils. Fluorescence increases during the seeded aggregation of α-synuclein seeds with α-synuclein monomeric protein (blue curve) but not when α-synuclein seeds are incubated with β-synuclein monomeric protein (black curve), thus showing that no seeded growth occurred in this case.

Protein amyloids develop an intrinsic fluorescence signature during aggregation

We report observations of an intrinsic fluorescence in the visible range, which develops during the aggregation of a range of polypeptides, including the disease-related human peptides amyloid-β(1-40) and (1-42), lysozyme and tau. Characteristic fluorescence properties such as the emission lifetime and spectra were determined experimentally. This intrinsic fluorescence is independent of the presence of aromatic side-chain residues within the polypeptide structure. Rather, it appears to result from electronic levels that become available when the polypeptide chain folds into a cross-β sheet scaffold similar to what has been reported to take place in crystals. We use these findings to quantify protein aggregation in vitro by fluorescence imaging in a label-free manner.

Design and analysis of multi-color confocal microscopy with a wavelength scanning detector

Spectral (or multi-color) microscopy has the ability to detect the fluorescent light of biological specimens with a broad range of wavelengths. Currently, the acousto-optic tunable filter (AOTF) is widely used in spectral microscopy as a substitute for a multiple-dichroic mirror to divide excitation and emission signals while maintaining sufficient light efficiency. In addition, systems which utilize an AOTF have a very fast switching speed and high resolution for wavelength selection. In this paper, confocal-spectral microscopy is proposed with a particular spectrometer design with a wavelength-scanning galvano-mirror. This enables the detection of broadband (480-700 nm) fluorescence signals by a single point detector (photomultiplier tube) instead of a CCD pixel array. For this purpose, a number of optical elements were applicably designed. A prism is used to amplify the dispersion angle, and the design of the relay optics matches the signals to the diameter of the wavelength-scanning galvano-mirror. Also, a birefringent material known as calcite is used to offset the displacement error at the image plane depending on the polarization states. The proposed multi-color confocal microscopy with the unique detection body has many advantages in comparison with commercial devices. In terms of the detection method, it can be easily applied to other imaging modalities.

Periodic interactions between solitons and dispersive waves during the generation of non-coherent supercontinuum radiation

We present a numerical study of interactions between dispersive waves (DWs) and solitons during supercontinuum generation in photonic crystal fibers pumped with picosecond laser pulses. We show how the soliton-induced trapping potential evolves along the fiber and affects the dynamics of a DW-soliton pair. Individual frequency components of the DW periodically interact with the soliton resulting in stepwise frequency blue shifts. In contrast, the ensemble blue shifts of all frequency components in the DW appear to be quasi-continuous. The step size of frequency up-conversion and the temporal separation between subsequent soliton-DW interactions are governed by the potential well which confines the soliton-DW pair and which changes in time.

Streak camera crosstalk reduction using a multiple delay optical fiber bundle

The streak camera is one of the fastest photodetection systems, while its capability of multiplexing is particularly attractive to many applications requiring parallel data acquisition. The degree of multiplexing in a streak camera is limited by the crosstalk between input channels. We developed a technique that introducing a fixed time delay between adjacent fiber channels in a customized two-dimensional to one-dimensional fiber array to significantly reduce crosstalk both at the sample plane and at the input of a streak camera. A prototype system has been developed that supports 100 input channels, and its performance in fluorescence microscopy is demonstrated.

Hyperspectral imaging microscopy for identification and quantitative analysis of fluorescently-labeled cells in highly autofluorescent tissue

Standard fluorescence microscopy approaches rely on measurements at single excitation and emission bands to identify specific fluorophores and the setting of thresholds to quantify fluorophore intensity. This is often insufficient to reliably resolve and quantify fluorescent labels in tissues due to high autofluorescence. Here we describe the use of hyperspectral analysis techniques to resolve and quantify fluorescently labeled cells in highly autofluorescent lung tissue. This approach allowed accurate detection of green fluorescent protein (GFP) emission spectra, even when GFP intensity was as little as 15% of the autofluorescence intensity. GFP-expressing cells were readily quantified with zero false positives detected. In contrast, when the same images were analyzed using standard (single-band) thresholding approaches, either few GFP cells (high thresholds) or substantial false positives (intermediate and low thresholds) were detected. These results demonstrate that hyperspectral analysis approaches uniquely offer accurate and precise detection and quantification of fluorescence signals in highly autofluorescent tissues.

Noise reduction of supercontinua via optical feedback

The impact of delayed optical feedback on the supercontinuum noise properties is investigated numerically and experimentally. The supercontinuum is generated by coupling femtosecond laser pulses into a microstructured fiber within a ring resonator, which introduces the optical feedback. The power noise and spectral amplitude noise properties of this feedback system are numerically and experimentally compared with single-pass supercontinuum generation. In a demonstrative experiment via optical feedback the power noise could be reduced by 15 dB and the spectral amplitude noise could be reduced by up to 28 dB.

A FRET sensor for non-invasive imaging of amyloid formation in vivo

Misfolding and aggregation of amyloidogenic polypeptides lie at the root of many neurodegenerative diseases. Whilst protein aggregation can be readily studied in vitro by established biophysical techniques, direct observation of the nature and kinetics of aggregation processes taking place in vivo is much more challenging. We describe here, however, a Förster resonance energy transfer sensor that permits the aggregation kinetics of amyloidogenic proteins to be quantified in living systems by exploiting our observation that amyloid assemblies can act as energy acceptors for variants of fluorescent proteins. The observed lifetime reduction can be attributed to fluorescence energy transfer to intrinsic energy states associated with the growing amyloid species. Indeed, for a-synuclein, a protein whose aggregation is linked to Parkinson's disease, we have used this sensor to follow the kinetics of the self-association reactions taking place in vitro and in vivo and to reveal the nature of the ensuing aggregated species. Experiments were conducted in vitro, in cells in culture and in living Caenorhabditis elegans. For the latter the readout correlates directly with the appearance of a toxic phenotype. The ability to measure the appearance and development of pathogenic amyloid species in a living animal and the ability to relate such data to similar processes observed in vitro provides a powerful new tool in the study of the pathology of the family of misfolding disorders. Our study confirms the importance of the molecular environment in which aggregation reactions take place, highlighting similarities as well as differences between the processes occurring in vitro and in vivo, and their significance for defining the molecular physiology of the diseases with which they are associated.

Design and application of a confocal microscope for spectrally resolved anisotropy imaging

Biophysical imaging tools exploit several properties of fluorescence to map cellular biochemistry. However, the engineering of a cost-effective and user-friendly detection system for sensing the diverse properties of fluorescence is a difficult challenge. Here, we present a novel architecture for a spectrograph that permits integrated characterization of excitation, emission and fluorescence anisotropy spectra in a quantitative and efficient manner. This sensing platform achieves excellent versatility of use at comparatively low costs. We demonstrate the novel optical design with example images of plant cells and of mammalian cells expressing fluorescent proteins undergoing energy transfer.

HomoFRET fluorescence anisotropy imaging as a tool to study molecular self-assembly in live cells

Molecular self-assembly is a defining feature of numerous biological functions and dysfunctions, ranging from basic cell signalling to diseases mediated by protein aggregation. There is current demand for novel experimental methods to study molecular self-assembly in live cells, and thereby in its physiological context. Förster resonance energy transfer (FRET) between fluorophores of a single type, known as homoFRET, permits noninvasive detection and quantification of molecular clusters in live cells. It can thus provide powerful insights into the molecular physiology of living systems and disease. HomoFRET is detected by measuring the loss of fluorescence anisotropy upon excitation with polarised light. This article reviews recent key developments in homoFRET fluorescence anisotropy imaging for the detection and quantification of molecular self-assembly reactions in biological systems. A summary is given of the current state-of-the-art and case studies are presented of successful implementations, highlighting technical aspects which have to be mastered to bridge the gap between proof-of-concept experiments and biological discoveries.

Control of pulse-to-pulse fluctuations in visible supercontinuum

Long-pulse supercontinuum sources are initiated by modulation instability and consequently suffer from stochastic shot-to-shot variations of their spectral power density. In this paper, we provide a measurement of pulse-to-pulse fluctuations over the whole supercontinuum spectrum, and we show that their spectral dependence follows the group index curve of the fiber. Then, we demonstrate a significant reduction of supercontinuum pulse-to-pulse fluctuations in the visible by using a photonic crystal fiber with longitudinally tailored guidance properties. We finally show numerically that this new source would allow a significant improvement of the signal-to-noise ratio in fluorescence microscopy.

Predicting supercontinuum pulse collisions with simulations exhibiting temporal aliasing

Interactions between supercontinuum (SC) light pulses, produced by the propagation of rapidly sequenced picosecond pump laser pulses along a photonic crystal fiber, result in spectral broadening, which we attribute to interpulse soliton collisions. This phenomenon was measured experimentally, following our observation of spectral broadening in numerical simulations that exhibit so-called "pulse wraparound" or "temporal aliasing." This occurs in simulations with narrow time grids: as early parts of the SC pulse leave the computational time domain, they "reenter" at the beginning and so interact with later parts of the evolving SC pulse. We show that this provides an effective model to predict the experimentally observed spectral changes.

An adaptive filter for studying the life cycle of optical rogue waves

We present an adaptive numerical filter for analyzing fiber-length dependent properties of optical rogue waves, which are highly intense and extremely red-shifted solitons that arise during supercontinuum generation in photonic crystal fiber. We use this filter to study a data set of 1000 simulated supercontinuum pulses, produced from 5 ps pump pulses containing random noise. Optical rogue waves arise in different supercontinuum pulses at various positions along the fiber, and exhibit a lifecycle: their intensity peaks over a finite range of fiber length before declining slowly.

Adjustment of supercontinua via the optical feedback phase--experimental verifications

The manipulation of a supercontinuum via delayed optical feedback is investigated experimentally. The supercontinuum is generated in a microstructured fiber and a feedback ring resonator introduces the optical feedback and leads to the formation of different regimes of nonlinear dynamics. Via the feedback phase the optical spectrum and the regimes of nonlinear dynamics can be adjusted systematically. The impact of delay detuning on two different length scales, namely on a sub-wavelength scale and on a larger scale in the order of 10 μm are discussed. Additionally, the adjustment of the optical spectrum without changing the regime of nonlinear dynamics is demonstrated.

Experimental investigations on nonlinear dynamics in supercontinuum generation with feedback

A system for supercontinuum generation by using a photonic crystal fiber within a synchronously pumped ring cavity is presented. The feedback led to an interaction of the generated supercontinuum with the following femtosecond laser pulses and thus to the formation of a nonlinear oscillator. The nonlinear dynamical behavior of this system was investigated experimentally and compared with numerical simulations. Steady state, period doubling and higher order multiplication of the repetition rate as well as limit cycle and chaotic behavior were observed in the supercontinuum generating system.

Rotaviruses associate with cellular lipid droplet components to replicate in viroplasms, and compounds disrupting or blocking lipid droplets inhibit viroplasm formation and viral replication

Rotaviruses are a major cause of acute gastroenteritis in children worldwide. Early stages of rotavirus assembly in infected cells occur in viroplasms. Confocal microscopy demonstrated that viroplasms associate with lipids and proteins (perilipin A, ADRP) characteristic of lipid droplets (LDs). LD-associated proteins were also found to colocalize with viroplasms containing a rotaviral NSP5-enhanced green fluorescent protein (EGFP) fusion protein and with viroplasm-like structures in uninfected cells coexpressing viral NSP2 and NSP5. Close spatial proximity of NSP5-EGFP and cellular perilipin A was confirmed by fluorescence resonance energy transfer. Viroplasms appear to recruit LD components during the time course of rotavirus infection. NSP5-specific siRNA blocked association of perilipin A with NSP5 in viroplasms. Viral double-stranded RNA (dsRNA), NSP5, and perilipin A cosedimented in low-density gradient fractions of rotavirus-infected cell extracts. Chemical compounds interfering with LD formation (isoproterenol plus isobutylmethylxanthine; triacsin C) decreased the number of viroplasms and inhibited dsRNA replication and the production of infectious progeny virus; this effect correlated with significant protection of cells from virus-associated cytopathicity. Rotaviruses represent a genus of another virus family utilizing LD components for replication, pointing at novel therapeutic targets for these pathogens.

phi2FLIM: a technique for alias-free frequency domain fluorescence lifetime imaging

A new approach to alias-free wide-field fluorescence lifetime imaging in the frequency domain is demonstrated using a supercontinuum source for fluorescence excitation and a phase-modulated image intensifier for detection. This technique is referred to as phi-squared fluorescence lifetime imaging (phi(2)FLIM). The phase modulation and square-wave gating of the image intensifier eliminate aliasing by the effective suppression of higher harmonics. The ability to use picosecond excitation pulses without aliasing expands the range of excitation sources available for frequency-domain fluorescence lifetime imaging (fd-FLIM) and improves the modulation depth of conventional homodyne fd-FLIM measurements, which use sinusoidal intensity modulation of the excitation source. The phi(2)FLIM results are analyzed using AB-plots, which facilitate the identification of mono-exponential and multi-exponential fluorescence decays and provide measurements of the fluorophore fractions in two component mixtures. The rapid acquisition speed of the technique enables lifetime measurements in dynamic systems, such as temporally evolving samples and samples that are sensitive to photo-bleaching. Rapid phi(2)FLIM measurements are demonstrated by imaging the dynamic mixing of two different dye solutions at 5.5 Hz. The tunability of supercontinuum radiation enables excitation wavelength resolved FLIM measurements, which facilitates analysis of samples containing multiple fluorophores with different absorption spectra.

A method to unmix multiple fluorophores in microscopy images with minimal a priori information

The ability to quantify the fluorescence signals from multiply labeled biological samples is highly desirable in the life sciences but often difficult, because of spectral overlap between fluorescent species and the presence of autofluorescence. Several so called unmixing algorithms have been developed to address this problem. Here, we present a novel algorithm that combines measurements of lifetime and spectrum to achieve unmixing without a priori information on the spectral properties of the fluorophore labels. The only assumption made is that the lifetimes of the fluorophores differ. Our method combines global analysis for a measurement of lifetime distributions with singular value decomposition to recover individual fluorescence spectra. We demonstrate the technique on simulated datasets and subsequently by an experiment on a biological sample. The method is computationally efficient and straightforward to implement. Applications range from histopathology of complex and multiply labelled samples to functional imaging in live cells.

Towards multiparametric fluorescent imaging of amyloid formation: studies of a YFP model of alpha-synuclein aggregation

Misfolding and aggregation of proteins are characteristics of a range of increasingly prevalent neurodegenerative disorders including Alzheimer's and Parkinson's diseases. In Parkinson's disease and several closely related syndromes, the protein alpha-synuclein (AS) aggregates and forms amyloid-like deposits in specific regions of the brain. Fluorescence microscopy using fluorescent proteins, for instance the yellow fluorescent protein (YFP), is the method of choice to image molecular events such as protein aggregation in living organisms. The presence of a bulky fluorescent protein tag, however, may potentially affect significantly the properties of the protein of interest; for AS in particular, its relative small size and, as an intrinsically unfolded protein, its lack of defined secondary structure could challenge the usefulness of fluorescent-protein-based derivatives. Here, we subject a YFP fusion of AS to exhaustive studies in vitro designed to determine its potential as a means of probing amyloid formation in vivo. By employing a combination of biophysical and biochemical studies, we demonstrate that the conjugation of YFP does not significantly perturb the structure of AS in solution and find that the AS-YFP protein forms amyloid deposits in vitro that are essentially identical with those observed for wild-type AS, except that they are fluorescent. Of the several fluorescent properties of the YFP chimera that were assayed, we find that fluorescence anisotropy is a particularly useful parameter to follow the aggregation of AS-YFP, because of energy migration Förster resonance energy transfer (emFRET or homoFRET) between closely positioned YFP moieties occurring as a result of the high density of the fluorophore within the amyloid species. Fluorescence anisotropy imaging microscopy further demonstrates the ability of homoFRET to distinguish between soluble, pre-fibrillar aggregates and amyloid fibrils of AS-YFP. Our results validate the use of fluorescent protein chimeras of AS as representative models for studying protein aggregation and offer new opportunities for the investigation of amyloid aggregation in vivo using YFP-tagged proteins.

Temporally resolved fluorescence spectroscopy of a microarray-based vapor sensing system

This paper describes a method to measure the complete fluorescence spectrum from numerous fluorescent microspheres in a microarray simultaneously during exposure to a vapor. The technique, called spectrally resolved sensor imaging (SRSI), positions a transmission grating directly in front of the microscope objective on a standard epi-fluorescence microscope. This modification produces a hybrid image on the CCD camera that contains a conventional fluorescence image in the zero-order diffracted light and a fluorescence spectral image in the first-order diffracted light. Three types of surface-functionalized silica microspheres were coated with a solvatochromic dye. The surface functionality on the microspheres influences the maximum emission wavelength of the dye and generates a fluorescence spectral signature that is used to identify each sensor type. These sensors were randomly distributed into a photolithographically fabricated microarray platform, and the spectral signature of each individual sensor was measured. The time resolution of spectral acquisition is short enough to capture dynamic changes in the fluorescence emission as a vapor is presented to the array. The ability to measure the entire fluorescence spectrum from each sensor simultaneously during a vapor exposure increases the dimensionality of the response data and significantly improves the classification accuracy of the system.

Ultraviolet-visible non-supercontinuum ultrafast source enabled by switching single silicon strand-like photonic crystal fibers

Cherenkov radiation from short photonic crystal fiber with a high air-fill fraction can selectively convert the 1020 nm fs pump pulses from a laser oscillator to the fundamental-mode signal pulses at a significantly shorter wavelength. Across the ultraviolet-visible spectral region, the typical fiber output is characterized by a single isolated Cherenkov band having a multimilliwatt-level average power, a Gaussian-shaped spectrum, and a 3-dB bandwidth of 15 nm. By selecting photonic crystal fibers with smaller cores, the central wavelength of the Cherenkov band can be easily extended to 347 nm in the ultraviolet, in sharp contrast to various supercontinuum or non-supercontinuum fiber sources that have difficulty extending their emission spectra below 400 nm. The supercontinuum generation often associated with fs pulse-pumped fibers is efficiently suppressed by detuning the zero-dispersion wavelength of the photonic crystal fiber far shorter than the pump wavelength, a condition termed as the short nonlinear-interaction condition.