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

Separation of spectrally overlapping fluorophores using intra-exposure excitation modulation

Multicolor fluorescence imaging is an excellent method for the simultaneous visualization of multiple structures, although it is limited by the available spectral window. More labels can be measured by distinguishing these on properties, such as their fluorescence dynamics, but usually these dynamics must be directly resolvable by the instrument. We propose an approach to distinguish emitters over a much broader range of light-induced dynamics by combining fast modulation of the light source with the detection of the time-integrated fluorescence. We demonstrate our method by distinguishing four spectrally overlapping photochromic fluorophores within Escherichia coli bacteria, showing that we can accurately classify all four probes by acquiring just two to four fluorescence images. Our strategy expands the range of probes and processes that can be used for fluorescence multiplexing.

Two-photon fluorescence and second harmonic generation hyperspectral imaging of old and modern spruce woods

Spruce is the commonly-used tonewood for the top plate of violin-family instruments, such as violins and cellos. The wood properties can critically determine the acoustic quality. It's been shown the wood of famous old instruments differ from modern ones due to chemical treatment and aging. To reveal the differences microscopically in both spatial and spectral domains, a two-photon hyperspectral system has been applied to investigate the autofluorescence and second harmonic generation within wood samples. Not only the cellular structures were observed through optical sectioning, but the spectral variations were revealed among different age wood samples and different cellular structures.

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.

Line-scanning hyperspectral imaging based on structured illumination optical sectioning

Line-scanning hyperspectral imaging (LHSI) is known to have a higher acquisition rate but lower sectioning capability than point-scanning hyperspectral imaging. To further increase the axial imaging contrast of LHSI, structured illumination was integrated into line excitation to remove the off-focus and scattered on-focus fluorescence signals. In an unsectioned leaf, the imaging contrast can be enhanced by 8 times, while in sectioned mouse skin tissues, a 4.5-fold enhancement can be achieved. With a spectral resolution of 1.15 nm, the fluorophores with seriously-overlapped spectra was proved to be separated without cross-talk by applying linear unmixing to the recorded spectral information.

Fast and simple spectral FLIM for biochemical and medical imaging

Spectrally resolved fluorescence lifetime imaging microscopy (λFLIM) has powerful potential for biochemical and medical imaging applications. However, long acquisition times, low spectral resolution and complexity of λFLIM often narrow its use to specialized laboratories. Therefore, we demonstrate here a simple spectral FLIM based on a solid-state detector array providing in-pixel histrogramming and delivering faster acquisition, larger dynamic range, and higher spectral elements than state-of-the-art λFLIM. We successfully apply this novel microscopy system to biochemical and medical imaging demonstrating that solid-state detectors are a key strategic technology to enable complex assays in biomedical laboratories and the clinic.

Attenuation-corrected fluorescence spectra unmixing for spectroscopy and microscopy

In fluorescence measurements, light is often absorbed and scattered by a sample both for excitation and emission, resulting in the measured spectra to be distorted. Conventional linear unmixing methods computationally separate overlapping spectra but do not account for these effects. We propose a new algorithm for fluorescence unmixing that accounts for the attenuation-related distortion effect on fluorescence spectra. Using a matrix representation, we derive forward measurement formation and a corresponding inverse method; the unmixing algorithm is based on nonnegative matrix factorization. We also demonstrate how this method can be extended to a higher-dimensional tensor form, which is useful for unmixing overlapping spectra observed under the attenuation effect in spectral imaging microscopy. We evaluate the proposed methods in simulation and experiments and show that it outperforms a conventional, linear unmixing method when absorption and scattering contributes to the measured signals, as in deep tissue imaging.

Non-de-scanned parallel recording two-photon hyperspectral microscopy with high spectral and spatial resolution

A two-photon hyperspectral microscope with non-de-scanned geometry and parallel recording scheme was constructed which had a low dwell time, high spectral resolution, and high spatial resolution. The dwell time was effectively decreased to reduce photodamage through parallel recording, while the non-de-scanned geometry led to a considerable reduction in the signal loss and spectrum distortion. Two experiments were performed to show that this system can solve crosstalk issues and spectrally resolve the intrinsic fluorophores in optically-thick tissues without staining and sectioning.

High speed multispectral fluorescence lifetime imaging

We report a spectrally resolved fluorescence lifetime imaging system based on time gated single photon detection with a fixed gate width of 200 ps and 7 spectral channels. Time gated systems can operate at high count rates but usually have large gate widths and sample only part of the fluorescence decay curve. In the system presented in this work, the fluorescence signal is sampled using a high speed transceiver. An error analysis is carried out to characterize the performance of both lifetime and spectral detection. The effect of gate width and spectral channel width on the accuracy of estimated lifetimes and spectral widths is described. The performance of the whole instrument is evaluated at count rates of up to 12 MHz. Accurate fluorescence lifetimes (error < 2%) are recorded at count rates as high as 5 MHz. This is limited by the PMT performance, not by the electronics. Analysis of the large spectral lifetime image sets is challenging and time-consuming. Here, we demonstrate the use of lifetime and spectral phasors for analyzing images of fibroblast cells with 2 different labeled components. The phasor approach provides a fast and intuitive way of analyzing the results of spectrally resolved fluorescence lifetime imaging experiments.

A fully constrained optimization method for time-resolved multispectral fluorescence lifetime imaging microscopy data unmixing

This paper presents a new unmixing methodology of multispectral fluorescence lifetime imaging microscopy (m-FLIM) data, in which the spectrum is defined as the combination of time-domain fluorescence decays at multiple emission wavelengths. The method is based on a quadratic constrained optimization (CO) algorithm that provides a closed-form solution under equality and inequality restrictions. In this paper, it is assumed that the time-resolved fluorescence spectrum profiles of the constituent components are linearly independent and known a priori. For comparison purposes, the standard least squares (LS) solution and two constrained versions nonnegativity constrained least squares (NCLS) and fully constrained least squares (FCLS) (Heinz and Chang, 2001) are also tested. Their performance was evaluated by using synthetic simulations, as well as imaged samples from fluorescent dyes and ex vivo tissue. In all the synthetic evaluations, the CO obtained the best accuracy in the estimations of the proportional contributions. CO could achieve an improvement ranging between 41% and 59% in the relative error compared to LS, NCLS, and FCLS at different signal-to-noise ratios. A liquid mixture of fluorescent dyes was also prepared and imaged in order to provide a controlled scenario with real data, where CO and FCLS obtained the best performance. The CO and FCLS were also tested with 20 ex vivo samples of human coronary arteries, where the expected concentrations are qualitatively known. A certainty measure was employed to assess the confidence in the estimations made by each algorithm. The experiments confirmed a better performance of CO, since this method is optimal with respect to equality and inequality restrictions in the linear unmixing formulation. Thus, the evaluation showed that CO achieves an accurate characterization of the samples. Furthermore, CO is a computational efficient alternative to estimate the abundance of components in m-FLIM data, since a global optimal solution is always guaranteed in a closed form.

Application of non-negative matrix factorization to multispectral FLIM data analysis

Existing methods of interpreting fluorescence lifetime imaging microscopy (FLIM) images are based on comparing the intensity and lifetime values at each pixel with those of known fluorophores. This method becomes unwieldy and subjective in many practical applications where there are several fluorescing species contributing to the bulk fluorescence signal, and even more so in the case of multispectral FLIM. Non-negative matrix factorization (NMF) is a multivariate data analysis technique aimed at extracting non-negative signatures of pure components and their non-negative abundances from an additive mixture of those components. In this paper, we present the application of NMF to multispectral time-domain FLIM data to obtain a new set of FLIM features (relative abundance of constituent fluorophores). These features are more intuitive and easier to interpret than the standard fluorescence intensity and lifetime values. The proposed approach, unlike several FLIM data analysis methods, is not limited by the number of constituent fluorescing species or their possibly complex decay dynamics. Moreover, the new set of FLIM features can be obtained by processing raw multispectral FLIM intensity data, thereby rendering time deconvolution unnecessary and resulting in lesser computational time and relaxed SNR requirements. The performance of the NMF method was validated on simulated and experimental multispectral time-domain FLIM data. The NMF features were also compared against the standard intensity and lifetime features, in terms of their ability to discriminate between different types of atherosclerotic plaques.

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.

Spectral resolution in conjunction with polar plots improves the accuracy and reliability of FLIM measurements and estimates of FRET efficiency

A spectrograph with continuous wavelength resolution has been integrated into a frequency-domain fluorescence lifetime-resolved imaging microscope (FLIM). The spectral information assists in the separation of multiple lifetime components, and helps resolve signal cross-talking that can interfere with an accurate analysis of multiple lifetime processes. This extends the number of different dyes that can be measured simultaneously in a FLIM measurement. Spectrally resolved FLIM (spectral-FLIM) also provides a means to measure more accurately the lifetime of a dim fluorescence component (as low as 2% of the total intensity) in the presence of another fluorescence component with a much higher intensity. A more reliable separation of the donor and acceptor fluorescence signals are possible for Förster resonance energy transfer (FRET) measurements; this allows more accurate determinations of both donor and acceptor lifetimes. By combining the polar plot analysis with spectral-FLIM data, the spectral dispersion of the acceptor signal can be used to derive the donor lifetime - and thereby the FRET efficiency - without iterative fitting. The lifetime relation between the donor and acceptor, in conjunction with spectral dispersion, is also used to separate the FRET pair signals from the donor alone signal. This method can be applied further to quantify the signals from separate FRET pairs, and provide information on the dynamics of the FRET pair between different states.

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.

Two-photon spectral imaging with high temporal and spectral resolution

We introduce a fast spectral imaging system using an electron-multiplying charge-coupled device (EM-CCD) as a detector. Our system is combined with a custom-built two-photon excitation laser scanning microscope and has 80 detection channels, which allow for high spectral resolution and fast frame acquisition without any loss of spectral information. To demonstrate the efficiency of our approach, we applied this technology to monitor fluorescent proteins and quantum dot-labeled G protein-coupled receptors in living cells as well as autofluorescence in tissue samples.

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.