Theoretical investigation of the photon efficiency in frequency-domain fluorescence lifetime imaging microscopy

Use of nanosecond excitation pulses in fluorescence lifetime measurement via phasor analysis

We investigated the possibility of using long excitation pulses in fluorescence lifetime imaging microscopy (FLIM) using phasor analysis. It has long been believed that the pulse width of an excitation laser must be shorter than the lifetime of a fluorophore in a time-domain FLIM system. Even though phasor analysis can effectively minimize the pulse effect by using deconvolution, the precision of a measured lifetime can be degraded seriously. Here, we provide a fundamental theory on pulse-width-dependent measurement precisions in lifetime measurement in the phasor plane. Our theory predicts that high-precision lifetimes can be obtained even with a laser whose pulse width is four times larger than the lifetime of a fluorophore. We have experimentally demonstrated this by measuring the lifetimes of fluorescence probes with 2.57 ns and 3.75 ns lifetimes by using various pulse widths (0.52-38 ns) and modulation frequencies (10-200 MHz). We believe our results open a new possibility of using long pulse-width lasers for high-precision FLIM.

Fourier Multiplexed Fluorescence Lifetime Imaging

Fluorescence lifetime imaging microscopy (FLIM) is a widely used functional imaging method in bioscience. Fourier multiplexed FLIM (FmFLIM), a frequency-domain lifetime measurement method, explores the principle of Fourier (frequency) multiplexing to achieve parallel lifetime detection on multiple fluorescence labels. Combining FmFLIM with a confocal scanning microscope allows multiplexed 3D lifetime imaging of cells and tissues. FmFLIM can also be integrated with the scanning laser tomography imaging method to perform 3D multiplex lifetime imaging of whole embryos and thick tissues.

Direct Photon-by-Photon Analysis of Time-Resolved Pulsed Excitation Data using Bayesian Nonparametrics

Lifetimes of chemical species are typically estimated by either fitting time-correlated single-photon counting (TCSPC) histograms or phasor analysis from time-resolved photon arrivals. While both methods yield lifetimes in a computationally efficient manner, their performance is limited by choices made on the number of distinct chemical species contributing photons. However, the number of species is encoded in the photon arrival times collected for each illuminated spot and need not be set by hand a priori. Here, we propose a direct photon-by-photon analysis of data drawn from pulsed excitation experiments to infer, simultaneously and self-consistently, the number of species and their associated lifetimes from a few thousand photons. We do so by leveraging new mathematical tools within the Bayesian nonparametric. We benchmark our method for both simulated and experimental data for 1-4 species.

How many photons are needed for FRET imaging?

Förster resonance energy transfer (FRET) imaging is an essential analytical method in biomedical research. The limited photon-budget experimentally available, however, imposes compromises between spatiotemporal and biochemical resolutions, photodamage and phototoxicity. The study of photon-statistics in biochemical imaging is thus important in guiding the efficient design of instrumentation and assays. Here, we show a comparative analysis of photon-statistics in FRET imaging demonstrating how the precision of FRET imaging varies vastly with imaging parameters. Therefore, we provide analytical and numerical tools for assay optimization. Fluorescence lifetime imaging microscopy (FLIM) is a very robust technique with excellent photon-efficiencies. However, we show that also intensity-based FRET imaging can reach high precision by utilizing information from both donor and acceptor fluorophores.

Reference-independent wide field fluorescence lifetime measurements using Frequency-Domain (FD) technique based on phase and amplitude crossing point

Fluorescence lifetime imaging microscopy (FLIM) is an essential tool in many scientific fields such as biology and medicine thanks to the known advantages of the fluorescence lifetime (FLT) over the classical fluorescence intensity (FI). However, the frequency domain (FD) FLIM technique suffers from its strong dependence on the reference and its compliance to the sample. In this paper, we suggest a new way to calculate the FLT by using the crossing point (CRPO) between the modulation and phase FLTs measured over several light emitting diode (LED) DC currents values instead of either method alone. This new technique was validated by measuring homogeneous substances with known FLT, where the CRPO appears to be the optimal measuring point. Furthermore, the CRPO method was applied in heterogeneous samples. It was found that the CRPO in known mixed solutions is the weighted average of the used solutions. While measuring B16 and lymphocyte cells, the CRPO of the DAPI compound in single FLT regions was measured at 3.5 ± 0.06 ns and at 2.83 ± 0.07 ns, respectively, both of which match previous reports and multi-frequency analyses. This paper suggests the CRPO as a new method to extract the FLT in problematic cases such as high MCP gains and heterogeneous environments. In traditional FD FLIM measurements, the variation in phase angle and modulation are measured. By measuring over varying DC currents, another variation is detected in the FLT determined through the phase and modulation methods, with the CRPO indicating the true FLT.

Multidie LED combined with homogenizing optics to improve frequency response and intensity for FLIM applications

Application of light-emitting diodes (LEDs) in frequency-domain fluorescence lifetime imaging microscopy (FLIM) has been limited by the trade-off between modulation frequency and illumination intensity of LEDs, which affects the signal-to-noise ratio in fluorescence lifetime measurements. To increase modulation frequency without sacrificing output power of LEDs, we propose to use LEDs with multiple dice connected in series. The LED capacitance was reduced with series connection; therefore, the frequency response of multidie LED was significantly increased. LEDs in visible light, including blue, green, amber and red, were all applicable in FLIM. We also present a homogenizing optics design, so that multidie LEDs produced uniform illumination on the same focal spot. When the homogenizing optics was combined with multicolour emitters, it provides multiple colour selection in a compact and convenient design.

Investigation of signal-to-noise ratio in frequency-domain multiphoton fluorescence lifetime imaging microscopy

Multiphoton microscopy (MPM) combined with fluorescence lifetime imaging microscopy (FLIM) has enabled three-dimensional quantitative molecular microscopy in vivo. The signal-to-noise ratio (SNR), and thus the imaging rate of MPM-FLIM, which is fundamentally limited by the shot noise and fluorescence saturation, has not been quantitatively studied yet. In this paper, we investigate the SNR performance of the frequency-domain (FD) MPM-FLIM with two figures of merit: the photon economy in the limit of shot noise, and the normalized SNR in the limit of saturation. The theoretical results and Monte Carlo simulations find that two-photon FD-FLIM requires 50% fewer photons to achieve the same SNR as conventional one-photon FLIM. We also analytically show that the MPM-FD-FLIM can exploit the DC and higher harmonic components generated by nonlinear optical mixing of the excitation light to improve SNR, reducing the required number of photons by an additional 50%. Finally, the effect of fluorophore saturation on the experimental SNR performance is discussed.

Modulated CMOS camera for fluorescence lifetime microscopy

Widefield frequency-domain fluorescence lifetime imaging microscopy (FD-FLIM) is a fast and accurate method to measure the fluorescence lifetime of entire images. However, the complexity and high costs involved in construction of such a system limit the extensive use of this technique. PCO AG recently released the first luminescence lifetime imaging camera based on a high frequency modulated CMOS image sensor, QMFLIM2. Here we tested and provide operational procedures to calibrate the camera and to improve the accuracy using corrections necessary for image analysis. With its flexible input/output options, we are able to use a modulated laser diode or a 20 MHz pulsed white supercontinuum laser as the light source. The output of the camera consists of a stack of modulated images that can be analyzed by the SimFCS software using the phasor approach. The nonuniform system response across the image sensor must be calibrated at the pixel level. This pixel calibration is crucial and needed for every camera settings, e.g. modulation frequency and exposure time. A significant dependency of the modulation signal on the intensity was also observed and hence an additional calibration is needed for each pixel depending on the pixel intensity level. These corrections are important not only for the fundamental frequency, but also for the higher harmonics when using the pulsed supercontinuum laser. With these post data acquisition corrections, the PCO CMOS-FLIM camera can be used for various biomedical applications requiring a large frame and high speed acquisition.

FPGA-based multi-channel fluorescence lifetime analysis of Fourier multiplexed frequency-sweeping lifetime imaging

We report a fast non-iterative lifetime data analysis method for the Fourier multiplexed frequency-sweeping confocal FLIM (Fm-FLIM) system [Opt. Express 22, 10221 (2014)]. The new method, named R-method, allows fast multi-channel lifetime image analysis in the system's FPGA data processing board. Experimental tests proved that the performance of the R-method is equivalent to that of single-exponential iterative fitting, and its sensitivity is well suited for time-lapse FLIM-FRET imaging of live cells, for example cyclic adenosine monophosphate (cAMP) level imaging with GFP-Epac-mCherry sensors. With the R-method and its FPGA implementation, multi-channel lifetime images can now be generated in real time on the multi-channel frequency-sweeping FLIM system, and live readout of FRET sensors can be performed during time-lapse imaging.

Analyzing receptor assemblies in the cell membrane using fluorescence anisotropy imaging with TIRF microscopy

Signaling within and between animal cells is controlled by the many receptor proteins in their membrane. They variously operate as trans-membrane monomers and homo- or hetero-dimers, and may assemble with ion-channels: analyses thereof are needed in studies of receptor actions in tissue physiology and pathology. Interactions between membrane proteins are detectable when pre-labeled with fluorophores, but a much fuller analysis is achievable via advanced optical techniques on living cells. In this context, the measurement of polarization anisotropy in the emitted fluorescence has been the least exploited. Here we demonstrate its methodology and particular advantages in the study of receptor protein assembly. Through excitation in both TIRF and EPI fluorescence illumination modes we are able to quantify and suppress contributions to the signal from extraneous intra-cellular fluorescence, and we show that the loss of fluorescence-polarization measured in membrane proteins reports on receptor protein assembly in real time. Receptor monomers and homo-dimers in the cell membrane can be analyzed quantitatively and for homo-dimers only a single fluorescent marker is needed, thus suppressing ambiguities that arise in alternative assays, which require multiple label moieties and which are thus subject to stoichiometric uncertainty.

Parallel excitation-emission multiplexed fluorescence lifetime confocal microscopy for live cell imaging

We present a novel excitation-emission multiplexed fluorescence lifetime microscopy (FLIM) method that surpasses current FLIM techniques in multiplexing capability. The method employs Fourier multiplexing to simultaneously acquire confocal fluorescence lifetime images of multiple excitation wavelength and emission color combinations at 44,000 pixels/sec. The system is built with low-cost CW laser sources and standard PMTs with versatile spectral configuration, which can be implemented as an add-on to commercial confocal microscopes. The Fourier lifetime confocal method allows fast multiplexed FLIM imaging, which makes it possible to monitor multiple biological processes in live cells. The low cost and compatibility with commercial systems could also make multiplexed FLIM more accessible to biological research community.

A practical implementation of multifrequency widefield frequency-domain fluorescence lifetime imaging microscopy

Widefield frequency-domain fluorescence lifetime imaging microscopy (FD-FLIM) is a fast and accurate method to measure the fluorescence lifetime, especially in kinetic studies in biomedical researches. However, the small range of modulation frequencies available in commercial instruments makes this technique limited in its applications. Herein, we describe a practical implementation of multifrequency widefield FD-FLIM using a pulsed supercontinuum laser and a direct digital synthesizer. In this instrument we use a pulse to modulate the image intensifier rather than the more conventional sine-wave modulation. This allows parallel multifrequency FLIM measurement using the Fast Fourier Transform and the cross-correlation technique, which permits precise and simultaneous isolation of individual frequencies. In addition, the pulse modulation at the cathode of image intensifier restores the loss of optical resolution caused by the defocusing effect when the cathode is sinusoidally modulated. Furthermore, in our implementation of this technique, data can be graphically analyzed by the phasor method while data are acquired, which allows easy fit-free lifetime analysis of FLIM images. Here, our measurements of standard fluorescent samples and a Föster resonance energy transfer pair demonstrate that the widefield multifrequency FLIM system is a valuable and simple tool in fluorescence imaging studies.

Single-laser shot fluorescence lifetime imaging on the nanosecond timescale using a Dual Image and Modeling Evaluation algorithm

A novel technique, designated dual imaging and modeling evaluation (DIME), for evaluating single-laser shot fluorescence lifetimes is presented. The technique is experimentally verified in a generic gas mixing experiment to provide a clear demonstration of the rapidness and sensitivity of the detector scheme. Single-laser shot fluorescence lifetimes of roughly 800 ps with a standard deviation of ~120 ps were determined. These results were compared to streak camera measurements. Furthermore, a general fluorescence lifetime determination algorithm is proposed. The evaluation algorithm has an analytic, linear relationship between the fluorescence lifetime and detector signal ratio. In combination with the DIME detector scheme, it is a faster, more accurate and more sensitive approach for rapid fluorescence lifetime imaging than previously proposed techniques. Monte Carlo simulations were conducted to analyze the sensitivity of the detector scheme as well as to compare the proposed evaluation algorithm to previously presented rapid lifetime determination algorithms.

Effect of noise on modulation amplitude and phase in frequency-domain diffusive imaging

We theoretically investigate the effect of noise on frequency-domain heterodyne and/or homodyne measurements of intensity-modulated beams propagating through diffusive media, such as a photon density wave. We assumed that the attenuated amplitude and delayed phase are estimated by taking the Fourier transform of the noisy, modulated output data. We show that the estimated amplitude and phase are biased when the number of output photons is small. We also show that the use of image intensifiers for photon amplification in heterodyne or homodyne measurements increases the amount of biases. Especially, it turns out that the biased estimation is independent of AC-dependent noise in sinusoidal heterodyne or homodyne outputs. Finally, the developed theory indicates that the previously known variance model of modulation amplitude and phase is not valid in low light situations. Monte-Carlo simulations with varied numbers of input photons verify our theoretical trends of the bias.

Noise characteristics of heterodyne/homodyne frequency-domain measurements

We theoretically develop and experimentally validate the noise characteristics of heterodyne and/or homodyne measurements that are widely used in frequency-domain diffusive imaging. The mean and covariance of the modulated heterodyne output are derived by adapting the random amplification of a temporal point process. A multinomial selection rule is applied to the result of the temporal noise analysis to additionally model the spatial distribution of intensified photons measured by a charge-coupled device (CCD), which shows that the photon detection efficiency of CCD pixels plays an important role in the noise property of detected photons. The approach of using a multinomial probability law is validated from experimental results. Also, experimentally measured characteristics of means and variances of homodyne outputs are in agreement with the developed theory. The developed noise model can be applied to all photon amplification processes.

Three-dimensional Fluorescence Lifetime Imaging with a Single Plane Illumination Microscope provides an improved signal to noise ratio

We designed a widefield frequency domain Fluorescence Lifetime Imaging Microscopy (FLIM)setup, which is based on a Single Plane Illumination Microscope (SPIM). A SPIM provides an inherent optical sectioning capability and reduces photobleaching compared to conventional widefield and confocal fluorescence microscopes. The lifetime precision of the FLIM was characterized with Rhodamine 6G solutions of different quencher concentrations [KI]. We demonstrate the high spatial resolution of the SPIM-FLIM combination in the intensity domain as well as in the lifetime domain with latex bead samples and multiple recordings of three-dimensional live Madine-Darby Canine Kidney (MDCK) cysts. We estimate that the bleaching rate after 600 images have been recorded is below 5%.

Photon budget analysis for fluorescence lifetime imaging microscopy

We have constructed a mathematical model to analyze the photon efficiency of frequency-domain fluorescence lifetime imaging microscopy (FLIM). The power of the light source needed for illumination in a FLIM system and the signal-to-noise ratio of the detector have led us to a photon "budget." These measures are relevant to many fluorescence microscope users and the results are not restricted to FLIM but applicable to widefield fluorescence microscopy in general. Limitations in photon numbers, however, are more of an issue with FLIM compared to other less quantitative types of imaging. By modeling a typical experimental configuration, examples are given for fluorophores whose absorption peaks span the visible spectrum from Fura-2 to Cy5. We have performed experiments to validate the assumptions and parameters used in our mathematical model. The influence of fluorophore concentration on the intensity of the fluorescence emission light and the Poisson distribution assumption of the detected fluorescence emission light have been validated. The experimental results agree well with the mathematical model. This photon budget is important in order to characterize the constraints involved in current fluorescent microscope systems that are used for lifetime as well as intensity measurements and to design and fabricate new systems.

Multiplexed fluorescence lifetime measurements by frequency-sweeping Fourier spectroscopy

We report simultaneous measurements of fluorescence lifetimes at multiple excitation wavelengths with a Fourier transform frequency domain fluorescence lifetime spectrometer. The spectrometer uses a Michelson interferometer with its differential optical path length scanning at a 22,000 Hz scan rate. The scan speed of the optical delay varies linearly during each scan and creates interference modulations that sweep from -150 to 150 MHz in 45.5 micros. The frequency-sweeping modulation allows nanosecond fluorescence lifetime measurements within 45.5 micros. Because the interference modulation frequency is wavelength dependent, under the Fourier multiplexing principle, the spectrometer can perform lifetime measurements on multiple excitation wavelengths simultaneously.

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.

mhFLIM: resolution of heterogeneous fluorescence decays in widefield lifetime microscopy

Frequency-domain fluorescence lifetime imaging microscopy (FD-FLIM) is a fast and accurate way of measuring fluorescence lifetimes in widefield microscopy. However, the resolution of multiple exponential fluorescence decays has remained beyond the reach of most practical FD-FLIM systems. In this paper we describe the implementation of FD-FLIM using a 40 MHz pulse train derived from a supercontinuum source for excitation. The technique, which we term multi-harmonic FLIM (mhFLIM), makes it possible to accurately resolve biexponential decays of fluorophores without any a priori information. The system's performance is demonstrated using a mixture of spectrally similar dyes of known composition and also on a multiply-labeled biological sample. The results are compared to those obtained from time correlated single photon counting (TCSPC) microscopy and a good level of agreement is achieved. We also demonstrate the first practical application of an algorithm derived by G. Weber [1] for analysing mhFLIM data. Because it does not require nonlinear minimisation, it offers potential for realtime analysis during acquisition.