Instrumental, optical and geometrical parameters affecting time-gated diffuse optical measurements: a systematic study

In time-domain diffuse optics the sensitivity to localized absorption changes buried inside a diffusive medium depends strongly on the interplay between instrumental, optical and geometrical parameters, which can hinder the theoretical advantages of novel measurement strategies like the short source-detector distance approach. Here, we present a study based on experimental measurements and simulations to comprehensively evaluate the effect of all different parameters. Results are evaluated exploiting standardized figures of merit, like contrast and contrast-to-noise ratio, to quantify the system sensitivity to deep localized absorption perturbations. Key findings show that the most critical hardware parameter is the memory effect which ultimately limits the dynamic range. Further, a choice of the source-detector distance around 10 mm seems to be a good compromise to compensate non-idealities in practical systems still preserving the advantages of short distances. This work provides both indications for users about the best measurement conditions and strategies, and for technology developers to identify the most crucial hardware features in view of next generation diffuse optics systems.

Single-shot ultrafast optical imaging

Single-shot ultrafast optical imaging can capture two-dimensional transient scenes in the optical spectral range at ≥100 million frames per second. This rapidly evolving field surpasses conventional pump-probe methods by possessing the real-time imaging capability, which is indispensable for recording non-repeatable and difficult-to-reproduce events and for understanding physical, chemical, and biological mechanisms. In this mini-review, we survey comprehensively the state-of-the-art single-shot ultrafast optical imaging. Based on the illumination requirement, we categorized the field into active-detection and passive-detection domains. Depending on the specific image acquisition and reconstruction strategies, these two categories are further divided into a total of six sub-categories. Under each sub-category, we describe operating principles, present representative cutting-edge techniques with a particular emphasis on their methodology and applications, and discuss their advantages and challenges. Finally, we envision prospects of technical advancement in this field.

Multi-beam scan analysis with a clinical LINAC for high resolution Cherenkov-excited molecular luminescence imaging in tissue

Cherenkov-excited luminescence scanned imaging (CELSI) is achieved with external beam radiotherapy to map out molecular luminescence intensity or lifetime in tissue. Just as in fluorescence microscopy, the choice of excitation geometry can affect the imaging time, spatial resolution and contrast recovered. In this study, the use of spatially patterned illumination was systematically studied comparing scan shapes, starting with line scan and block patterns and increasing from single beams to multiple parallel beams and then to clinically used treatment plans for radiation therapy. The image recovery was improved by a spatial-temporal modulation-demodulation method, which used the ability to capture simultaneous images of the excitation Cherenkov beam shape to deconvolve the CELSI images. Experimental studies used the multi-leaf collimator on a clinical linear accelerator (LINAC) to create the scanning patterns, and image resolution and contrast recovery were tested at different depths of tissue phantom material. As hypothesized, the smallest illumination squares achieved optimal resolution, but at the cost of lower signal and slower imaging time. Having larger excitation blocks provided superior signal but at the cost of increased radiation dose and lower resolution. Increasing the scan beams to multiple block patterns improved the performance in terms of image fidelity, lower radiation dose and faster acquisition. The spatial resolution was mostly dependent upon pixel area with an optimized side length near 38mm and a beam scan pitch of P = 0.33, and the achievable imaging depth was increased from 14mm to 18mm with sufficient resolving power for 1mm sized test objects. As a proof-of-concept, in-vivo tumor mouse imaging was performed to show 3D rendering and quantification of tissue pO2 with values of 5.6mmHg in a tumor and 77mmHg in normal tissue.

Label-free assessment of carotid artery biochemical composition using fiber-based fluorescence lifetime imaging

Novel diagnostic tools with the ability to monitor variations in biochemical composition and provide benchmark indicators of vascular tissue maturation are needed to create functional tissue replacements. We investigated the ability of fiber-based, label-free multispectral fluorescent lifetime imaging (FLIm) to quantify the anatomical variations in biochemical composition of native carotid arteries and validated these results against biochemical assays. FLIm-derived parameters in spectral band 415-455 nm correlated with tissue collagen content (R² = 0.64) and cell number (R² = 0.61) and in spectral band 465-553 nm strongly correlated with elastin content (R² = 0.89). These results suggest that FLIm holds great potential for assessing vascular tissue maturation and functional properties based on tissue autofluorescence.

Multiwavelength time-resolved near-infrared spectroscopy of the adult head: assessment of intracerebral and extracerebral absorption changes

An optical technique based on diffuse reflectance measurement combined with indocyanine green (ICG) bolus tracking is extensively tested as a method for the clinical assessment of brain perfusion at the bedside. We report on multiwavelength time-resolved diffuse reflectance spectroscopy measurements carried out on the head of a healthy adult during the intravenous administration of a bolus of ICG. Intracerebral and extracerebral changes in absorption were estimated from an analysis of changes in statistical moments (total number of photons, mean time of flight and variance) of the distributions of times of flight (DTOF) of photons recorded simultaneously at 16 wavelengths from the range of 650-850 nm using sensitivity factors estimated by diffusion approximation based on a layered model of the studied medium. We validated the proposed method in a series of phantom experiments and in-vivo measurements. The results obtained show that changes in the concentration of the ICG can be assessed as a function of time of the experiment and depth in the tissue. Thus, the separation of changes in ICG concentration appearing in intra- and extracerebral tissues can be estimated from optical data acquired at a single source-detector pair of fibers/fiber bundles positioned on the surface of the head.

A spread spectrum approach to time-domain near-infrared diffuse optical imaging using inexpensive optical transceiver modules

We introduce a compact time-domain system for near-infrared spectroscopy using a spread spectrum technique. The proof-of-concept single channel instrument utilises a low-cost commercially available optical transceiver module as a light source, controlled by a Kintex 7 field programmable gate array (FPGA). The FPGA modulates the optical transceiver with maximum-length sequences at line rates up to 10Gb/s, allowing us to achieve an instrument response function with full width at half maximum under 600ps. The instrument is characterised through a set of detailed phantom measurements as well as proof-of-concept in vivo measurements, demonstrating performance comparable with conventional pulsed time-domain near-infrared spectroscopy systems.

Tomographic fluorescence lifetime multiplexing in the spatial frequency domain

The ability to simultaneously recover multiple fluorophores within biological tissue (multiplexing) can have important applications for tracking parallel disease processes in vivo. Here we present a novel method for rapid and quantitative multiplexing within a scattering medium, such as biological tissue, based on fluorescence lifetime contrast. This method employs a tomographic inversion of the asymptotic (late) portion of time-resolved spatial frequency (SF) domain measurements. Using Monte Carlo simulations and phantom experiments, we show that the SF-asymptotic time domain (SF-ATD) approach provides a several-fold improvement in relative quantitation and localization accuracy over conventional SF-time domain inversion. We also show that the SF-ATD approach can exploit selective filtering of high spatial frequencies to dramatically improve reconstruction accuracy for fluorophores with subnanosecond lifetimes, which is typical of most near-infrared fluorophores. These results suggest that the SF-ATD approach will serve as a powerful new tool for whole-body lifetime multiplexing.

High throughput detection chain for time domain optical mammography

A novel detection chain, based on 8 Silicon Photomultipliers (forming a wide-area custom-made detection probe) and on a time-to-digital converter, was developed to improve the signal level in multi-wavelength (635-1060 nm) time domain optical mammography. The performances of individual components and of the overall chain were assessed using established protocols (BIP and MEDPHOT). The photon detection efficiency was improved by up to 3 orders of magnitude, and the maximum count rate level was increased by a factor of 10 when compared to the previous system, based on photomultiplier tubes and conventional time-correlated single-photon counting boards. In the estimate of optical parameters, the novel detection chain provides performances comparable to the previous system, widely validated in clinics, but with higher signal level, higher robustness, and at a lower price per channel, thus targeting important requirements for clinical applications.

Towards two-photon excited endogenous fluorescence lifetime imaging microendoscopy

In situ fluorescence lifetime imaging microscopy (FLIM) in an endoscopic configuration of the endogenous biomarker nicotinamide adenine dinucleotide (NADH) has a great potential for malignant tissue diagnosis. Moreover, two-photon nonlinear excitation provides intrinsic optical sectioning along with enhanced imaging depth. We demonstrate, for the first time to our knowledge, nonlinear endogenous FLIM in a fibered microscope with proximal detection, applied to NADH in cultured cells, as a first step to a nonlinear endomicroscope, using a double-clad microstructured fiber with convenient fiber length (> 3 m) and excitation pulse duration (≈50 fs). Fluorescence photons are collected by the fiber inner cladding and we show that its contribution to the impulse response function (IRF), which originates from its intermodal and chromatic dispersions, is small (< 600 ps) and stable for lengths up to 8 m and allows for short lifetime measurements. We use the phasor representation as a quick visualization tool adapted to the endoscopy speed requirements.

Analytical models for time-domain diffuse correlation spectroscopy for multi-layer and heterogeneous turbid media

A novel approach for time-domain diffuse correlation spectroscopy (TD-DCS) has been recently proposed, which has the unique advantage by simultaneous measurements of optical and dynamical properties in a scattering medium. In this study, analytical models for calculating the time-resolved electric-field autocorrelation function is presented for a multi-layer turbid sample, as well as a semi-infinite medium embedded with a small dynamic heterogeneity. To verify the analytical models, we used Monte Carlo simulations, which demonstrated that the theoretical prediction for the time-resolved autocorrelation function was highly consistent with the Monte Carlo simulation, validating the proposed analytical models. Using these analytical models, we also showed that TD-DCS has a higher sensitivity compared to conventional continuous-wave (CW) DCS for detecting the deeper dynamics. The presented analytical models and simulations can be utilized for quantification of optical and dynamical properties from future TD-DCS experimental data as well as for optimization of the experimental design to achieve maximum contrast for deep tissue dynamics.

Time domain diffuse correlation spectroscopy with a high coherence pulsed source: in vivo and phantom results

Diffuse correlation spectroscopy (DCS), combined with time-resolved reflectance spectroscopy (TRS) or frequency domain spectroscopy, aims at path length (i.e. depth) resolved, non-invasive and simultaneous assessment of tissue composition and blood flow. However, while TRS provides a path length resolved data, the standard DCS does not. Recently, a time domain DCS experiment showed path length resolved measurements for improved quantification with respect to classical DCS, but was limited to phantoms and small animal studies. Here, we demonstrate time domain DCS for in vivo studies on the adult forehead and the arm. We achieve path length resolved DCS by means of an actively mode-locked Ti:Sapphire laser that allows high coherence pulses, thus enabling adequate signal-to-noise ratio in relatively fast (~1 s) temporal resolution. This work paves the way to the translation of this approach to practical in vivo use.

Chromophore decomposition in multispectral time-resolved diffuse optical tomography

Multicomponent phantom measurements are carried out to evaluate the ability of multispectral time domain diffuse optical tomography in reflectance geometry to quantify the position and the composition of small heterogeneities at depths of 1-1.5 cm in turbid media. Time-resolved data were analyzed with the Mellin-Laplace transform. Results show good localization and correct composition gradation of objects but still a lack of absolute material composition accuracy when no a priori geometry information is known.

Ballistic and snake photon imaging for locating optical endomicroscopy fibres

We demonstrate determination of the location of the distal-end of a fibre-optic device deep in tissue through the imaging of ballistic and snake photons using a time resolved single-photon detector array. The fibre was imaged with centimetre resolution, within clinically relevant settings and models. This technique can overcome the limitations imposed by tissue scattering in optically determining the in vivo location of fibre-optic medical instruments.

Transient absorption imaging of hemes with 2-color, independently tunable visible-wavelength ultrafast source

Pump probe microscopy is a time-resolved multiphoton imaging technique capable of generating contrast between non-fluorescent pigments based on differences in excited-state lifetimes. Here we describe a fiber-based ultrafast system designed for imaging heme proteins with an independently-tunable pulse pair in the visible-wavelength regime. Starting with a 1060 nm fiber amplifier (1.3 W at 63 MHz, 140 fs pulses), visible pulses were produced in the vicinity of 488 nm and 532 nm by doubling the output of a short photonic crystal fiber with a pair of periodically-poled lithium niobate crystals, providing 5-20 mW power in each beam. This was sufficient for acquiring transient absorption images from unstained cryosectioned tissue.

Can time-resolved NIRS provide the sensitivity to detect brain activity during motor imagery consistently?

Previous functional magnetic resonance imaging (fMRI) studies have shown that a subgroup of patients diagnosed as being in a vegetative state are aware and able to communicate by performing a motor imagery task in response to commands. Due to the fMRI's cost and accessibility, there is a need for exploring different imaging modalities that can be used at the bedside. A promising technique is functional near infrared spectroscopy (fNIRS) that has been successfully applied to measure brain oxygenation in humans. Due to the limited depth sensitivity of continuous-wave NIRS, time-resolved (TR) detection has been proposed as a way of enhancing the sensitivity to the brain, since late arriving photons have a higher probability of reaching the brain. The goal of this study was to assess the feasibility and sensitivity of TR fNIRS in detecting brain activity during motor imagery. Fifteen healthy subjects were recruited in this study, and the fNIRS results were validated using fMRI. The change in the statistical moments of the distribution of times of flight (number of photons, mean time of flight and variance) were calculated for each channel to determine the presence of brain activity. The results indicate up to an 86% agreement between fMRI and TR-fNIRS and the sensitivity ranging from 64 to 93% with the highest value determined for the mean time of flight. These promising results highlight the potential of TR-fNIRS as a portable brain computer interface for patients with disorder of consciousness.

AlliGator: A Phasor Computational Platform for Fast in vivo Lifetime Analysis

A fast time-gated phasor analysis tool was developed and used to monitor kinetics of NIR FLIM-FRET in vitro and in vivo. The results were validated by comparison with standard two-component fluorescence decay fitting analysis.

Geometrically complex 3D-printed phantoms for diffuse optical imaging

Tissue-equivalent phantoms that mimic the optical properties of human and animal tissues are commonly used in diffuse optical imaging research to characterize instrumentation or evaluate an image reconstruction method. Although many recipes have been produced for generating solid phantoms with specified absorption and transport scattering coefficients at visible and near-infrared wavelengths, the construction methods are generally time-consuming and are unable to create complex geometries. We present a method of generating phantoms using a standard 3D printer. A simple recipe was devised which enables printed phantoms to be produced with precisely known optical properties. To illustrate the capability of the method, we describe the creation of an anatomically accurate, tissue-equivalent premature infant head optical phantom with a hollow brain space based on MRI atlas data. A diffuse optical image of the phantom is acquired when a high contrast target is inserted into the hollow space filled with an aqueous scattering solution.

Dynamic imaging and quantitative analysis of cranial neural tube closure in the mouse embryo using optical coherence tomography

Neural tube closure is a critical feature of central nervous system morphogenesis during embryonic development. Failure of this process leads to neural tube defects, one of the most common forms of human congenital defects. Although molecular and genetic studies in model organisms have provided insights into the genes and proteins that are required for normal neural tube development, complications associated with live imaging of neural tube closure in mammals limit efficient morphological analyses. Here, we report the use of optical coherence tomography (OCT) for dynamic imaging and quantitative assessment of cranial neural tube closure in live mouse embryos in culture. Through time-lapse imaging, we captured two neural tube closure mechanisms in different cranial regions, zipper-like closure of the hindbrain region and button-like closure of the midbrain region. We also used OCT imaging for phenotypic characterization of a neural tube defect in a mouse mutant. These results suggest that the described approach is a useful tool for live dynamic analysis of normal neural tube closure and neural tube defects in the mouse model.

Subtraction-based approach for enhancing the depth sensitivity of time-resolved NIRS

The aim of this study was to evaluate enhancing of the depth sensitivity of time-resolved near-infrared spectroscopy with a subtraction-based approach. Due to the complexity of light propagation in a heterogeneous media, and to prove the validity of the proposed method in a heterogeneous turbid media we conducted a broad analysis taking into account a number of parameters related to the method as well as various parameters of this media. The results of these experiments confirm that the depth sensitivity of the subtraction-based approach is better than classical approaches using continuous-wave or time-resolved methods. Furthermore, the results showed that the subtraction-based approach has a unique, selective sensitivity to a layer at a specific depth. In vivo application of the proposed method resulted in a greater magnitude of the hemodynamic changes during functional activation than with the standard approach.

Quantification in time-domain diffuse optical tomography using Mellin-Laplace transforms

Simulations and phantom measurements are used to evaluate the ability of time-domain diffuse optical tomography using Mellin-Laplace transforms to quantify the absorption perturbation of centimetric objects immersed at depth 1-2 cm in turbid media. We find that the estimated absorption coefficient varies almost linearly with the absorption change in the range of 0-0.15 cm^-1 but is underestimated by a factor that depends on the inclusion depth (~2, 3 and 6 for depths of 1.0, 1.5 and 2.0 cm respectively). For larger absorption changes, the variation is sublinear with ~20% decrease for δμ_a = 0.37 cm^-1. By contrast, constraining the absorption change to the actual volume of the inclusion may considerably improve the accuracy and linearity of the reconstructed absorption.

Automated analysis of multimodal fluorescence lifetime imaging and optical coherence tomography data for the diagnosis of oral cancer in the hamster cheek pouch model

It is known that the progression of oral cancer is accompanied by changes in both tissue biochemistry and morphology. A multimodal imaging approach combining functional and structural imaging modalities could therefore provide a more comprehensive prognosis of oral cancer. This idea forms the central theme of the current study, wherein this premise is examined in the context of a multimodal imaging system that combines fluorescence lifetime imaging (FLIM) and optical coherence tomography (OCT). Towards this end, in the first part of the present study, the diagnostic advantage obtained by using both fluorescence intensity and lifetime information is assessed. In the second part of the study, the diagnostic potential of FLIM-derived biochemical features is compared with that of OCT-derived morphological features. For an objective assessment, several quantitative biochemical and morphological features from FLIM and OCT data, respectively, were obtained using signal and image processing techniques. These features were subsequently used in a statistical classification framework to quantify the diagnostic potential of different features. The classification accuracy for combined FLIM and OCT features was estimated to be 87.4%, which was statistically higher than accuracy based on only FLIM (83.2%) or OCT (81.0%) features. Moreover, the complimentary information provided by FLIM and OCT features, resulted in highest sensitivity and specificity for the combined FLIM and OCT features for discriminating benign (88.2% sens., 92.0% spec.), pre-cancerous (81.5% sens., 96.0% spec.), and cancerous (90.1% sens., 92.0% spec.) classes.

Temporal binning of time-correlated single photon counting data improves exponential decay fits and imaging speed

Time-correlated single photon counting (TCSPC) enables acquisition of fluorescence lifetime decays with high temporal resolution within the fluorescence decay. However, many thousands of photons per pixel are required for accurate lifetime decay curve representation, instrument response deconvolution, and lifetime estimation, particularly for two-component lifetimes. TCSPC imaging speed is inherently limited due to the single photon per laser pulse nature and low fluorescence event efficiencies (<10%) required to reduce bias towards short lifetimes. Here, simulated fluorescence lifetime decays are analyzed by SPCImage and SLIM Curve software to determine the limiting lifetime parameters and photon requirements of fluorescence lifetime decays that can be accurately fit. Data analysis techniques to improve fitting accuracy for low photon count data were evaluated. Temporal binning of the decays from 256 time bins to 42 time bins significantly (p<0.0001) improved fit accuracy in SPCImage and enabled accurate fits with low photon counts (as low as 700 photons/decay), a 6-fold reduction in required photons and therefore improvement in imaging speed. Additionally, reducing the number of free parameters in the fitting algorithm by fixing the lifetimes to known values significantly reduced the lifetime component error from 27.3% to 3.2% in SPCImage (p<0.0001) and from 50.6% to 4.2% in SLIM Curve (p<0.0001). Analysis of nicotinamide adenine dinucleotide-lactate dehydrogenase (NADH-LDH) solutions confirmed temporal binning of TCSPC data and a reduced number of free parameters improves exponential decay fit accuracy in SPCImage. Altogether, temporal binning (in SPCImage) and reduced free parameters are data analysis techniques that enable accurate lifetime estimation from low photon count data and enable TCSPC imaging speeds up to 6x and 300x faster, respectively, than traditional TCSPC analysis.

Dynamics of cell and tissue growth acquired by means of extended field of view lensfree microscopy

In this paper, we discuss a new methodology based on lensfree imaging to perform wound healing assay with unprecedented statistics. Our video lensfree microscopy setup is a simple device featuring only a CMOS sensor and a semi coherent illumination system. Yet it is a powerful mean for the real-time monitoring of cultivated cells. It presents several key advantages, e.g. integration into standard incubator, compatibility with standard cell culture protocol, simplicity and ease of use. It can perform the follow-up in a large field of view (25 mm(2)) of several crucial parameters during the culture of cells i.e. their motility, their proliferation rate or their death. Consequently the setup can gather large statistics both in space and time. Here we uses this facility in the context of wound healing assay to perform label-free measurements of the velocities of the fronts of proliferation of the cell layer as a function of time by means of particle image velocimetry (PIV) processing. However, for such tissue growth experiments, the field of view of 25 mm(2) remains not sufficient and results can be biased depending on the position of the device with respect to the recipient of the cell culture. Hence, to conduct exhaustive wound healing assays, we propose to enlarge the field of view up to 10 cm(2) through a raster scan, by moving the source/sensor with respect to the Petri dish. We have performed acquisitions of wound healing assay (keratinocytes HaCaT) both in real-time (25 mm(2)) and in final point (10 cm(2)) to assess the combination of velocimetry measurements and final point wide field imaging. In the future, we aim at combining directly our extended field of view acquisitions (>10 cm(2)) with real time ability inside the incubator.

Effect of a thin superficial layer on the estimate of hemodynamic changes in a two-layer medium by time domain NIRS

In order to study hemodynamic changes involved in muscular metabolism by means of time domain fNIRS, we need to discriminate in the measured signal contributions coming from different depths. Muscles are, in fact, typically located under other tissues, e.g. skin and fat. In this paper, we study the possibility to exploit a previously proposed method for analyzing time-resolved fNIRS measurements in a two-layer structure with a thin superficial layer. This method is based on the calculation of the time-dependent mean partial pathlengths. We validated it by simulating venous and arterial arm cuff occlusions and then applied it on in vivo measurements.

Generalized mesh-based Monte Carlo for wide-field illumination and detection via mesh retessellation

Monte Carlo methods are commonly used as the gold standard in modeling photon transport through turbid media. With the rapid development of structured light applications, an accurate and efficient method capable of simulating arbitrary illumination patterns and complex detection schemes over large surface area is in great need. Here we report a generalized mesh-based Monte Carlo algorithm to support a variety of wide-field illumination methods, including spatial-frequency-domain imaging (SFDI) patterns and arbitrary 2-D patterns. The extended algorithm can also model wide-field detectors such as a free-space CCD camera. The significantly enhanced flexibility of source and detector modeling is achieved via a fast mesh retessellation process that combines the target domain and the source/detector space in a single tetrahedral mesh. Both simulations of complex domains and comparisons with phantom measurements are included to demonstrate the flexibility, efficiency and accuracy of the extended algorithm. Our updated open-source software is provided at http://mcx.space/mmc.

Time-resolved singlet-oxygen luminescence detection with an efficient and practical semiconductor single-photon detector

In clinical applications, such as PhotoDynamic Therapy, direct singlet-oxygen detection through its luminescence in the near-infrared range (1270 nm) has been a challenging task due to its low emission probability and the lack of suitable single-photon detectors. Here, we propose a practical setup based on a negative-feedback avalanche diode detector that is a viable alternative to the current state-of-the art for different clinical scenarios, especially where geometric collection efficiency is limited (e.g. fiber-based systems, confocal microscopy, scanning systems etc.). The proposed setup is characterized with Rose Bengal as a standard photosensitizer and it is used to measure the singlet-oxygen quantum yield of a new set of photosensitizers for site-selective photodynamic therapy.

Multiplexed fluorescence tomography with spectral and temporal data: demixing with intrinsic regularization

We consider the joint use of spectral and temporal data for multiplexed fluorescence molecular tomography to enable high-throughput imaging of multiple fluorescent targets in bulk tissue. This is a challenging problem due to the narrow near-infrared diagnostic window and relatively broad emission spectra of common fluorophores, and the distortion ("redshift") that the fluorophore signals undergo as they propagate through tissue. We show through a Cramér-Rao lower bound analysis that demixing with spectral-temporal data could result in an order of magnitude improvement in performance over either modality alone. To cope with the resulting large data set, we propose a novel two-stage algorithm that decouples the demixing and tomographic reconstruction operations. In this work we concentrate on the demixing stage. We introduce an approach which incorporates ideas from sparse subspace clustering and compressed sensing and does not require a regularization parameter. We report on simulations in which we simultaneously demixed four fluorophores with closely overlapping spectral and temporal profiles in a 25 mm diameter cross-sectional area with a root-mean-square error of less than 3% per fluorophore, as well as on studies of sensitivity of the method to model mismatch.

Wide-field fluorescence molecular tomography with compressive sensing based preconditioning

Wide-field optical tomography based on structured light illumination and detection strategies enables efficient tomographic imaging of large tissues at very fast acquisition speeds. However, the optical inverse problem based on such instrumental approach is still ill-conditioned. Herein, we investigate the benefit of employing compressive sensing-based preconditioning to wide-field structured illumination and detection approaches. We assess the performances of Fluorescence Molecular Tomography (FMT) when using such preconditioning methods both in silico and with experimental data. Additionally, we demonstrate that such methodology could be used to select the subset of patterns that provides optimal reconstruction performances. Lastly, we compare preconditioning data collected using a normal base that offers good experimental SNR against that directly acquired with optimal designed base. An experimental phantom study is provided to validate the proposed technique.

Effect of recombinant interleukin-12 on murine skin regeneration and cell dynamics using in vivo multimodal microscopy

Interleukin-12 (IL-12) is a pro-inflammatory cytokine known for its role in immunity, and previous studies have shown that IL-12 provides mitigation of radiation injury. In this study, we utilize a multimodal microscopy system equipped with second harmonic generation (SHG) and fluorescence lifetime imaging microscopy (FLIM) to examine the effect of IL-12 on collagen structure and cellular metabolic activity in vivo during skin wound healing. This preliminary study illustrates the highly dynamic and heterogeneous in vivo microenvironment of the wounded skin. In addition, results suggest that IL-12 triggers a significantly more rapid and greater cellular metabolic response in the wounded animals. These results can elucidate insights into the response mechanism of IL-12 in both wound healing and acute radiation syndrome.

Simultaneous FRAP, FLIM and FAIM for measurements of protein mobility and interaction in living cells

We present a novel integrated multimodal fluorescence microscopy technique for simultaneous fluorescence recovery after photobleaching (FRAP), fluorescence lifetime imaging (FLIM) and fluorescence anisotropy imaging (FAIM). This approach captures a series of polarization-resolved fluorescence lifetime images during a FRAP recovery, maximizing the information available from a limited photon budget. We have applied this method to analyse the behaviour of GFP-labelled coxsackievirus and adenovirus receptor (CAR) in living human epithelial cells. Our data reveal that CAR exists in oligomeric states throughout the cell, and that these complexes occur in conjunction with high immobile fractions of the receptor at cell-cell junctions. These findings shed light on previously unknown molecular associations between CAR receptors in intact cells and demonstrate the power of combined FRAP, FLIM and FAIM microscopy as a robust method to analyse complex multi-component dynamics in living cells.

Fast single photon avalanche photodiode-based time-resolved diffuse optical tomography scanner

Resolution in diffuse optical tomography (DOT) is a persistent problem and is primarily limited by high degree of light scatter in biological tissue. We showed previously that the reduction in photon scatter between a source and detector pair at early time points following a laser pulse in time-resolved DOT is highly dependent on the temporal response of the instrument. To this end, we developed a new single-photon avalanche photodiode (SPAD) based time-resolved DOT scanner. This instrument uses an array of fast SPADs, a femto-second Titanium Sapphire laser and single photon counting electronics. In combination, the overall instrument temporal impulse response function width was 59 ps. In this paper, we report the design of this instrument and validate its operation in symmetrical and irregularly shaped optical phantoms of approximately small animal size. We were able to accurately reconstruct the size and position of up to 4 absorbing inclusions, with increasing image quality at earlier time windows. We attribute these results primarily to the rapid response time of our instrument. These data illustrate the potential utility of fast SPAD detectors in time-resolved DOT.

In vivo visualization of skin inflammation by optical coherence tomography and two-photon microscopy

Inflammation is a non-specific immune response to injury intended to protect biological tissue from harmful stimuli such as pathogens, irritants, and damaged cells. In vivo optical tissue imaging has been used to provide spatial and dynamic characteristics of inflammation within the tissue. In this paper, we report in vivo visualization of inflammation in the skin at both cellular and physiological levels by using a combination of label-free two-photon microscopy (TPM) and optical coherence tomography (OCT). Skin inflammation was induced by topically applying lipopolysaccharide (LPS) on the mouse ear. Temporal OCT imaging visualized tissue swelling, vasodilation, and increased capillary density 30 min and 1 hour after application. TPM imaging showed immune cell migration within the inflamed skin. Combined OCT and TPM was applied to obtain complementary information from each modality in the same region of interest. The information provided by each modality were consistent with previous reports about the characteristics of inflammation. Therefore, the combination of OCT and TPM holds potential for studying inflammation of the skin.

Extended output phasor representation of multi-spectral fluorescence lifetime imaging microscopy

In this paper, we investigate novel low-dimensional and model-free representations for multi-spectral fluorescence lifetime imaging microscopy (m-FLIM) data. We depart from the classical definition of the phasor in the complex plane to propose the extended output phasor (EOP) and extended phasor (EP) for multi-spectral information. The frequency domain properties of the EOP and EP are analytically studied based on a multiexponential model for the impulse response of the imaged tissue. For practical implementations, the EOP is more appealing since there is no need to perform deconvolution of the instrument response from the measured m-FLIM data, as in the case of EP. Our synthetic and experimental evaluations with m-FLIM datasets of human coronary atherosclerotic plaques show that low frequency indexes have to be employed for a distinctive representation of the EOP and EP, and to reduce noise distortion. The tissue classification of the m-FLIM datasets by EOP and EP also improves with low frequency indexes, and does not present significant differences by using either phasor.

Gated STED microscopy with time-gated single-photon avalanche diode

Stimulated emission depletion (STED) microscopy provides fluorescence imaging with sub-diffraction resolution. Experimentally demonstrated at the end of the 90s, STED microscopy has gained substantial momentum and impact only in the last few years. Indeed, advances in many fields improved its compatibility with everyday biological research. Among them, a fundamental step was represented by the introduction in a STED architecture of the time-gated detection, which greatly reduced the complexity of the implementation and the illumination intensity needed. However, the benefits of the time-gated detection came along with a reduction of the fluorescence signal forming the STED microscopy images. The maximization of the useful (within the time gate) photon flux is then an important aspect to obtain super-resolved images. Here we show that by using a fast-gated single-photon avalanche diode (SPAD), i.e. a detector able to rapidly (hundreds picoseconds) switch-on and -off can improve significantly the signal-to-noise ratio (SNR) of the gated STED image. In addition to an enhancement of the image SNR, the use of the fast-gated SPAD reduces also the system complexity. We demonstrate these abilities both on calibration and biological sample. The experiments were carried on a gated STED microscope based on a STED beam operating in continuous-wave (CW), although the fast-gated SPAD is fully compatible with gated STED implementations based on pulsed STED beams.

Spectral and lifetime domain measurements of rat brain tumors

During glioblastoma surgery, delineation of the brain tumor margins is difficult because the infiltrated and normal tissues have the same visual appearance. We use a fiber-optical fluorescence probe for spectroscopic and time domain measurements to assist surgeon in differentiating the healthy and the infiltrated tissues. First study was performed on rats that were previously injected with tumorous cells. Measurements of endogenous tissue fluorescence were performed on fresh and fixed rat tumor brain slices. Spectral characteristics, fluorescence redox ratios and fluorescence lifetime measurements were analyzed. The study aimed at defining an optical index that can act as an indicator for discriminating healthy from tumorous tissue.

Mesoscopic in vivo 3-D tracking of sparse cell populations using angular multiplexed optical projection tomography

We describe an angular multiplexed imaging technique for 3-D in vivo cell tracking of sparse cell distributions and optical projection tomography (OPT) with superior time-lapse resolution and a significantly reduced light dose compared to volumetric time-lapse techniques. We demonstrate that using dual axis OPT, where two images are acquired simultaneously at different projection angles, can enable localization and tracking of features in 3-D with a time resolution equal to the camera frame rate. This is achieved with a 200x reduction in light dose compared to an equivalent volumetric time-lapse single camera OPT acquisition with 200 projection angles. We demonstrate the application of this technique to mapping the 3-D neutrophil migration pattern observed over ~25.5 minutes in a live 2 day post-fertilisation transgenic LysC:GFP zebrafish embryo following a tail wound.

Optical metabolic imaging quantifies heterogeneous cell populations

The genetic and phenotypic heterogeneity of cancers can contribute to tumor aggressiveness, invasion, and resistance to therapy. Fluorescence imaging occupies a unique niche to investigate tumor heterogeneity due to its high resolution and molecular specificity. Here, heterogeneous populations are identified and quantified by combined optical metabolic imaging and subpopulation analysis (OMI-SPA). OMI probes the fluorescence intensities and lifetimes of metabolic enzymes in cells to provide images of cellular metabolism, and SPA models cell populations as mixed Gaussian distributions to identify cell subpopulations. In this study, OMI-SPA is characterized by simulation experiments and validated with cell experiments. To generate heterogeneous populations, two breast cancer cell lines, SKBr3 and MDA-MB-231, were co-cultured at varying proportions. OMI-SPA correctly identifies two populations with minimal mean and proportion error using the optical redox ratio (fluorescence intensity of NAD(P)H divided by the intensity of FAD), mean NAD(P)H fluorescence lifetime, and OMI index. Simulation experiments characterized the relationships between sample size, data standard deviation, and subpopulation mean separation distance required for OMI-SPA to identify subpopulations.

Linear regression models and k-means clustering for statistical analysis of fNIRS data

We propose a new algorithm, based on a linear regression model, to statistically estimate the hemodynamic activations in fNIRS data sets. The main concern guiding the algorithm development was the minimization of assumptions and approximations made on the data set for the application of statistical tests. Further, we propose a K-means method to cluster fNIRS data (i.e. channels) as activated or not activated. The methods were validated both on simulated and in vivo fNIRS data. A time domain (TD) fNIRS technique was preferred because of its high performances in discriminating cortical activation and superficial physiological changes. However, the proposed method is also applicable to continuous wave or frequency domain fNIRS data sets.

Spatial resolution in depth for time-resolved diffuse optical tomography using short source-detector separations

Diffuse optical tomography for medical applications can require probes with small dimensions involving short source-detector separations. Even though this configuration is seen at first as a constraint due to the challenge of depth sensitivity, we show here that it can potentially be an asset for spatial resolution in depth. By comparing two fiber optic probes on a test object, we first show with simulations that short source-detector separations improve the spatial resolution down to a limit depth. We then confirm these results in an experimental study with a state-of-the-art setup involving a fast-gated single-photon avalanche diode allowing maximum depth sensitivity. We conclude that short source-detector separations are an option to consider for the design of probes so as to improve image quality for diffuse optical tomography in reflectance.

Estimate of tissue composition in malignant and benign breast lesions by time-domain optical mammography

The optical characterization of malignant and benign breast lesions is presented. Time-resolved transmittance measurements were performed in the 630-1060 nm range by means of a 7-wavelength optical mammograph, providing both imaging and spectroscopy information. A total of 62 lesions were analyzed, including 33 malignant and 29 benign lesions. The characterization of breast lesions was performed applying a perturbation model based on the high-order calculation of the pathlength of photons inside the lesion, which led to the assessment of oxy- and deoxy-hemoglobin, lipids, water and collagen concentrations. Significant variations between tumor and healthy tissue were observed in terms of both absorption properties and constituents concentration. In particular, benign lesions and tumors show a statistically significant discrimination in terms of absorption at several wavelengths and also in terms of oxy-hemoglobin and collagen content.

Calcium imaging at kHz frame rates resolves millisecond timing in neuronal circuits and varicosities

We have configured a widefield fast imaging system that allows imaging at 1000 frames per second (512x512 pixels). The system was extended with custom processing tools including a time correlation method to facilitate the analysis of static subcellular compartments (e.g. neuronal varicosities) with enhanced contrast, as well as a dynamic intensity processing (DIP) algorithm that aids in data size reduction and fast visualization and interpretation of timing and directionality in neuronal circuits. This system, together with our custom developed processing tools enables efficient detection of fast physiological events, such as action potential dependent calcium steps. We show, using a specific blocker of nerve communication, that with this setup it is possible to discriminate between a pre and post synaptic event in an all optical way.

Separation of superficial and cerebral hemodynamics using a single distance time-domain NIRS measurement

In functional near-infrared spectroscopy (fNIRS) superficial hemodynamics can mask optical signals related to brain activity. We present a method to separate superficial and cerebral absorption changes based on the analysis of changes in moments of time-of-flight distributions and a two-layered model. The related sensitivity factors were calculated from individual optical properties. The method was validated on a two-layer liquid phantom. Absorption changes in the lower layer were retrieved with an accuracy better than 20%. The method was successfully applied to in vivo data and compared to the reconstruction of homogeneous absorption changes.

Spatial light modulator based active wide-field illumination for ex vivo and in vivo quantitative NIR FRET imaging

Fluorescence lifetime imaging is playing an increasing role in drug development by providing a sensitive method to monitor drug delivery and receptor-ligand interactions. However, the wide dynamic range of fluorescence intensity emitted by ex vivo and in vivo samples presents challenges in retrieving information over the whole subject accurately and quantitatively. To overcome this challenge, we developed an active wide-field illumination (AWFI) strategy based on a spatial light modulator that acquires optimal fluorescence signals by enhancing the dynamic range, signal to noise ratio, and estimation of lifetime-based parameters. We demonstrate the ability of AWFI to estimate Förster resonance energy transfer (FRET) donor fraction from dissected organs with high accuracy (standard deviation <6%) over the whole field of view, in contrast with the homogenous wide-field illumination. We further report its successful application to quantitative FRET imaging in a live mouse. AWFI allows improved detection of weak signals and enhanced quantitative accuracy in ex vivo and in vivo molecular fluorescence quantitative imaging. The technique allows for robust quantitative estimation of the bio-distribution of molecular probes and lifetime-based parameters over an extended imaging field exhibiting a large range of fluorescence intensities and at a high acquisition speed (less than 1 min).

Non-contact in vivo diffuse optical imaging using a time-gated scanning system

We report on the design and first in vivo tests of a novel non-contact scanning imaging system for time-domain near-infrared spectroscopy. Our system is based on a null source-detector separation approach and utilizes polarization-selective detection and a fast-gated single-photon avalanche diode to record late photons only. The in-vivo tests included the recording of hemodynamics during arm occlusion and two brain activation tasks. Localized and non-localized changes in oxy- and deoxyhemoglobin concentration were detected for motor and cognitive tasks, respectively. The tests demonstrate the feasibility of non-contact imaging of absorption changes in deeper tissues.

Multi-channel medical device for time domain functional near infrared spectroscopy based on wavelength space multiplexing

We have designed a compact dual wavelength (687 nm, 826 nm) multi-channel (16 sources, 8 detectors) medical device for muscle and brain imaging based on time domain functional near infrared spectroscopy. The system employs the wavelength space multiplexing approach to reduce wavelength cross-talk and increase signal-to-noise ratio. System performances have been tested on homogeneous and heterogeneous tissue phantoms following specifically designed protocols for photon migration instruments. Preliminary in vivo measurements have been performed to validate the instrument capability to monitor hemodynamic parameters changes in the arm muscle during arterial occlusion and in the adult head during a motor task experiment.

Subcellular localization-dependent changes in EGFP fluorescence lifetime measured by time-resolved flow cytometry

Intracellular protein transport and localization to subcellular regions are processes necessary for normal protein function. Fluorescent proteins can be fused to proteins of interest to track movement and determine localization within a cell. Currently, fluorescence microscopy combined with image processing is most often used to study protein movement and subcellular localization. In this contribution we evaluate a high-throughput time-resolved flow cytometry approach to correlate intracellular localization of human LC3 protein with the fluorescence lifetime of enhanced green fluorescent protein (EGFP). Subcellular LC3 localization to autophagosomes is a marker of the cellular process called autophagy. In breast cancer cells expressing native EGFP and EGFP-LC3 fusion proteins, we measured the fluorescence intensity and lifetime of (i) diffuse EGFP (ii) punctate EGFP-LC3 and (iii) diffuse EGFP-ΔLC3 after amino acid starvation to induce autophagy-dependent LC3 localization. We verify EGFP-LC3 localization with low-throughput confocal microscopy and compare to fluorescence intensity measured by standard flow cytometry. Our results demonstrate that time-resolved flow cytometry can be correlated to subcellular localization of EGFP fusion proteins by measuring changes in fluorescence lifetime.

Time-domain reflectance diffuse optical tomography with Mellin-Laplace transform for experimental detection and depth localization of a single absorbing inclusion

We show how to apply the Mellin-Laplace transform to process time-resolved reflectance measurements for diffuse optical tomography. We illustrate this method on simulated signals incorporating the main sources of experimental noise and suggest how to fine-tune the method in order to detect the deepest absorbing inclusions and optimize their localization in depth, depending on the dynamic range of the measurement. To finish, we apply this method to measurements acquired with a setup including a femtosecond laser, photomultipliers and a time-correlated single photon counting board. Simulations and experiments are illustrated for a probe featuring the interfiber distance of 1.5 cm and show the potential of time-resolved techniques for imaging absorption contrast in depth with this geometry.

Variance of time-of-flight distribution is sensitive to cerebral blood flow as demonstrated by ICG bolus-tracking measurements in adult pigs

Variance of time-of-flight distributions have been shown to be more sensitive to cerebral blood flow (CBF) during dynamic-contrast enhanced monitoring of neurotrauma patients than attenuation. What is unknown is the degree to which variance is affected by changes in extracerebral blood flow. Furthermore, the importance of acquiring the arterial input function (AIF) on quantitative analysis of the data is not yet clear. This animal study confirms that variance is both sensitive and specific to changes occurring in the brain when measurements are acquired on the surface of the scalp. Furthermore, when the variance data along with the measured AIF is analyzed using a nonparametric deconvolution method, the recovered change in CBF is in good agreement with CT perfusion values.

Combined hemoglobin and fluorescence diffuse optical tomography for breast tumor diagnosis: a pilot study on time-domain methodology

A combined time-domain fluorescence and hemoglobin diffuse optical tomography (DOT) system and the image reconstruction methods are proposed for enhancing the reliability of breast-dedicated optical measurement. The system equipped with two pulsed laser diodes at wavelengths of 780 nm and 830 nm that are specific to the peak excitation and emission of the FDA-approved ICG agent, and works with a 4-channel time-correlated single photon counting device to acquire the time-resolved distributions of the light re-emissions at 32 boundary sites of tissues in a tandem serial-to-parallel mode. The simultaneous reconstruction of the two optical (absorption and scattering) and two fluorescent (yield and lifetime) properties are achieved with the respective featured-data algorithms based on the generalized pulse spectrum technique. The performances of the methodology are experimentally assessed on breast-mimicking phantoms for hemoglobin- and fluorescence-DOT alone, as well as for fluorescence-guided hemoglobin-DOT. The results demonstrate the efficacy of improving the accuracy of hemoglobin-DOT based on a priori fluorescence localization.

Method for the discrimination of superficial and deep absorption variations by time domain fNIRS

A method for the discrimination of superficial and deep absorption variations by time domain functional near infrared spectroscopy is presented. The method exploits the estimate of the photon time-dependent pathlength in different domains of the sampled medium and makes use of an approach based on time-gating of the photon distribution of time-of-flights. Validation of the method is performed in the two-layer geometry to focus on muscle and head applications. Numerical simulations varied the thickness of the upper layer, the interfiber distance, the shape of the instrument response function and the photon counts. Preliminary results from in vivo data are also shown.