Real-time in vivo computed optical interferometric tomography

Recent Advances and Current Trends in Transmission Tomographic Diffraction Microscopy

Optical microscopy techniques are among the most used methods in biomedical sample characterization. In their more advanced realization, optical microscopes demonstrate resolution down to the nanometric scale. These methods rely on the use of fluorescent sample labeling in order to break the diffraction limit. However, fluorescent molecules' phototoxicity or photobleaching is not always compatible with the investigated samples. To overcome this limitation, quantitative phase imaging techniques have been proposed. Among these, holographic imaging has demonstrated its ability to image living microscopic samples without staining. However, for a 3D assessment of samples, tomographic acquisitions are needed. Tomographic Diffraction Microscopy (TDM) combines holographic acquisitions with tomographic reconstructions. Relying on a 3D synthetic aperture process, TDM allows for 3D quantitative measurements of the complex refractive index of the investigated sample. Since its initial proposition by Emil Wolf in 1969, the concept of TDM has found a lot of applications and has become one of the hot topics in biomedical imaging. This review focuses on recent achievements in TDM development. Current trends and perspectives of the technique are also discussed.

Computational 3D resolution enhancement for optical coherence tomography with a narrowband visible light source

Phase-preserving spectral estimation optical coherence tomography (SE-OCT) enables combining axial resolution improvement with computational depth of field (DOF) extension. We show that the combination of SE-OCT with interferometric synthetic aperture microscopy (ISAM) and computational adaptive optics (CAO) results in high 3D resolution over a large depth range for an OCT system with a narrow bandwidth visible light super-luminescent diode (SLD). SE-OCT results in up to five times axial resolution improvement from 8 µm to 1.5 µm. The combination with ISAM gives a sub-micron lateral resolution over a 400 µm axial range, which is at least 16 times the conventional depth of field. CAO can be successfully applied after SE and ISAM and removes residual aberrations, resulting in high quality images. The results show that phase-preserving SE-OCT is sufficiently accurate for coherent post-processing, enabling the use of cost-effective SLDs in the visible light range for high spatial resolution OCT.

Label-free metabolic and structural profiling of dynamic biological samples using multimodal optical microscopy with sensorless adaptive optics

Label-free optical microscopy has matured as a noninvasive tool for biological imaging; yet, it is criticized for its lack of specificity, slow acquisition and processing times, and weak and noisy optical signals that lead to inaccuracies in quantification. We introduce FOCALS (Fast Optical Coherence, Autofluorescence Lifetime imaging, and Second harmonic generation) microscopy capable of generating NAD(P)H fluorescence lifetime, second harmonic generation (SHG), and polarization-sensitive optical coherence microscopy (OCM) images simultaneously. Multimodal imaging generates quantitative metabolic and morphological profiles of biological samples in vitro, ex vivo, and in vivo. Fast analog detection of fluorescence lifetime and real-time processing on a graphical processing unit enables longitudinal imaging of biological dynamics. We detail the effect of optical aberrations on the accuracy of FLIM beyond the context of undistorting image features. To compensate for the sample-induced aberrations, we implemented a closed-loop single-shot sensorless adaptive optics solution, which uses computational adaptive optics of OCM for wavefront estimation within 2 s and improves the quality of quantitative fluorescence imaging in thick tissues. Multimodal imaging with complementary contrasts improves the specificity and enables multidimensional quantification of the optical signatures in vitro, ex vivo, and in vivo, fast acquisition and real-time processing improve imaging speed by 4-40 × while maintaining enough signal for quantitative nonlinear microscopy, and adaptive optics improves the overall versatility, which enable FOCALS microscopy to overcome the limits of traditional label-free imaging techniques.

Lateral Resolution of a Commercial Optical Coherence Tomography Instrument

Purpose

The lateral resolution of an optical coherence tomography (OCT) instrument was considered to be equal to the illumination spot size on the retina. To evaluate the potential lateral resolution of the Spectralis OCT, an instrument calculated to have a 14 µm resolution.

Methods

The lateral point spread function (PSF) was evaluated using diamond abrasive powder 0 to 1 µm in diameter in silicone elastomer and a validated target with 800 nm FeO particles in urethane. The amplitude transfer function was calculated from human OCT images. Finally, resolution was measured using the 1951 USAF target.

Results

Measurement of the lateral PSF from 1215 diamond particle images yielded a full-width half maximum (FWHM) to be 5.11 µm and for 732 FeO particles, 4.9 µm. From the amplitude transfer function, the FWHM of the diffraction limited PSF was calculated to be 5.0 µm. The USAF target imaging showed a lateral resolution of 4.6 µm.

Conclusions

Although a calculation of the spot size of the illumination beam was reported in the past as the lateral resolution of the OCT instrument, the actual lateral resolution is better by a factor of at least 2.5 times. The clinically used A-scan spacing was derived from the calculated, and not the true resolution, and results in under sampling. This set of findings likely apply to all commercial clinical instruments.

Translational Relevance

The scan density parameters of past and present commercial OCT instruments were based on earlier translational concepts, which now appear to have been incorrect.

Resolution-enhanced OCT and expanded framework of information capacity and resolution in coherent imaging

Spatial resolution in conventional optical microscopy has traditionally been treated as a fixed parameter of the optical system. Here, we present an approach to enhance transverse resolution in beam-scanned optical coherence tomography (OCT) beyond its aberration-free resolution limit, without any modification to the optical system. Based on the theorem of invariance of information capacity, resolution-enhanced (RE)-OCT navigates the exchange of information between resolution and signal-to-noise ratio (SNR) by exploiting efficient noise suppression via coherent averaging and a simple computational bandwidth expansion procedure. We demonstrate a resolution enhancement of 1.5 × relative to the aberration-free limit while maintaining comparable SNR in silicone phantom. We show that RE-OCT can significantly enhance the visualization of fine microstructural features in collagen gel and ex vivo mouse brain. Beyond RE-OCT, our analysis in the spatial-frequency domain leads to an expanded framework of information capacity and resolution in coherent imaging that contributes new implications to the theory of coherent imaging. RE-OCT can be readily implemented on most OCT systems worldwide, immediately unlocking information that is beyond their current imaging capabilities, and so has the potential for widespread impact in the numerous areas in which OCT is utilized, including the basic sciences and translational medicine.

Manifestation of aberrations in full-field optical coherence tomography

We report on a theoretical model for image formation in full-field optical coherence tomography (FFOCT). Because the spatial incoherence of the illumination acts as a virtual confocal pinhole in FFOCT, its imaging performance is equivalent to a scanning time-gated coherent confocal microscope. In agreement with optical experiments enabling a precise control of aberrations, FFOCT is shown to have nearly twice the resolution of standard imaging at moderate aberration level. Beyond a rigorous study on the sensitivity of FFOCT with respect to aberrations, this theoretical model paves the way towards an optimized design of adaptive optics and computational tools for high-resolution and deep imaging of biological tissues.

Neural network enabled time stretch spectral regression

Spectral interferometry is utilized in a wide range of biomedical and scientific applications and metrology. Retrieving the magnitude and phase of the complex electric field from the interferogram is central to all its applications. We report a spectral interferometry system that utilizes a neural network to infer the magnitude and phase of femtosecond interferograms directly from the measured single-shot interference patterns and compare its performance with the widely used Hilbert transform. Our approach does not require apriori knowledge of the shear frequency, and achieves higher accuracy under our experimental conditions. To train the network, we introduce an experimental technique that generates a large number of femtosecond interferograms with known (labeled) phase and magnitude profiles. While the profiles for these pulses are digitally generated, they obey causality by satisfying the Kramer-Kronig relation. This technique is resilient against nonlinear optical distortions, quantization noise, and the sampling rate limit of the backend digitizer - valuable properties that relax instrument complexity and cost.

Fast simulation and design of the fiber probe with a fiber-based pupil filter for optical coherence tomography using the eigenmode expansion approach

Fiber probes for optical coherence tomography (OCT) recently employ a short section of step-index multimode fiber (SIMMF) to generate output beams with extended depth of focus (DOF). As the focusing region of the output beam is generally close to the probe end, it is not feasible to adopt the methods for bulk-optics with spatial pupil filters to the fiber probes with fiber-based filters. On the other hand, the applicable method of the beam propagation method (BPM) to the fiber probes is computationally inefficient to perform parameter scan and exhaustive search optimization. In this paper, we propose the method which analyzes the non-Gaussian beams from the fiber probes with fiber-based filters using the eigenmode expansion (EME) method. Furthermore, we confirm the power of this method in designing fiber-based filters with increased DOF gain and uniformly focusing by introducing more and higher-order fiber modes. These results using the EME method are in good agreement with that by the BPM, while the latter takes 1-2 orders more computation time. With higher-order fiber modes involved, a novel probe design with increased DOF gain and suppressed sidelobe is proposed. Our findings reveal that the fiber probes based on SIMMFs are able to achieve about four times DOF gain at maximum with uniformly focusing under acceptable modal dispersion. The EME method enables fast and accurate simulation of fiber probes based on SIMMFs, which is important in the design of high-performance fiber-based micro-imaging systems for biomedical applications.

Automated fast computational adaptive optics for optical coherence tomography based on a stochastic parallel gradient descent algorithm

The transverse resolution of optical coherence tomography is decreased by aberrations introduced from optical components and the tested samples. In this paper, an automated fast computational aberration correction method based on a stochastic parallel gradient descent (SPGD) algorithm is proposed for aberration-corrected imaging without adopting extra adaptive optics hardware components. A virtual phase filter constructed through combination of Zernike polynomials is adopted to eliminate the wavefront aberration, and their coefficients are stochastically estimated in parallel through the optimization of the image metrics. The feasibility of the proposed method is validated by a simulated resolution target image, in which the introduced aberration wavefront is estimated accurately and with fast convergence. The computation time for the aberration correction of a 512 × 512 pixel image from 7 terms to 12 terms requires little change, from 2.13 s to 2.35 s. The proposed method is then applied for samples with different scattering properties including a particle-based phantom, ex-vivo rabbit adipose tissue, and in-vivo human retina photoreceptors, respectively. Results indicate that diffraction-limited optical performance is recovered, and the maximum intensity increased nearly 3-fold for out-of-focus plane in particle-based tissue phantom. The SPGD algorithm shows great potential for aberration correction and improved run-time performance compared to our previous Resilient backpropagation (Rprop) algorithm when correcting for complex wavefront distortions. The fast computational aberration correction suggests that after further optimization our method can be integrated for future applications in real-time clinical imaging.

Single-shot two-dimensional spectroscopic magnetomotive optical coherence elastography with graphics processing unit acceleration

Biomechanical contrast within tissues can be assessed based on the resonant frequency probed by spectroscopic magnetomotive optical coherence elastography (MM-OCE). However, to date, in vivo MM-OCE imaging has not been achieved, mainly due to the constraints on imaging speed. Previously, spatially-resolved spectroscopic contrast was achieved in a "multiple-excitation, multiple-acquisition" manner, where seconds of coil cooling time set between consecutive imaging frames lead to total acquisition times of tens of minutes. Here, we demonstrate an improved data acquisition speed by providing a single chirped force excitation prior to magnetomotion imaging with a BM-scan configuration. In addition, elastogram reconstruction was accelerated by exploiting the parallel computing capability of a graphics processing unit (GPU). The accelerated MM-OCE platform achieved data acquisition in 2.9 s and post-processing in 0.6 s for a 2048-frame BM-mode stack. In addition, the elasticity sensing functionality was validated on tissue-mimicking phantoms with high spatial resolution. For the first time, to the best of our knowledge, MM-OCE images were acquired from the skin of a living mouse, demonstrating its feasibility for in vivo imaging.

Angular compounding for speckle reduction in optical coherence tomography using geometric image registration algorithm and digital focusing

Optical coherence tomography (OCT) suffers from speckle noise due to the high spatial coherence of the utilized light source, leading to significant reductions in image quality and diagnostic capabilities. In the past, angular compounding techniques have been applied to suppress speckle noise. However, existing image registration methods usually guarantee pure angular compounding only within a relatively small field of view in the focal region, but produce spatial averaging in the other regions, resulting in resolution loss and image blur. This work develops an image registration model to correctly localize the real-space location of every pixel in an OCT image, for all depths. The registered images captured at different angles are fused into a speckle-reduced composite image. Digital focusing, based on the convolution of the complex OCT images and the conjugate of the point spread function (PSF), is studied to further enhance lateral resolution and contrast. As demonstrated by experiments, angular compounding with our improved image registration techniques and digital focusing, can effectively suppress speckle noise, enhance resolution and contrast, and reveal fine structures in ex-vivo imaged tissue.

Ten Years of Gabor-Domain Optical Coherence Microscopy

Gabor-domain optical coherence microscopy (GDOCM) is a high-definition imaging technique leveraging principles of low-coherence interferometry, liquid lens technology, high-speed imaging, and precision scanning. GDOCM achieves isotropic 2 μm resolution in 3D, effectively breaking the cellular resolution limit of optical coherence tomography (OCT). In the ten years since its introduction, GDOCM has been used for cellular imaging in 3D in a number of clinical applications, including dermatology, oncology and ophthalmology, as well as to characterize materials in industrial applications. Future developments will enhance the structural imaging capability of GDOCM by adding functional modalities, such as fluorescence and elastography, by estimating thicknesses on the nano-scale, and by incorporating machine learning techniques.

Live video rate volumetric OCT imaging of the retina with multi-MHz A-scan rates

Surgical microscopes are vital tools for ophthalmic surgeons. The recent development of an integrated OCT system for the first time allows to look at tissue features below the surface. Hence, these systems can drastically improve the quality and reduce the risk of surgical interventions. However, current commercial OCT-enhanced ophthalmic surgical microscopes provide only one additional cross sectional view to the standard microscope image and feature a low update rate. To present volumetric data at a high update rate, much faster OCT systems than the ones applied in today's surgical microscopes need to be developed. We demonstrate live volumetric retinal OCT imaging, which may provide a sufficiently large volume size (330x330x595 Voxel) and high update frequency (24.2 Hz) such that the surgeon may even purely rely on the OCT for certain surgical maneuvers. It represents a major technological step towards the possible application of OCT-only surgical microscopes in the future which would be much more compact thus enabling many additional minimal invasive applications. We show that multi-MHz A-scan rates are essential for such a device. Additionally, advanced phase-based OCT techniques require 3D OCT volumes to be detected with a stable optical phase. These techniques can provide additional functional information of the retina. Up to now, classical OCT was to slow for this, so our system can pave the way to holographic OCT with a traditional confocal flying spot approach. For the first time, we present point scanning volumetric OCT imaging of the posterior eye with up to 191.2 Hz volume rate. We show that this volume rate is high enough to enable a sufficiently stable optical phase to a level, where remaining phase errors can be corrected. Applying advanced post processing concepts for numerical refocusing or computational adaptive optics should be possible in future with such a system.

Live video rate volumetric OCT imaging of the retina with multi-MHz A-scan rates

Surgical microscopes are vital tools for ophthalmic surgeons. The recent development of an integrated OCT system for the first time allows to look at tissue features below the surface. Hence, these systems can drastically improve the quality and reduce the risk of surgical interventions. However, current commercial OCT-enhanced ophthalmic surgical microscopes provide only one additional cross sectional view to the standard microscope image and feature a low update rate. To present volumetric data at a high update rate, much faster OCT systems than the ones applied in today's surgical microscopes need to be developed. We demonstrate live volumetric retinal OCT imaging, which may provide a sufficiently large volume size (330x330x595 Voxel) and high update frequency (24.2 Hz) such that the surgeon may even purely rely on the OCT for certain surgical maneuvers. It represents a major technological step towards the possible application of OCT-only surgical microscopes in the future which would be much more compact thus enabling many additional minimal invasive applications. We show that multi-MHz A-scan rates are essential for such a device. Additionally, advanced phase-based OCT techniques require 3D OCT volumes to be detected with a stable optical phase. These techniques can provide additional functional information of the retina. Up to now, classical OCT was to slow for this, so our system can pave the way to holographic OCT with a traditional confocal flying spot approach. For the first time, we present point scanning volumetric OCT imaging of the posterior eye with up to 191.2 Hz volume rate. We show that this volume rate is high enough to enable a sufficiently stable optical phase to a level, where remaining phase errors can be corrected. Applying advanced post processing concepts for numerical refocusing or computational adaptive optics should be possible in future with such a system.

Disintegration of simulated drinking water biofilms with arrays of microchannel plasma jets

Biofilms exist and thrive within drinking water distribution networks, and can present human health concerns. Exposure of simulated drinking water biofilms, grown from groundwater, to a 9 × 9 array of microchannel plasma jets has the effect of severely eroding the biofilm and deactivating the organisms they harbor. In-situ measurements of biofilm structure and thickness with an optical coherence tomography (OCT) system show the biofilm thickness to fall from 122 ± 17 µm to 55 ± 13 µm after 15 min. of exposure of the biofilm to the microplasma column array, when the plasmas are dissipating a power density of 58 W/cm². All biofilms investigated vanish with 20 min. of exposure. Confocal laser scanning microscopy (CLSM) demonstrates that the number of living cells in the biofilms declines by more than 93% with 15 min. of biofilm exposure to the plasma arrays. Concentrations of several oxygen-bearing species, generated by the plasma array, were found to be 0.4–21 nM/s for the hydroxyl radical (OH), 85–396 nM/s for the ¹O₂ excited molecule, 98–280 µM for H₂O₂, and 24–42 µM for O₃ when the power density delivered to the array was varied between 3.6 W/cm² and 79 W/cm². The data presented here demonstrate the potential of microplasma arrays as a tool for controlling, through non-thermal disruption and removal, mixed-species biofilms prevalent in commercial and residential water systems.

Biofilms in drinking water premise plumbing systems can be disrupted and their microorganisms deactivated by exposure to jets of ionized gas known as plasma. Researchers at the University of Illinois, USA, led by Thanh (Helen) Nguyen and J. Gary Eden, explored the potential of low temperature plasma jets in disrupting & removing drinking water biofilms. The plasma was directed through fabricated microchannels and onto samples that the simulated biofilms. The interaction of the plasma with air and water generated reactive chemical species and ultraviolet radiation that disrupted the biofilms and deactivated the microorganisms within them. The biofilms studied vanished within 20 min. of plasma exposure. Plasma jets offer an inexpensive, low temperature and chlorine-free method for combating harmful biofilms in drinking water premise plumbing systems.

Extending axial focus of optical coherence tomography using parallel multiple aperture synthesis

Compromising the inherent trade-off between transverse resolution and depth of focus (DOF) remains a long-standing issue in optical coherence tomography (OCT). In this work, we report a novel technique-parallel multiple aperture synthesis (pMAS) to simultaneously generate multiple optical apertures in an OCT sample arm by employing a two-surface coated mirror. In the proposed pMAS, the DOF is extended by a factor of 16.49 without sacrificing the transverse resolution for proof-of-concept experiments when multiple distinctive apertures are digitally synthesized. The microparticles and tissue experiments demonstrate the feasibility of pMAS to address the fundamental problem of limited DOF in high-resolution OCT.

Wavefront measurement using computational adaptive optics

In many optical imaging applications, it is necessary to correct for aberrations to obtain high quality images. Optical coherence tomography (OCT) provides access to the amplitude and phase of the backscattered optical field for three-dimensional (3D) imaging samples. Computational adaptive optics (CAO) modifies the phase of the OCT data in the spatial frequency domain to correct optical aberrations without using a deformable mirror, as is commonly done in hardware-based adaptive optics (AO). This provides improvement of image quality throughout the 3D volume, enabling imaging across greater depth ranges and in highly aberrated samples. However, the CAO aberration correction has a complicated relation to the imaging pupil and is not a direct measurement of the pupil aberrations. Here we present new methods for recovering the wavefront aberrations directly from the OCT data without the use of hardware adaptive optics. This enables both computational measurement and correction of optical aberrations.

Multiple aperture synthetic optical coherence tomography for biological tissue imaging

An inherent compromise must be made between transverse resolution and depth of focus (DOF) in spectral domain optical coherence tomography (SD-OCT). Thus far, OCT has not been capable of providing a sufficient DOF to stably acquire cellular-resolution images. We previously reported a novel technique named multiple aperture synthesis (MAS) to extend the DOF in high-resolution OCT [Optica4, 701 (2017)]. In this technique, the illumination beam is scanned across the objective lens pupil plane by being steered at the pinhole using a custom-made microcylindrical lens. Images captured via multiple distinctive apertures were digitally refocused, which is similar to synthetic aperture radar. In this study, we applied this technique for the first time to image both a homemade microparticle sample and biological tissue. The results demonstrated the feasibility and efficacy of high-resolution biological tissue imaging with a dramatic DOF extension.

Interferometric synthetic aperture microscopy for extended focus optical coherence microscopy

Optical coherence microscopy (OCM) is an interferometric technique providing 3D images of biological samples with micrometric resolution and penetration depth of several hundreds of micrometers. OCM differs from optical coherence tomography (OCT) in that it uses a high numerical aperture (NA) objective to achieve high lateral resolution. However, the high NA also reduces the depth-of-field (DOF), scaling with 1/NA². Interferometric synthetic aperture microscopy (ISAM) is a computed imaging technique providing a solution to this trade-off between resolution and DOF. An alternative hardware method to achieve an extended DOF is to use a non-Gaussian illumination. Extended focus OCM (xfOCM) uses a Bessel beam to obtain a narrow and extended illumination volume. xfOCM detects back-scattered light using a Gaussian mode in order to maintain good sensitivity. However, the Gaussian detection mode limits the DOF. In this work, we present extended ISAM (xISAM), a method combining the benefits of both ISAM and xfOCM. xISAM uses the 3D coherent transfer function (CTF) to generalize the ISAM algorithm to different system configurations. We demonstrate xISAM both on simulated and experimental data, showing that xISAM attains a combination of high transverse resolution and extended DOF which has so far been unobtainable through conventional ISAM or xfOCM individually.

Extended depth of focus for coherence-based cellular imaging

Improving lateral resolution for cross-sectional optical coherence tomography (OCT) imaging is difficult due to the rapid divergence of light once it is focused to a small spot. To overcome this obstacle, we introduce a fiber optics system that generates a coaxially focused multimode (CAFM) beam for depth of focus (DOF) extension. We fabricated a CAFM beam OCT probe and show that the DOF is more than fivefold that of a conventional Gaussian beam, enabling cross-sectional imaging of biological tissues with clearly resolved cellular and subcellular structures over more than a 400 μm depth range. The compact and straightforward design and high-resolution extended DOF imaging capabilities of this technique suggests that it will be very useful for endoscopic cross-sectional imaging of human internal organs in vivo.

Label-free volumetric optical imaging of intact murine brains

A central effort of today’s neuroscience is to study the brain’s ’wiring diagram’. The nervous system is believed to be a network of neurons interacting with each other through synaptic connection between axons and dendrites, therefore the neuronal connectivity map not only depicts the underlying anatomy, but also has important behavioral implications. Different approaches have been utilized to decipher neuronal circuits, including electron microscopy (EM) and light microscopy (LM). However, these approaches typically demand extensive sectioning and reconstruction for a brain sample. Recently, tissue clearing methods have enabled the investigation of a fully assembled biological system with greatly improved light penetration. Yet, most of these implementations, still require either genetic or exogenous contrast labeling for light microscopy. Here we demonstrate a high-speed approach, termed as Clearing Assisted Scattering Tomography (CAST), where intact brains can be imaged at optical resolution without labeling by leveraging tissue clearing and the scattering contrast of optical frequency domain imaging (OFDI).

Quasi-needle-like focus synthesized by optical coherence tomography

It is known that lateral resolution and depth of focus (DOF) in an optical imaging system are coupled, and a compromise between them has to be made. In this Letter, we propose to resolve the trade-off between lateral resolution and the DOF by a synthetic effective point spread function in optical path length (OPL) domain. A quasi-needle-like focus is synthesized by optical coherence tomography. We demonstrate that the synthesized quasi-needle-like focus provides a four-fold extension of a conventional DOF, while maintaining a high lateral resolution of 2.5 μm over a depth range of approximately 240 μm. The focal range can be further extended with more optical path length coded beams for synthesis involved.

Computational optical coherence tomography [Invited]

Optical coherence tomography (OCT) has become an important imaging modality with numerous biomedical applications. Challenges in high-speed, high-resolution, volumetric OCT imaging include managing dispersion, the trade-off between transverse resolution and depth-of-field, and correcting optical aberrations that are present in both the system and sample. Physics-based computational imaging techniques have proven to provide solutions to these limitations. This review aims to outline these computational imaging techniques within a general mathematical framework, summarize the historical progress, highlight the state-of-the-art achievements, and discuss the present challenges.

En face coherence microscopy [Invited]

En face coherence microscopy or flying spot or full field optical coherence tomography or microscopy (FF-OCT/FF-OCM) belongs to the OCT family because the sectioning ability is mostly linked to the source coherence length. In this article we will focus our attention on the advantages and the drawbacks of the following approaches: en face versus B scan tomography in terms of resolution, coherent versus incoherent illumination and influence of aberrations, and scanning versus full field imaging. We then show some examples to illustrate the diverse applications of en face coherent microscopy and show that endogenous or exogenous contrasts can add valuable information to the standard morphological image. To conclude we discuss a few domains that appear promising for future development of en face coherence microscopy.

Acoustic-actuated optical coherence angiography

Optical coherence tomography (OCT) angiography requires high sensitivity and image penetration for detailed microvascular monitoring. Unfortunately, no effective contrast-medium-enhanced scheme is currently available for imaging improvement. We here propose the simultaneous use of gas-filled microbubbles (MBs) and acoustic actuation to enhance the imaging contrast of OCT angiography. OCT-synchronized acoustic actuation was applied in the presence of MBs, and different moving object tracking angiographic algorithms were tested in in vitro tubing and in vivo mouse experiments. This scheme significantly enhanced the OCT angiography performance, including its sensitivity and penetration, and should advance the utilization of OCT as an effective microvascular diagnostic tool.

Evaluation of Laser-Assisted Trans-Nail Drug Delivery with Optical Coherence Tomography

The nail provides a functional protection to the fingertips and surrounding tissue from external injuries. The nail plate consists of three layers including dorsal, intermediate, and ventral layers. The dorsal layer consists of compact, hard keratins, limiting topical drug delivery through the nail. In this study, we investigate the application of fractional CO₂ laser that produces arrays of microthermal ablation zones (MAZs) to facilitate drug delivery in the nails. We utilized optical coherence tomography (OCT) for real-time monitoring of the laser-skin tissue interaction, sparing the patient from an invasive surgical sampling procedure. The time-dependent OCT intensity variance was used to observe drug diffusion through an induced MAZ array. Subsequently, nails were treated with cream and liquid topical drugs to investigate the feasibility and diffusion efficacy of laser-assisted drug delivery. Our results show that fractional CO₂ laser improves the effectiveness of topical drug delivery in the nail plate and that OCT could potentially be used for in vivo monitoring of the depth of laser penetration as well as real-time observations of drug delivery.

Aberration-free volumetric high-speed imaging of in vivo retina

Certain topics in research and advancements in medical diagnostics may benefit from improved temporal and spatial resolution during non-invasive optical imaging of living tissue. However, so far no imaging technique can generate entirely diffraction-limited tomographic volumes with a single data acquisition, if the target moves or changes rapidly, such as the human retina. Additionally, the presence of aberrations may represent further difficulties. We show that a simple interferometric setup–based on parallelized optical coherence tomography–acquires volumetric data with 10 billion voxels per second, exceeding previous imaging speeds by an order of magnitude. This allows us to computationally obtain and correct defocus and aberrations resulting in entirely diffraction-limited volumes. As demonstration, we imaged living human retina with clearly visible nerve fiber layer, small capillary networks, and photoreceptor cells. Furthermore, the technique can also obtain phase-sensitive volumes of other scattering structures at unprecedented acquisition speeds.

Computed Optical Interferometric Imaging: Methods, Achievements, and Challenges

Three-dimensional high-resolution optical imaging systems are generally restricted by the trade-off between resolution and depth-of-field as well as imperfections in the imaging system or sample. Computed optical interferometric imaging is able to overcome these longstanding limitations using methods such as interferometric synthetic aperture microscopy (ISAM) and computational adaptive optics (CAO) which manipulate the complex interferometric data. These techniques correct for limited depth-of-field and optical aberrations without the need for additional hardware. This paper aims to outline these computational methods, making them readily available to the research community. Achievements of the techniques will be highlighted, along with past and present challenges in implementing the techniques. Challenges such as phase instability and determination of the appropriate aberration correction have been largely overcome so that imaging of living tissues using ISAM and CAO is now possible. Computed imaging in optics is becoming a mature technology poised to make a significant impact in medicine and biology.

Real-time imaging through strongly scattering media: seeing through turbid media, instantly

Numerous everyday situations like navigation, medical imaging and rescue operations require viewing through optically inhomogeneous media. This is a challenging task as photons propagate predominantly diffusively (rather than ballistically) due to random multiple scattering off the inhomogenieties. Real-time imaging with ballistic light under continuous-wave illumination is even more challenging due to the extremely weak signal, necessitating voluminous data-processing. Here we report imaging through strongly scattering media in real-time and at rates several times the critical flicker frequency of the eye, so that motion is perceived as continuous. Two factors contributed to the speedup of more than three orders of magnitude over conventional techniques - the use of a simplified algorithm enabling processing of data on the fly, and the utilisation of task and data parallelization capabilities of typical desktop computers. The extreme simplicity of the technique, and its implementation with present day low-cost technology promises its utility in a variety of devices in maritime, aerospace, rail and road transport, in medical imaging and defence. It is of equal interest to the common man and adventure sportsperson like hikers, divers, mountaineers, who frequently encounter situations requiring realtime imaging through obscuring media. As a specific example, navigation under poor visibility is examined.

Automated interferometric synthetic aperture microscopy and computational adaptive optics for improved optical coherence tomography

In this paper, we introduce an algorithm framework for the automation of interferometric synthetic aperture microscopy (ISAM). Under this framework, common processing steps such as dispersion correction, Fourier domain resampling, and computational adaptive optics aberration correction are carried out as metrics-assisted parameter search problems. We further present the results of this algorithm applied to phantom and biological tissue samples and compare with manually adjusted results. With the automated algorithm, near-optimal ISAM reconstruction can be achieved without manual adjustment. At the same time, the technical barrier for the nonexpert using ISAM imaging is also significantly lowered.

Intraoperative optical coherence tomography for assessing human lymph nodes for metastatic cancer

Background

Evaluation of lymph node (LN) status is an important factor for detecting metastasis and thereby staging breast cancer. Currently utilized clinical techniques involve the surgical disruption and resection of lymphatic structure, whether nodes or axillary contents, for histological examination. While reasonably effective at detection of macrometastasis, the majority of the resected lymph nodes are histologically negative. Improvements need to be made to better detect micrometastasis, minimize or eliminate lymphatic disruption complications, and provide immediate and accurate intraoperative feedback for in vivo cancer staging to better guide surgery.

Methods

We evaluated the use of optical coherence tomography (OCT), a high-resolution, real-time, label-free imaging modality for the intraoperative assessment of human LNs for metastatic disease in patients with breast cancer. We assessed the sensitivity and specificity of double-blinded trained readers who analyzed intraoperative OCT LN images for presence of metastatic disease, using co-registered post-operative histopathology as the gold standard.

Results

Our results suggest that intraoperative OCT examination of LNs is an appropriate real-time, label-free, non-destructive alternative to frozen-section analysis, potentially offering faster interpretation and results to empower superior intraoperative decision-making.

Conclusions

Intraoperative OCT has strong potential to supplement current post-operative histopathology with real-time in situ assessment of LNs to preserve both non-cancerous nodes and their lymphatic vessels, and thus reduce the associated risks and complications from surgical disruption of lymphoid structures following biopsy.

Response of Simulated Drinking Water Biofilm Mechanical and Structural Properties to Long-Term Disinfectant Exposure

Mechanical and structural properties of biofilms influence the accumulation and release of pathogens in drinking water distribution systems (DWDS). Thus, understanding how long-term residual disinfectants exposure affects biofilm mechanical and structural properties is a necessary aspect for pathogen risk assessment and control. In this study, elastic modulus and structure of groundwater biofilms was monitored by atomic force microscopy (AFM) and optical coherence tomography (OCT) during three months of exposure to monochloramine or free chlorine. After the first month of disinfectant exposure, the mean stiffness of monochloramine- or free-chlorine-treated biofilms was 4 to 9 times higher than those before treatment. Meanwhile, the biofilm thickness decreased from 120 ± 8 μm to 93 ± 6-107 ± 11 μm. The increased surface stiffness and decreased biofilm thickness within the first month of disinfectant exposure was presumably due to the consumption of biomass. However, by the second to third month during disinfectant exposure, the biofilm mean stiffness showed a 2- to 4-fold decrease, and the biofilm thickness increased to 110 ± 7-129 ± 8 μm, suggesting that the biofilms adapted to disinfectant exposure. After three months of the disinfectant exposure process, the disinfected biofilms showed 2-5 times higher mean stiffness (as determined by AFM) and 6-13-fold higher ratios of protein over polysaccharide, as determined by differential staining and confocal laser scanning microscopy (CLSM), than the nondisinfected groundwater biofilms. However, the disinfected biofilms and nondisinfected biofilms showed statistically similar thicknesses (t test, p > 0.05), suggesting that long-term disinfection may not significantly remove net biomass. This study showed how biofilm mechanical and structural properties vary in response to a complex DWDS environment, which will contribute to further research on the risk assessment and control of biofilm-associated-pathogens in DWDS.

Real-time Imaging of the Resection Bed Using a Handheld Probe to Reduce Incidence of Microscopic Positive Margins in Cancer Surgery

Wide local excision (WLE) is a common surgical intervention for solid tumors such as those in melanoma, breast, pancreatic, and gastrointestinal cancer. However, adequate margin assessment during WLE remains a significant challenge, resulting in surgical reinterventions to achieve adequate local control. Currently, no label-free imaging method is available for surgeons to examine the resection bed in vivo for microscopic residual cancer. Optical coherence tomography (OCT) enables real-time high-resolution imaging of tissue microstructure. Previous studies have demonstrated that OCT analysis of excised tissue specimens can distinguish between normal and cancerous tissues by identifying the heterogeneous and disorganized microscopic tissue structures indicative of malignancy. In this translational study involving 35 patients, a handheld surgical OCT imaging probe was developed for in vivo use to assess margins both in the resection bed and on excised specimens for the microscopic presence of cancer. The image results from OCT showed structural differences between normal and cancerous tissue within the resection bed following WLE of the human breast. The ex vivo images were compared with standard postoperative histopathology to yield sensitivity of 91.7% [95% confidence interval (CI), 62.5%-100%] and specificity of 92.1% (95% CI, 78.4%-98%). This study demonstrates in vivo OCT imaging of the resection bed during WLE with the potential for real-time microscopic image-guided surgery.

Polarization-sensitive interferometric synthetic aperture microscopy

Three-dimensional optical microscopy suffers from the well-known compromise between transverse resolution and depth-of-field. This is true for both structural imaging methods and their functional extensions. Interferometric synthetic aperture microscopy (ISAM) is a solution to the 3D coherent microscopy inverse problem that provides depth-independent transverse resolution. We demonstrate the extension of ISAM to polarization sensitive imaging, termed polarization-sensitive interferometric synthetic aperture microscopy (PS-ISAM). This technique is the first functionalization of the ISAM method and provides improved depth-of-field for polarization-sensitive imaging. The basic assumptions of polarization-sensitive imaging are explored, and refocusing of birefringent structures is experimentally demonstrated. PS-ISAM enables high-resolution volumetric imaging of birefringent materials and tissue.

Optical coherence tomography-guided laser microsurgery for blood coagulation with continuous-wave laser diode

Blood coagulation is the clotting and subsequent dissolution of the clot following repair to the damaged tissue. However, inducing blood coagulation is difficult for some patients with homeostasis dysfunction or during surgery. In this study, we proposed a method to develop an integrated system that combines optical coherence tomography (OCT) and laser microsurgery for blood coagulation. Also, an algorithm for positioning of the treatment location from OCT images was developed. With OCT scanning, 2D/3D OCT images and angiography of tissue can be obtained simultaneously, enabling to noninvasively reconstruct the morphological and microvascular structures for real-time monitoring of changes in biological tissues during laser microsurgery. Instead of high-cost pulsed lasers, continuous-wave laser diodes (CW-LDs) with the central wavelengths of 450 nm and 532 nm are used for blood coagulation, corresponding to higher absorption coefficients of oxyhemoglobin and deoxyhemoglobin. Experimental results showed that the location of laser exposure can be accurately controlled with the proposed approach of imaging-based feedback positioning. Moreover, blood coagulation can be efficiently induced by CW-LDs and the coagulation process can be monitored in real-time with OCT. This technology enables to potentially provide accurate positioning for laser microsurgery and control the laser exposure to avoid extra damage by real-time OCT imaging.

Swept-source optical coherence tomography powered by a 1.3-μm vertical cavity surface emitting laser enables 2.3-mm-deep brain imaging in mice in vivo

We report noninvasive, in vivo optical imaging deep within a mouse brain by swept-source optical coherence tomography (SS-OCT), enabled by a 1.3-μm vertical cavity surface emitting laser (VCSEL). VCSEL SS-OCT offers a constant signal sensitivity of 105 dB throughout an entire depth of 4.25 mm in air, ensuring an extended usable imaging depth range of more than 2 mm in turbid biological tissue. Using this approach, we show deep brain imaging in mice with an open-skull cranial window preparation, revealing intact mouse brain anatomy from the superficial cerebral cortex to the deep hippocampus. VCSEL SS-OCT would be applicable to small animal studies for the investigation of deep tissue compartments in living brains where diseases such as dementia and tumor can take their toll.

Noninvasive in vivo imaging reveals differences between tectorial membrane and basilar membrane traveling waves in the mouse cochlea

Sound is encoded within the auditory portion of the inner ear, the cochlea, after propagating down its length as a traveling wave. For over half a century, vibratory measurements to study cochlear traveling waves have been made using invasive approaches such as laser Doppler vibrometry. Although these studies have provided critical information regarding the nonlinear processes within the living cochlea that increase the amplitude of vibration and sharpen frequency tuning, the data have typically been limited to point measurements of basilar membrane vibration. In addition, opening the cochlea may alter its function and affect the findings. Here we describe volumetric optical coherence tomography vibrometry, a technique that overcomes these limitations by providing depth-resolved displacement measurements at 200 kHz inside a 3D volume of tissue with picometer sensitivity. We studied the mouse cochlea by imaging noninvasively through the surrounding bone to measure sound-induced vibrations of the sensory structures in vivo, and report, to our knowledge, the first measures of tectorial membrane vibration within the unopened cochlea. We found that the tectorial membrane sustains traveling wave propagation. Compared with basilar membrane traveling waves, tectorial membrane traveling waves have larger dynamic ranges, sharper frequency tuning, and apically shifted positions of peak vibration. These findings explain discrepancies between previously published basilar membrane vibration and auditory nerve single unit data. Because the tectorial membrane directly overlies the inner hair cell stereociliary bundles, these data provide the most accurate characterization of the stimulus shaping the afferent auditory response available to date.

Depth-encoded synthetic aperture optical coherence tomography of biological tissues with extended focal depth

Optical coherence tomography (OCT) has proven to be able to provide three-dimensional (3D) volumetric images of scattering biological tissues for in vivo medical diagnostics. Unlike conventional optical microscopy, its depth-resolving ability (axial resolution) is exclusively determined by the laser source and therefore invariant over the full imaging depth. In contrast, its transverse resolution is determined by the objective's numerical aperture and the wavelength which is only approximately maintained over twice the Rayleigh range. However, the prevailing laser sources for OCT allow image depths of more than 5 mm which is considerably longer than the Rayleigh range. This limits high transverse resolution imaging with OCT. Previously, we reported a novel method to extend the depth-of-focus (DOF) of OCT imaging in Mo et al.Opt. Express 21, 10048 (2013)]. The approach is to create three different optical apertures via pupil segmentation with an annular phase plate. These three optical apertures produce three OCT images from the same sample, which are encoded to different depth positions in a single OCT B-scan. This allows for correcting the defocus-induced curvature of wave front in the pupil so as to improve the focus. As a consequence, the three images originating from those three optical apertures can be used to reconstruct a new image with an extended DOF. In this study, we successfully applied this method for the first time to both an artificial phantom and biological tissues over a four times larger depth range. The results demonstrate a significant DOF improvement, paving the way for 3D high resolution OCT imaging beyond the conventional Rayleigh range.

Computational high-resolution optical imaging of the living human retina

High-resolution in vivo imaging is of great importance for the fields of biology and medicine. The introduction of hardware-based adaptive optics (HAO) has pushed the limits of optical imaging, enabling high-resolution near diffraction-limited imaging of previously unresolvable structures^1,2. In ophthalmology, when combined with optical coherence tomography, HAO has enabled a detailed three-dimensional visualization of photoreceptor distributions^3,4 and individual nerve fibre bundles⁵ in the living human retina. However, the introduction of HAO hardware and supporting software adds considerable complexity and cost to an imaging system, limiting the number of researchers and medical professionals who could benefit from the technology. Here we demonstrate a fully automated computational approach that enables high-resolution in vivo ophthalmic imaging without the need for HAO. The results demonstrate that computational methods in coherent microscopy are applicable in highly dynamic living systems.

Three-dimensional motion correction using speckle and phase for in vivo computed optical interferometric tomography

Over the years, many computed optical interferometric techniques have been developed to perform high-resolution volumetric tomography. By utilizing the phase and amplitude information provided with interferometric detection, post-acquisition corrections for defocus and optical aberrations can be performed. The introduction of the phase, though, can dramatically increase the sensitivity to motion (most prominently along the optical axis). In this paper, we present two algorithms which, together, can correct for motion in all three dimensions with enough accuracy for defocus and aberration correction in computed optical interferometric tomography. The first algorithm utilizes phase differences within the acquired data to correct for motion along the optical axis. The second algorithm utilizes the addition of a speckle tracking system using temporally- and spatially-coherent illumination to measure motion orthogonal to the optical axis. The use of coherent illumination allows for high-contrast speckle patterns even when imaging apparently uniform samples or when highly aberrated beams cannot be avoided.

Depth extension and sidelobe suppression in optical coherence tomography using pupil filters

We demonstrate a new focus engineering scheme to achieve both extended depth of focus (DOF) and sidelobe suppression in spectral-domain optical coherence tomography (SD-OCT) system. Each of the illumination pupil function and the detection pupil function is modulated using an annular pupil filter implemented by center obscuration. The two pupil filters are arranged in a dark-field configuration such that the first sidelobe of the illumination point-spread function (PSF) matches the first minimum of the detection PSF in the lateral focal plane. We tested the feasibility of the proposed scheme numerically, and then constructed a dark-field OCT (DF-OCT) system to further verify its effectiveness experimentally. Simulation results show that a DOF gain of 4.2 can be achieved compared with a full aperture OCT (FA-OCT) system, with a suppression ratio of 2.9 dB for the first sidelobe compared with an annular-aperture bright-field OCT (BF-OCT) system. Experimental results show that the constructed DF-OCT extends the DOF by three-fold compared with the constructed FA-OCT, and suppresses the first sidelobe by 3.1 dB compared with the BF-OCT. The penalty for the extended DOF is an ~11.6 dB drop in sensitivity compared with the FA-OCT system.

Feasibility of ablative fractional laser-assisted drug delivery with optical coherence tomography

Fractional resurfacing creates hundreds of microscopic wounds in the skin without injuring surrounding tissue. This technique allows rapid wound healing owing to small injury regions, and has been proven as an effective method for repairing photodamaged skin. Recently, ablative fractional laser (AFL) treatment has been demonstrated to facilitate topical drug delivery into skin. However, induced fractional photothermolysis depends on several parameters, such as incident angle, exposure energy, and spot size of the fractional laser. In this study, we used fractional CO2 laser to induce microscopic ablation array on the nail for facilitating drug delivery through the nail. To ensure proper energy delivery without damaging tissue structures beneath the nail plate, optical coherence tomography (OCT) was implemented for quantitative evaluation of induced microscopic ablation zone (MAZ). Moreover, to further study the feasibility of drug delivery, normal saline was dripped on the exposure area of fingernail and the speckle variance in OCT signal was used to observe water diffusion through the ablative channels into the nail plate. In conclusion, this study establishes OCT as an effective tool for the investigation of fractional photothermolysis and water/drug delivery through microscopic ablation channels after nail fractional laser treatment.

Computed optical interferometric tomography for high-speed volumetric cellular imaging

Three-dimensional high-resolution imaging methods are important for cellular-level research. Optical coherence microscopy (OCM) is a low-coherence-based interferometry technology for cellular imaging with both high axial and lateral resolution. Using a high-numerical-aperture objective, OCM normally has a shallow depth of field and requires scanning the focus through the entire region of interest to perform volumetric imaging. With a higher-numerical-aperture objective, the image quality of OCM is affected by and more sensitive to aberrations. Interferometric synthetic aperture microscopy (ISAM) and computational adaptive optics (CAO) are computed imaging techniques that overcome the depth-of-field limitation and the effect of optical aberrations in optical coherence tomography (OCT), respectively. In this work we combine OCM with ISAM and CAO to achieve high-speed volumetric cellular imaging. Experimental imaging results of ex vivo human breast tissue, ex vivo mouse brain tissue, in vitro fibroblast cells in 3D scaffolds, and in vivo human skin demonstrate the significant potential of this technique for high-speed volumetric cellular imaging.

Stability in computed optical interferometric tomography (part I): stability requirements

As imaging systems become more advanced and acquire data at faster rates, increasingly dynamic samples can be imaged without concern of motion artifacts. For optical interferometric techniques such as optical coherence tomography, it often follows that initially, only amplitude-based data are utilized due to unstable or unreliable phase measurements. As systems progress, stable phase maps can also be acquired, enabling more advanced, phase-dependent post-processing techniques. Here we report an investigation of the stability requirements for a class of phase-dependent post-processing techniques - numerical defocus and aberration correction with further extensions to techniques such as Doppler, phase-variance, and optical coherence elastography. Mathematical analyses and numerical simulations over a variety of instabilities are supported by experimental investigations.

Stability in computed optical interferometric tomography (Part II): in vivo stability assessment

Stability is of utmost importance to a wide range of phase-sensitive processing techniques. In Doppler optical coherence tomography and optical coherence elastography, in addition to defocus and aberration correction techniques such as interferometric synthetic aperture microscopy and computational/digital adaptive optics, a precise understanding of the system and sample stability helps to guide the system design and choice of imaging parameters. This article focuses on methods to accurately and quantitatively measure the stability of an imaging configuration in vivo. These methods are capable of partially decoupling axial from transverse motion and are compared against the stability requirements for computed optical interferometric tomography laid out in the first part of this article.

Parallelized multi-graphics processing unit framework for high-speed Gabor-domain optical coherence microscopy

Gabor-domain optical coherence microscopy (GD-OCM) is a volumetric high-resolution technique capable of acquiring three-dimensional (3-D) skin images with histological resolution. Real-time image processing is needed to enable GD-OCM imaging in a clinical setting. We present a parallelized and scalable multi-graphics processing unit (GPU) computing framework for real-time GD-OCM image processing. A parallelized control mechanism was developed to individually assign computation tasks to each of the GPUs. For each GPU, the optimal number of amplitude-scans (A-scans) to be processed in parallel was selected to maximize GPU memory usage and core throughput. We investigated five computing architectures for computational speed-up in processing 1000×1000 A-scans. The proposed parallelized multi-GPU computing framework enables processing at a computational speed faster than the GD-OCM image acquisition, thereby facilitating high-speed GD-OCM imaging in a clinical setting. Using two parallelized GPUs, the image processing of a 1×1×0.6  mm3 skin sample was performed in about 13 s, and the performance was benchmarked at 6.5 s with four GPUs. This work thus demonstrates that 3-D GD-OCM data may be displayed in real-time to the examiner using parallelized GPU processing.

Numerical focusing methods for full field OCT: a comparison based on a common signal model

In this paper a theoretical model of the full field swept source (FF SS) OCT signal is presented based on the angular spectrum wave propagation approach which accounts for the defocus error with imaging depth. It is shown that using the same theoretical model of the signal, numerical defocus correction methods based on a simple forward model (FM) and inverse scattering (IS), the latter being similar to interferometric synthetic aperture microscopy (ISAM), can be derived. Both FM and IS are compared quantitatively with sub-aperture based digital adaptive optics (DAO). FM has the least numerical complexity, and is the fastest in terms of computational speed among the three. SNR improvement of more than 10 dB is shown for all the three methods over a sample depth of 1.5 mm. For a sample with non-uniform refractive index with depth, FM and IS both improved the depth of focus (DOF) by a factor of 7x for an imaging NA of 0.1. DAO performs the best in case of non-uniform refractive index with respect to DOF improvement by 11x.

Multifocal interferometric synthetic aperture microscopy

There is an inherent trade-off between transverse resolution and depth of field (DOF) in optical coherence tomography (OCT) which becomes a limiting factor for certain applications. Multifocal OCT and interferometric synthetic aperture microscopy (ISAM) each provide a distinct solution to the trade-off through modification to the experiment or via post-processing, respectively. In this paper, we have solved the inverse problem of multifocal OCT and present a general algorithm for combining multiple ISAM datasets. Multifocal ISAM (MISAM) uses a regularized combination of the resampled datasets to bring advantages of both multifocal OCT and ISAM to achieve optimal transverse resolution, extended effective DOF and improved signal-to-noise ratio. We present theory, simulation and experimental results.