Label-free CARS microscopy through a multimode fiber endoscope

Vibrational fiber photometry: label-free and reporter-free minimally invasive Raman spectroscopy deep in the mouse brain

Optical approaches to monitor neural activity are transforming neuroscience, owing to a fast-evolving palette of genetically encoded molecular reporters. However, the field still requires robust and label-free technologies to monitor the multifaceted biomolecular changes accompanying brain development, aging or disease. Here, we have developed vibrational fiber photometry as a low-invasive method for label-free monitoring of the biomolecular content of arbitrarily deep regions of the mouse brain in vivo through spontaneous Raman spectroscopy. Using a tapered fiber probe as thin as 1 µm at its tip, we elucidate the cytoarchitecture of the mouse brain, monitor molecular alterations caused by traumatic brain injury, as well as detect markers of brain metastasis with high accuracy. We view our approach, which introduces a deep learning algorithm to suppress probe background, as a promising complement to the existing palette of tools for the optical interrogation of neural function, with application to fundamental and preclinical investigations of the brain and other organs.

Polarization-resolved transmission matrices of specialty optical fibers

Transmission matrix measurements of multimode fibers are now routinely performed in numerous laboratories, enabling control of the electric field at the distal end of the fiber and paving the way for the potential application to ultrathin medical endoscopes with high resolution. The same concepts are applicable to other areas, such as space division multiplexing, targeted power delivery, fiber laser performance, and the general study of the mode coupling properties of the fiber. However, the process of building an experimental setup and developing the supporting code to measure the fiber's transmission matrix remains challenging and time consuming, with full details on experimental design, data collection, and supporting algorithms spread over multiple papers or lacking in detail. Here, we outline a complete and self-contained description of the specific experiment we use to measure fully polarization-resolved transmission matrices, which enable full control of the electric field, in contrast to the more common scalar setups. Our exact implementation of the full polarization experiment is new and is easy to align while providing flexibility to switch between full-polarization and scalar measurements if desired. We utilize a spatial light modulator to measure the transmission matrix using linear phase gratings to generate the basis functions and measure the distal electric field using phase-shifting interferometry with an independent reference beam derived from the same laser. We introduce a new method to measure and account for the phase and amplitude drift during the measurement using a Levenberg-Marquardt nonlinear fitting algorithm. Finally, we describe creating distal images through the multimode fiber using phase-to-amplitude shaping techniques to construct the correct input electric field through a superposition of the basis functions with the phase-only spatial light modulator. We show that results are insensitive to the choice of phase-to-amplitude shaping technique as quantified by measuring the contrast of a razor blade at the distal end of the fiber, indicating that the simplest but most power efficient method may be the best choice for many applications. We also discuss some of the possible variations on the setup and techniques presented here and highlight the details that we have found key in achieving high fidelity distal control. Throughout the paper, we discuss applications of our setup and measurement process to a variety of specialty fibers, including fibers with harsh environment coatings, coreless fibers, rectangular core fibers, pedestal fibers, and a pump-signal combiner based on a tapered fiber bundle. This demonstrates the usefulness of these techniques across a variety of application areas and shows the flexibility of our setup in studying various fiber types.

Unsupervised data driven approaches to Raman imaging through a multimode optical fiber

Raman spectroscopy is a label-free, chemically specific optical technique that provides detailed information about the chemical composition and structure of the excited analyte. Because of this, there is growing research interest in miniaturizing Raman probes to reach deep regions of the body. Typically, such probes utilize multiple optical fibers to act as separate excitation/collection channels with optical filters attached to the distal facet to separate the collected signal from the background optical signal from the probe itself. Although these probes have achieved impressive diagnostic performance, their use is limited by the overall size of the probe, which is typically several hundred micrometers to millimeters. Here, we show how a wavefront shaping technique can be used to measure Raman images through a single, hair-thin multimode fiber. The wavefront shaping technique transforms the tip of the fiber to a micrometer spatial resolution Raman microscope. The resultant Raman images were analyzed with a variety of state-of-the-art statistical techniques, including principal component analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE), uniform manifold approximation and projection (UMAP), and k-means clustering. Our data-driven approach enables us to create Raman images of microclusters of pharmaceuticals using fingerprint region Raman spectra through a standard silica multimode optical fiber.

Advantages of internal reference in holographic shaping ps supercontinuum pulses through multimode optical fibers

The use of wavefront shaping has found extensive application to develop ultra-thin endoscopic techniques based on multimode optical fibers (MMF), leveraging on the ability to control modal interference at the fiber's distal end. Although several techniques have been developed to achieve MMF-based laser-scanning imaging, the use of short laser pulses is still a challenging application. This is due to the intrinsic delay and temporal broadening introduced by the fiber itself, which requires additional compensation optics on the reference beam during the calibration procedure. Here we combine the use of a supercontinuum laser and an internal reference-based wavefront shaping system to produce focused spot scanning in multiple planes at the output of a step-index multimode fiber, without the requirement of a delay line or pulse pre-compensation. We benchmarked the performances of internal vs external reference during calibration, finding that the use of an internal reference grants better focusing efficiency. The system was characterized at different wavelengths, showcasing the wavelength resiliency of the different parameters. Lastly, the scanning of focal planes beyond the fiber facet was achieved by exploiting the chromato-axial memory effect.

Exploiting holographically encoded variance to transmit labelled images through a multimode optical fiber

Artificial intelligence has emerged as promising tool to decode an image transmitted through a multimode fiber (MMF) by applying deep learning techniques. By transmitting thousands of images through the MMF, deep neural networks (DNNs) are able to decipher the seemingly random output speckle patterns and unveil the intrinsic input-output relationship. High fidelity reconstruction is obtained for datasets with a large degree of homogeneity, which underutilizes the capacity of the combined MMF-DNN system. Here, we show that holographic modulation can encode an additional layer of variance on the output speckle pattern, improving the overall transmissive capabilities of the system. Operatively, we have implemented this by adding a holographic label to the original dataset and injecting the resulting phase image into the fiber facet through a Fourier transform lens. The resulting speckle pattern dataset can be clustered primarily by holographic label, and can be reconstructed without loss of fidelity. As an application, we describe how color images may be segmented into RGB components and each color component may then be labelled by distinct hologram. A ResUNet architecture was then used to decode each class of speckle patterns and reconstruct the color image without the need for temporal synchronization between sender and receiver.

Collagen organization and structure in FBLN5-/- mice using label-free microscopy: implications for pelvic organ prolapse

Pelvic organ prolapse (POP) is a gynecological disorder described by the descent of superior pelvic organs into or out of the vagina as a consequence of disrupted muscles and tissue. A thorough understanding of the etiology of POP is limited by the availability of clinically relevant samples, restricting longitudinal POP studies on soft-tissue biomechanics and structure to POP-induced models such as fibulin-5 knockout (FBLN5-/- ) mice. Despite being a principal constituent in the extracellular matrix, little is known about structural perturbations to collagen networks in the FBLN5-/- mouse cervix. We identify significantly different collagen network populations in normal and prolapsed cervical cross-sections using two label-free, nonlinear microscopy techniques. Collagen in the prolapsed mouse cervix tends to be more isotropic, and displays reduced alignment persistence via 2-D Fourier transform analysis of images acquired using second harmonic generation microscopy. Furthermore, coherent Raman hyperspectral imaging revealed elevated disorder in the secondary structure of collagen in prolapsed tissues. Our results underscore the need for in situ multimodal monitoring of collagen organization to improve POP predictive capabilities.

Highly efficient and widely tunable Si3N4 waveguide-based optical parametric oscillator

We demonstrate an efficient and widely tunable synchronously pumped optical parametric oscillator (OPO) exploiting four-wave mixing (FWM) in a silicon nitride (Si3N4) waveguide with inverted tapers. At a pump pulse duration of 2 ps, the waveguide-based OPO (WOPO) exhibited a high external pump-to-idler conversion efficiency of up to -7.64 dB at 74% pump depletion and a generation of up to 387 pJ output idler pulse energy around 1.13 μm wavelength. Additionally, the parametric oscillation resulted in a 64 dB amplification of idler power spectral density in comparison to spontaneous FWM, allowing for a wide idler wavelength tunability of 191 nm around 1.15 μm. Our WOPO represents a significant improvement of conversion efficiency as well as output energy among χ3 WOPOs, rendering an important step towards a highly efficient and widely tunable chip-based light source for, e.g., coherent anti-Stokes Raman scattering.

Generating Airy beams through multimode fibres

Focussing light through a multimode fibre (MMF) is the basis of holographic endoscopes, which currently enable detailed imaging of deep tissue. Achieving high fidelity and purity diffraction-limited foci has been shown to be possible, when fully controlling the amplitude, phase, and two orthogonal polarisation states of the input field. Yet, generating more complex field distributions with similar performance remains to be assessed. Here, we demonstrate the generation of Airy beams through an MMF containing in excess of 90 % of the optical power delivered by the fibre. We discuss two distinct methods for generating optical landscapes: the direct field and the Fourier domain synthesis. Moreover, we showcase the flexibility of the Fourier domain synthesis to modify the generated beam.

Collagen organization and structure in FLBN5-/- mice using label-free microscopy: implications for pelvic organ prolapse

Pelvic organ prolapse (POP) is a gynecological disorder described by the descent of superior pelvic organs into or out of the vagina as a consequence of disrupted muscles and tissue. A thorough understanding of the etiology of POP is limited by the availability of clinically relevant samples, restricting longitudinal POP studies on soft-tissue biomechanics and structure to POP-induced models such as fibulin-5 knockout (FBLN5-/-) mice. Despite being a principal constituent in the extracellular matrix, little is known about structural perturbations to collagen networks in the FBLN5-/- mouse cervix. We identify significantly different collagen network populations in normal and prolapsed cervical cross-sections using two label-free, nonlinear microscopy techniques. Collagen in the prolapsed mouse cervix tends to be more isotropic, and displays reduced alignment persistence via 2-D Fourier Transform analysis of images acquired using second harmonic generation microscopy. Furthermore, coherent Raman hyperspectral imaging revealed elevated disorder in the secondary structure of collagen in prolapsed tissues. Our results underscore the need for in situ multimodal monitoring of collagen organization to improve POP predictive capabilities.

Optimizing the internal phase reference to shape the output of a multimode optical fiber

Pre-shaping light to achieve desired amplitude distributions at the tip of a multimode fiber (MMF) has emerged as a powerful method allowing a wide range of imaging techniques to be implemented at the distal facet. Such techniques rely on measuring the transmission matrix of the optically turbid waveguide which scrambles the coherent input light into an effectively random speckle pattern. Typically, this is done by measuring the interferogram between the output speckle and a reference beam. In recent years, an optical setup where the reference beam passes through the MMF has become an attractive configuration because of the high interferometric stability of the common optical path. However, the merits and drawbacks of an internal reference beam remain controversial. The measurement of the transmission matrix is known to depend on the choice of internal reference and has been reported to result in "blind spots" due to phase singularities of the reference beam. Here, we describe how the focussing efficiency of the calibration can be increased by several percent by optimising the choice of internal reference beam.

Contribution of Intravital Neuroimaging to Study Animal Models of Multiple Sclerosis

Multiple sclerosis (MS) is a complex and long-lasting neurodegenerative disease of the central nervous system (CNS), characterized by the loss of myelin within the white matter and cortical fibers, axonopathy, and inflammatory responses leading to consequent sensory-motor and cognitive deficits of patients. While complete resolution of the disease is not yet a reality, partial tissue repair has been observed in patients which offers hope for therapeutic strategies. To address the molecular and cellular events of the pathomechanisms, a variety of animal models have been developed to investigate distinct aspects of MS disease. Recent advances of multiscale intravital imaging facilitated the direct in vivo analysis of MS in the animal models with perspective of clinical transfer to patients. This review gives an overview of MS animal models, focusing on the current imaging modalities at the microscopic and macroscopic levels and emphasizing the importance of multimodal approaches to improve our understanding of the disease and minimize the use of animals.

Learned end-to-end high-resolution lensless fiber imaging towards real-time cancer diagnosis

Recent advances in label-free histology promise a new era for real-time diagnosis in neurosurgery. Deep learning using autofluorescence is promising for tumor classification without histochemical staining process. The high image resolution and minimally invasive diagnostics with negligible tissue damage is of great importance. The state of the art is raster scanning endoscopes, but the distal lens optics limits the size. Lensless fiber bundle endoscopy offers both small diameters of a few 100 microns and the suitability as single-use probes, which is beneficial in sterilization. The problem is the inherent honeycomb artifacts of coherent fiber bundles (CFB). For the first time, we demonstrate an end-to-end lensless fiber imaging with exploiting the near-field. The framework includes resolution enhancement and classification networks that use single-shot CFB images to provide both high-resolution imaging and tumor diagnosis. The well-trained resolution enhancement network not only recovers high-resolution features beyond the physical limitations of CFB, but also helps improving tumor recognition rate. Especially for glioblastoma, the resolution enhancement network helps increasing the classification accuracy from 90.8 to 95.6%. The novel technique enables histological real-time imaging with lensless fiber endoscopy and is promising for a quick and minimally invasive intraoperative treatment and cancer diagnosis in neurosurgery.

A method for single particle tracking through a multimode fiber

Multimode optical fiber (MMF) endoscopes have recently gained widespread attention as a novel tool for imaging deep within tissue using light microscopy. We here present a method for particle tracking through the MMF, which overcomes the lack of a fast enough wide-field fluorescence imaging modality for this type of endoscope, namely a discrete implementation of orbital particle tracking. We achieve biologically relevant tracking speeds (up to 1.2 μm/s) despite using a slow SLM for the wavefront shaping. We demonstrate a tracking accuracy of λ/50 for a 0.3 NA fiber and show tracking of a pinhole moving to mimic Brownian motion with diffusion rates of up to 0.3 μm²/s.

Ultrathin, high-speed, all-optical photoacoustic endomicroscopy probe for guiding minimally invasive surgery

Photoacoustic (PA) endoscopy has shown significant potential for clinical diagnosis and surgical guidance. Multimode fibres (MMFs) are becoming increasingly attractive for the development of miniature endoscopy probes owing to their ultrathin size, low cost and diffraction-limited spatial resolution enabled by wavefront shaping. However, current MMF-based PA endomicroscopy probes are either limited by a bulky ultrasound detector or a low imaging speed that hindered their usability. In this work, we report the development of a highly miniaturised and high-speed PA endomicroscopy probe that is integrated within the cannula of a 20 gauge medical needle. This probe comprises a MMF for delivering the PA excitation light and a single-mode optical fibre with a plano-concave microresonator for ultrasound detection. Wavefront shaping with a digital micromirror device enabled rapid raster-scanning of a focused light spot at the distal end of the MMF for tissue interrogation. High-resolution PA imaging of mouse red blood cells covering an area 100 µm in diameter was achieved with the needle probe at ∼3 frames per second. Mosaicing imaging was performed after fibre characterisation by translating the needle probe to enlarge the field-of-view in real-time. The developed ultrathin PA endomicroscopy probe is promising for guiding minimally invasive surgery by providing functional, molecular and microstructural information of tissue in real-time.

All-optical thermometry using a single multimode fiber endoscope and diamond nanoparticles containing nitrogen vacancy centers

Photoluminescence (PL) spectra from diamond nanoparticles containing negative nitrogen vacancy centers were measured by using a single multimode fiber endoscope combined with a high-sensitivity spectroscopy system. A laser light spot was produced at the distal end of the endoscope and the PL spectra from a temperature-controlled ensemble of diamond nanoparticles were measured. After calibrating the sensitivity and wavelength of the spectroscopy system, the temperature dependence of the zero-phonon line peak wavelength similar to those previously reported was obtained.

Non-invasive chemically selective energy delivery and focusing inside a scattering medium guided by Raman scattering

Raman scattering is a chemically selective probing mechanism with diverse applications in industry and clinical settings. Yet, most samples are optically opaque limiting the applicability of Raman probing at depth. Here, we demonstrate chemically selective energy deposition behind a scattering medium by combining prior information on the chemical's spectrum with the measurement of a spectrally resolved Raman speckle as a feedback mechanism for wavefront shaping. We demonstrate unprecedented sixfold signal enhancement in an epi-geometry, realizing targeted energy deposition and focusing on individual Raman active particles.

Near perfect focusing through multimode fibres

Holographic, multimode fibre (MMF) based endoscopes envision high-quality in-vivo imaging inside previously inaccessible structures of living organisms, amongst other perspective applications. Within these instruments, a digital micro-mirror device (DMD) is deployed in order to holographically synthesise light fields which, after traversing the multimode fibre, form foci at desired positions behind the distal fibre facet. When applied in various imaging modalities, the purity and sharpness of the achieved foci are determinant for the imaging performance. Here we present diffraction-limited foci, which contain in excess of 96% of optical power delivered by the fibre which, to the best of our knowledge, represents the highest value reported to date. Further, we quantitatively study the impact of various conditions of the experimental procedure including input polarisation settings, influence of ghost diffraction orders, light modulation regimes, bias of the calibration camera and the influence of noise.

Suppression of the non-linear background in a multimode fibre CARS endoscope

Multimode fibres show great potential for use as miniature endoscopes for imaging deep in tissue with minimal damage. When used for coherent anti-Stokes Raman scattering (CARS) microscopy with femtosecond excitation sources, a high band-width probe is required to efficiently focus the broadband laser pulses at the sample plane. Although graded-index (GRIN) fibres have a large bandwidth, it is accompanied by a strong background signal from four-wave mixing and other non-linear processes occurring inside the fibre. We demonstrate that using a composite probe consisting of a GRIN fibre with a spliced on step-index fibre reduces the intensity of the non-linear background by more than one order of magnitude without significantly decreasing the focusing performance of the probe. Using this composite probe we acquire CARS images of biologically relevant tissue such as myelinated axons in the brain with good contrast.

Time-of-flight 3D imaging through multimode optical fibers

[Figure: see text].

Translational biophotonics with Raman imaging: clinical applications and beyond

Clinical medicine continues to seek novel rapid non-invasive tools capable of providing greater insight into disease progression and management. Raman scattering based technologies constitute a set of tools under continuing development to address outstanding challenges spanning diagnostic medicine, surgical guidance, therapeutic monitoring, and histopathology. Here we review the mechanisms and clinical applications of Raman scattering, specifically focusing on high-speed imaging methods that can provide spatial context for translational biomedical applications.

Multimodal nonlinear endomicroscopic imaging probe using a double-core double-clad fiber and focus-combining micro-optical concept

Multimodal non-linear microscopy combining coherent anti-Stokes Raman scattering, second harmonic generation, and two-photon excited fluorescence has proved to be a versatile and powerful tool enabling the label-free investigation of tissue structure, molecular composition, and correlation with function and disease status. For a routine medical application, the implementation of this approach into an in vivo imaging endoscope is required. However, this is a difficult task due to the requirements of a multicolour ultrashort laser delivery from a compact and robust laser source through a fiber with low losses and temporal synchronization, the efficient signal collection in epi-direction, the need for small-diameter but highly corrected endomicroobjectives of high numerical aperture and compact scanners. Here, we introduce an ultra-compact fiber-scanning endoscope platform for multimodal non-linear endomicroscopy in combination with a compact four-wave mixing based fiber laser. The heart of this fiber-scanning endoscope is an in-house custom-designed, single mode, double clad, double core pure silica fiber in combination with a 2.4 mm diameter NIR-dual-waveband corrected endomicroscopic objective of 0.55 numerical aperture and 180 µm field of view for non-linear imaging, allowing a background free, low-loss, high peak power laser delivery, and an efficient signal collection in backward direction. A linear diffractive optical grating overlays pump and Stokes laser foci across the full field of view, such that diffraction-limited performance is demonstrated for tissue imaging at one frame per second with sub-micron spatial resolution and at a high transmission of 65% from the laser to the specimen using a distal resonant fiber scanner.

Coherent Raman scattering microscopy for chemical imaging of biological systems

Coherent Raman scattering (CRS) processes, including both the coherent anti-Stokes Raman scattering and stimulated Raman scattering, have been utilized in state-of-the-art microscopy platforms for chemical imaging of biological samples. The key advantage of CRS microscopy over fluorescence microscopy is label-free, which is an attractive characteristic for modern biological and medical sciences. Besides, CRS has other advantages such as higher selectivity to metabolites, no photobleaching, and narrow peak width. These features have brought fast-growing attention to CRS microscopy in biological research. In this review article, we will first briefly introduce the history of CRS microscopy, and then explain the theoretical background of the CRS processes in detail using the classical approach. Next, we will cover major instrumentation techniques of CRS microscopy. Finally, we will enumerate examples of recent applications of CRS imaging in biological and medical sciences.

Compressively sampling the optical transmission matrix of a multimode fibre

The measurement of the optical transmission matrix (TM) of an opaque material is an advanced form of space-variant aberration correction. Beyond imaging, TM-based methods are emerging in a range of fields, including optical communications, micro-manipulation, and computing. In many cases, the TM is very sensitive to perturbations in the configuration of the scattering medium it represents. Therefore, applications often require an up-to-the-minute characterisation of the fragile TM, typically entailing hundreds to thousands of probe measurements. Here, we explore how these measurement requirements can be relaxed using the framework of compressive sensing, in which the incorporation of prior information enables accurate estimation from fewer measurements than the dimensionality of the TM we aim to reconstruct. Examples of such priors include knowledge of a memory effect linking the input and output fields, an approximate model of the optical system, or a recent but degraded TM measurement. We demonstrate this concept by reconstructing the full-size TM of a multimode fibre supporting 754 modes at compression ratios down to ∼5% with good fidelity. We show that in this case, imaging is still possible using TMs reconstructed at compression ratios down to ∼1% (eight probe measurements). This compressive TM sampling strategy is quite general and may be applied to a variety of other scattering samples, including diffusers, thin layers of tissue, fibre optics of any refractive profile, and reflections from opaque walls. These approaches offer a route towards the measurement of high-dimensional TMs either quickly or with access to limited numbers of measurements.

Spatiotemporal focusing through a multimode fiber via time-domain wavefront shaping

We shape fs optical pulses and deliver them in a single spatial mode to the input of a multimode fiber. The pulse is shaped in time such that at the output of the multimode fiber an ultrashort pulse appears at a predefined focus. Our result shows how to raster scan an ultrashort pulse at the output of a stiff piece of square-core step-index multimode fiber and in this way show the potential for making a nonlinear fluorescent image of the scene behind the fiber, while the connection to the multimode fiber can be established via a thin and flexible single-mode fiber. The experimental results match our numerical simulation well.

All-fiber single-cavity dual-comb for coherent anti-Stokes Raman scattering spectroscopy based on spectral focusing

We report an all-fiber free-running bidirectional dual-comb laser system for coherent anti-Stokes Raman scattering spectroscopy based on spectral focusing. The mode-locked oscillator is a bidirectional ring-cavity erbium fiber laser running at a repetition rate of ∼114MHz. One output of the bidirectional laser is wavelength-shifted from 1560 to 1060 nm via supercontinuum generation for use as the pump source. We have been able to record the Raman spectra of various samples such as polystyrene, olive oil, polymethyl methacrylate (PMMA), and polyethylene in the C-H stretching window. We believe that this all-fiber laser design has promising potential for coherent Raman spectroscopy and also label-free imaging for a variety of practical applications.

Volumetric two-photon fluorescence imaging of live neurons using a multimode optical fiber

Multimode optical fibers (MMFs), combined with wavefront control methods, have achieved minimally invasive in vivo imaging of neurons in deep-brain regions with diffraction-limited spatial resolution. Here, we report a method for volumetric two-photon fluorescence imaging with a MMF-based system requiring a single transmission matrix measurement. Central to this method is the use of a laser source able to generate both continuous wave light and femtosecond pulses. The chromatic dispersion of pulses generated an axially elongated excitation focus, which we used to demonstrate volumetric imaging of neurons and their dendrites in live rat brain slices through a 60 µm core MMF.

Non-linear label-free imaging through a multimode graded index optical fibre

In recent years, great advances have been made in developing minimal footprint micro-endoscopes using multimode optical fibres (MMF) [1]. By employing wavefront shaping methods the seemingly random speckle pattern resulting from the guiding of coherent light through an MMF can be formed into a diffraction limited spot. This enables the implementation of multiple laser scanning techniques. In this work we show that this approach can be employed to realize label-free non-linear microscopy techniques such as coherent anti-Stokes Raman scattering (CARS) and second harmonic generation (SHG). Backscattered light makes epi-detection possible even though these processes preferably emit light in the direction of beam propagation [2].