Fractal propagation method enables realistic optical microscopy simulations in biological tissues

Implantable photonic neural probes with out-of-plane focusing grating emitters

We have designed, fabricated, and characterized implantable silicon neural probes with nanophotonic grating emitters that focus the emitted light at a specified distance above the surface of the probe for spatially precise optogenetic targeting of neurons. Using the holographic principle, we designed gratings for wavelengths of 488 and 594 nm, targeting the excitation spectra of the optogenetic actuators Channelrhodopsin-2 and Chrimson, respectively. The measured optical emission pattern of these emitters in non-scattering medium and tissue matched well with simulations. To our knowledge, this is the first report of focused spots with the size scale of a neuron soma in brain tissue formed from implantable neural probes.

Airy-Gaussian vector beam and its application in generating flexible optical chains

In recent years, the manipulation of structured optical beam has become an attractive and promising area. The Gaussian beam is the most common beam as the output beam of the laser, and the Airy beam is recently proposed with fascinating properties and applications. In this paper, for the first time to our knowledge, the polarization is used as a tool to design a new kind of Airy-Gaussian vector beam by connecting the Gaussian and Airy functions, which opens a new avenue in designing new beams based on the existed beams. We realize the Airy-Gaussian vector beam with space-variant polarization distribution in theory and experiment, and find that the vector beam can autofocus twice during propagation. The optical chains with flexible intensity peaks are achieved with the Airy-Gaussian vector beam, which can be applied in trapping and delivering particles including biological cells and Rydberg atoms. Such optical chains can significantly improve the trapping efficiency, reduce the heat accumulation, and sweep away the impurity particles.

Fractal-based aberration-corrected full-field OCT

The Kolmogorov turbulence model has been validated as a quantitative 3D light scattering model of the inhomogeneous refraction index of biological tissue using full-field OCT (FF-OCT). A fractal-based computational compensation approach was proposed for correcting of depth-resolved aberrations with volumetric FF-OCT. First, the power-spectral density spectrum of the index inhomogeneities was measured by radial Fourier transformation of volumetric data. The spectrum's shape indicates the spatial correlation function and can be quantified as the fractal dimension of tissue. The defocusing correction matrix was built by applying fractal-based analysis as an image quality metric. For comparison, tissue-induced in-depth aberration models were built by phase compensation. After digital aberration correction of FF-OCT images, it enables extracting the temporal contrast indicating the sample dynamics in onion in mitosis and ex vivo mouse heart during delayed neuronal death. The proposed fractal-based contrast augmented images show subcellular resolution recording of dynamic scatters of the growing-up onion cell wall and some micro activities. In addition, low-frequency chamber and high-frequency cardiac muscle fibers from ex vivo mouse heart tissue. Therefore, the depth-resolved changes in fractal parameters may be regarded as a quantitative indicator of defocus aberration compensation. Also the enhanced temporal contrast in FF-OCT has the potential to be a label-free, non-invasive, and three-dimensional imaging tool to investigate sub-cellular activities in metabolism studies.

Modeling nonlinear optical microscopy in scattering media, part I. Propagation from lens to focal volume: tutorial

The development and application of nonlinear optical (NLO) microscopy methods in biomedical research have experienced rapid growth over the past three decades. Despite the compelling power of these methods, optical scattering limits their practical use in biological tissues. This tutorial offers a model-based approach illustrating how analytical methods from classical electromagnetism can be employed to comprehensively model NLO microscopy in scattering media. In Part I, we quantitatively model focused beam propagation in non-scattering and scattering media from the lens to focal volume. In Part II, we model signal generation, radiation, and far-field detection. Moreover, we detail modeling approaches for major optical microscopy modalities including classical fluorescence, multi-photon fluorescence, second harmonic generation, and coherent anti-Stokes Raman microscopy.

Ultra-thin boundary layer for high-accuracy simulations of light propagation

The modified Born series method is currently one of the most efficient methods available for simulating light scattering in large inhomogeneous media. However, to achieve high accuracy, the method requires thick gradually absorbing layers around the simulation domain. Here, we introduce new boundary conditions, combining a padding-free acyclic convolution with an ultra-thin boundary layer. Our new boundary conditions minimize the wrap-around and reflection artefacts originating from the edges of the simulation domain, while also greatly reducing the computational costs and the memory requirements of the method. Our GPU-accelerated Matlab implementation is available on GitHub.

Holistic Monte-Carlo optical modelling of biological imaging

The invention and advancement of biological microscopy depends critically on an ability to accurately simulate imaging of complex biological structures embedded within complex scattering media. Unfortunately no technique exists for rigorous simulation of the complete imaging process, including the source, instrument, sample and detector. Monte-Carlo modelling is the gold standard for the modelling of light propagation in tissue, but is somewhat laborious to implement and does not incorporate the rejection of scattered light by the microscope. On the other hand microscopes may be rigorously and rapidly modelled using commercial ray-tracing software, but excluding the interaction with the biological sample. We report a hybrid Monte-Carlo optical ray-tracing technique for modelling of complete imaging systems of arbitrary complexity. We make the software available to enable user-friendly and rigorous virtual prototyping of biological microscopy of arbitrary complexity involving light scattering, fluorescence, polarised light propagation, diffraction and coherence. Examples are presented for the modelling and optimisation of representative imaging of neural cells using light-sheet and micro-endoscopic fluorescence microscopy and imaging of retinal vasculature using confocal and non-confocal scanning-laser ophthalmoscopes.

Calculating coherent light-wave propagation in large heterogeneous media

Understanding the interaction of light with a highly scattering material is essential for optical microscopy of optically thick and heterogeneous biological tissues. Ensemble-averaged analytic solutions cannot provide more than general predictions for relatively simple cases. Yet, biological tissues contain chiral organic molecules and many of the cells' structures are birefringent, a property exploited by polarization microscopy for label-free imaging. Solving Maxwell's equations in such materials is a notoriously hard problem. Here we present an efficient method to determine the propagation of electro-magnetic waves in arbitrary anisotropic materials. We demonstrate how the algorithm enables large scale calculations of the scattered light field in complex birefringent materials, chiral media, and even materials with a negative refractive index.

Modified biological spectrum and SNR of Laguerre-Gaussian pulsed beams with orbital angular momentum in turbulent tissue

We propose a modified biological spectrum that contains both short length-scale and long length-scale to study light propagation through turbulent biological tissue. Based on the two-scale modified biological spectrum, we derive an analytic expression of the two-frequency mutual coherence function of Laguerre-Gaussian pulsed beam and establish a model of the signal-to-noise ratio (SNR) of Laguerre-Gaussian pulsed beam carrying orbital angular momentum in turbulent biological tissue. The results show that the modified biological spectrum agrees well with experimental results. In addition, the structural length-scale of biological tissue has a significant influence on the bandwidths and SNR of orbital angular momentum states. This work provides theoretical preparation for more accurately medical diagnosis and optical imaging.

Multidirectional digital scanned light-sheet microscopy enables uniform fluorescence excitation and contrast-enhanced imaging

Light-sheet fluorescence microscopy (LSFM) has emerged as a powerful method for rapid and optically efficient 3D microscopy. Initial LSFM designs utilized a static sheet of light, termed selective plane illumination microscopy (SPIM), which exhibited shadowing artifacts and deteriorated contrast due to light scattering. These issues have been addressed, in part, by multidirectional selective plane illumination microscopy (mSPIM), in which rotation of the light sheet is used to mitigate shadowing artifacts, and digital scanned light-sheet microscopy (DSLM), in which confocal line detection is used to reject scattered light. Here we present a simple and passive multidirectional digital scanned light-sheet microscopy (mDSLM) architecture that combines the benefits of mSPIM and DSLM. By utilizing an elliptical Gaussian beam with increased angular diversity in the imaging plane, mDSLM provides mitigation of shadowing artifacts and contrast-enhanced imaging of fluorescently labeled samples.

Biobeam-Multiplexed wave-optical simulations of light-sheet microscopy

Sample-induced image-degradation remains an intricate wave-optical problem in light-sheet microscopy. Here we present biobeam, an open-source software package that enables simulation of operational light-sheet microscopes by combining data from 10⁵–10⁶ multiplexed and GPU-accelerated point-spread-function calculations. The wave-optical nature of these simulations leads to the faithful reproduction of spatially varying aberrations, diffraction artifacts, geometric image distortions, adaptive optics, and emergent wave-optical phenomena, and renders image-formation in light-sheet microscopy computationally tractable.

Modern microscopes permit to acquire high quality images of large fields of view, which is the result of a decade-long development of computer aided optical design. However, this high image quality can only be obtained at the very surface of biological specimens: when trying to penetrate deeper into biological tissues, light scattering by cells rapidly leads to severe image blur and computers have so far been unable to model the process by which light forms images in such turbid optical environments. We developed a software that allows one to simulate how microscopes record images deep inside scattering biological samples. Our software reproduces a wide range of optical effects that underlie image blur in tissues. Hence strategies to improve image quality within three-dimensional samples can now be systematically tested by computers. Specifically, our software reproduces intricate wave-optical effects that have recently been proposed as strategies to gain perfect images even in the most turbid environments.This provides the chance for a new generation of microscopes, in which computer models guide the imaging process to enable highest possible resolution even deep inside biological specimens.

Bessel-beam illumination in dual-axis confocal microscopy mitigates resolution degradation caused by refractive heterogeneities

One of the main challenges for laser-scanning microscopy of biological tissues with refractive heterogeneities is the degradation in spatial resolution that occurs as a result of beam steering and distortion. This challenge is particularly significant for dual-axis confocal (DAC) microscopy, which achieves improved spatial-filtering and optical-sectioning performance over traditional confocal microscopy through off-axis illumination and collection of light with low-numerical aperture (NA) beams that must intersect precisely at their foci within tissues. DAC microscope image quality is sensitive to positional changes and distortions of these illumination- and collection-beam foci. Previous studies have shown that Bessel beams display improved positional stability and beam quality than Gaussian beams when propagating through tissues with refractive heterogeneities, which suggests that Bessel-beam illumination may enhance DAC microscopy of such tissues. Here, we utilize both Gaussian and Bessel illumination in a point-scanned DAC microscope and quantify the resultant degradation in resolution when imaging within heterogeneous optical phantoms and fresh tissues. Results indicate that DAC microscopy with Bessel illumination exhibits reduced resolution degradation from microscopic tissue heterogeneities compared to DAC microscopy with conventional Gaussian illumination.