Broadband CARS Hyperspectral Classification of Single Immune Cells.

Broadband CARS is a coherent Raman scattering technique that provides access to the full biological vibrational spectrum within milliseconds, facilitating the recording of widefield hyperspectral Raman images. In this work, BCARS hyperspectral images of unstained cells from two different cell lines of immune lineage (T cell [Jurkat] and pDCs [CAL-1]) were recorded and analyzed using multivariate statistical algorithms in order to determine the spectral differences between the cells. A classifier was trained which could distinguish the known cells with a 97% out-of-bag accuracy.

Optical diffraction tomography using a self-reference module.

Optical diffraction tomography enables label-free, 3D refractive index (RI) imaging of biological samples. We present a novel, cost-effective approach to ODT that employs a modular design incorporating a self-reference holographic capture module. This two-part system consists of an illumination module and a capture module that can be seamlessly integrated with any life-science microscope using an automated alignment protocol.

Nonlinear ray tracing in focused fields, part 3. Monochromatic wavefront aberration: tutorial.

Using the flux tracing algorithm developed in the previous two parts, we examine the nonlinear rays that pass through the focus of a lens containing monochromatic aberrations. Lens aberration is modeled differently in the numerical propagation algorithms relating to the thin lens and the ideal lens cases. For the former, an additive phase term is applied to the transmission function of the thin lens, which describes a distortion in the thickness function of the lens, and for the latter an additive phase term is added to the pupil function of the lens (the Fourier transform of the image plane).

Nonlinear ray tracing in focused fields, part 2. Tracing the flux: tutorial.

In this three-part paper series, we develop a method to trace the lines of flux through a three-dimensional wavefield by following a direction that is governed by the derivative of the phase at each point, a process that is best described as flux tracing but which we interchangeably name "nonlinear ray tracing." In the first part we focused on the high-speed calculation of focused three-dimensional complex wavefields in the paraxial approximation for and laser modes. The algorithms developed in the first paper are first used to generate the three-dimensional grid of samples of the complex wavefield in the focal region.

Nonlinear ray tracing in focused fields, part 1. Calculation of 3D focused wavefields: tutorial.

In this three-part paper series, we develop a method to trace the lines of flux through a three-dimensional wavefield by following a direction that is governed by the derivative of the phase at each point, a process that is best described as flux tracing but which we interchangeably name "nonlinear ray tracing." In this first part, we provide a tutorial on the high-speed calculation of three-dimensional complex wavefields, which is a necessary precursor to flux tracing. The basis of this calculation is the angular spectrum method, a well-known numerical algorithm that can be used to efficiently and accurately calculate diffracted fields for numerical apertures <0.

Wavenumber Calibration Protocol for Raman Spectrometers Using Physical Modelling and a Fast Search Algorithm.

A wavenumber calibration protocol is proposed that replaces polynomial fitting to relate the detector axis and the wavenumber shift. The physical model of the Raman spectrometer is used to derive a mathematical expression relating the detector plane to the wavenumber shift, in terms of the system parameters including the spectrograph focal length, the grating angle, and the laser wavelength; the model is general to both reflection and transmission gratings. A fast search algorithm detects the set of parameters that best explains the position of spectral lines recorded on the detector for a known reference standard.

Removing non-resonant background from broadband CARS using a physics-informed neural network.

Broadband coherent anti-Stokes Raman scattering (BCARS) is capable of producing high-quality Raman spectra spanning broad bandwidths, 400-4000 cm, with millisecond acquisition times. Raw BCARS spectra, however, are a coherent combination of vibrationally resonant (Raman) and non-resonant (electronic) components that may challenge or degrade chemical analyses. Recently, we demonstrated a deep convolutional autoencoder network, trained on pairs of simulated BCARS-Raman datasets, which could retrieve the Raman signal with high quality under ideal conditions.

Improved Wavelength Calibration by Modeling the Spectrometer.

Wavelength calibration is a necessary first step for a range of applications in spectroscopy. The relationship between wavelength and pixel position on the array detector is approximately governed by a low-order polynomial and traditional wavelength calibration involves first-, second-, and third-order polynomial fitting to the pixel positions of spectral lines from a well known reference lamp such as neon. However, these methods lose accuracy for bands outside of the outermost spectral line in the reference spectrum.

Automated Raman Micro-Spectroscopy of Epithelial Cell Nuclei for High-Throughput Classification.

Raman micro-spectroscopy is a powerful technique for the identification and classification of cancer cells and tissues. In recent years, the application of Raman spectroscopy to detect bladder, cervical, and oral cytological samples has been reported to have an accuracy greater than that of standard pathology. However, despite being entirely non-invasive and relatively inexpensive, the slow recording time, and lack of reproducibility have prevented the clinical adoption of the technology.

Convolution Network with Custom Loss Function for the Denoising of Low SNR Raman Spectra.

Raman spectroscopy is a powerful diagnostic tool in biomedical science, whereby different disease groups can be classified based on subtle differences in the cell or tissue spectra. A key component in the classification of Raman spectra is the application of multi-variate statistical models. However, Raman scattering is a weak process, resulting in a trade-off between acquisition times and signal-to-noise ratios, which has limited its more widespread adoption as a clinical tool.

Label-free color staining of quantitative phase images of biological cells by simulated Rheinberg illumination.

Modern microscopes are designed with functionalities that are tailored to enhance image contrast. Dark-field imaging, phase contrast, differential interference contrast, and other optical techniques enable biological cells and other phase-only objects to be visualized. Quantitative phase imaging refers to an emerging set of techniques that allow for the complex transmission function of the sample to be measured.

An Algorithm for the Removal of Cosmic Ray Artifacts in Spectral Data Sets.

Cosmic ray artifacts may be present in all photo-electric readout systems. In spectroscopy, they present as random unidirectional sharp spikes that distort spectra and may have an affect on post-processing, possibly affecting the results of multivariate statistical classification. A number of methods have previously been proposed to remove cosmic ray artifacts from spectra but the goal of removing the artifacts while making no other change to the underlying spectrum is challenging.

Multicomponent analysis using a confocal Raman microscope.

Measuring the concentration of multiple chemical components in a low-volume aqueous mixture by Raman spectroscopy has received significant interest in the literature. All of the contributions to date focus on the design of optical systems that facilitate the recording of spectra with high signal-to-noise ratio by collecting as many Raman scattered photons as possible. In this study, the confocal Raman microscope setup is investigated for multicomponent analysis.

Label-free discrimination analysis of de-differentiated vascular smooth muscle cells, mesenchymal stem cells and their vascular and osteogenic progeny using vibrational spectroscopy.

The accumulation of vascular smooth muscle (SMC)-like cells and stem cell-derived myogenic and osteogenic progeny contributes significantly to arteriosclerotic disease. This study established whether label-free vibrational spectroscopy can discriminate de-differentiated 'synthetic' SMCs from undifferentiated stem cells and their myogenic and osteogenic progeny in vitro, compared with conventional immunocytochemical and genetic analyses. TGF-β1- and Jagged1-induced myogenic differentiation of CD44 mesenchymal stem cells was confirmed in vitro by immunocytochemical analysis of specific SMC differentiation marker expression (α-actin, calponin and myosin heavy chain 11), an epigenetic histone mark (H3K4me2) at the myosin heavy chain 11 locus, promoter transactivation and mRNA transcript levels.

Single-shot speckle reduction in numerical reconstruction of digitally recorded holograms: comment.

We comment on a recent Letter by Hincapie et al. [Opt. Lett.

Multiwavefront digital holographic television.

This paper presents the full technology chain supporting wide angle digital holographic television from holographic capture of real world objects/scenes to holographic display with an extended viewing angle. The data are captured with multiple CCD cameras located around an object. The display system is based on multiple tilted spatial light modulators (SLMs) arranged in a circular configuration.

Extended viewing angle holographic display system with tilted SLMs in a circular configuration.

This paper presents an extended viewing angle holographic display for reconstruction of real world objects in which the capture and display systems are decoupled. This is achieved by employing multiple tilted spatial light modulators (SLMs) arranged in a circular configuration. In order to prove the proper reconstruction and visual perception of holographic images the Wigner distribution function is employed.

Digital computation of the complex linear canonical transform.

An efficient algorithm for the accurate computation of the linear canonical transform with complex transform parameters and with complex output variable is presented. Sampling issues are discussed and the requirements for different cases given. Simulations are provided to validate the results.

Quantization noise and its reduction in lensless Fourier digital holography.

Digital holography is an imaging technique that enables recovery of topographic 3D information about an object under investigation. In digital holography, an interference pattern is recorded on a digital camera. Therefore, quantization of the recorded hologram is an integral part of the imaging process.

Fixed-point numercial-reconstruction for digital holographic microscopy.

In this Letter, we study the reconstruction of digital holograms of microscopic objects using a fixed-point representation of the numercial-reconstruction process. For different bit levels in our fixed-point reconstruction algorithm, we investigate the errors introduced to both the reconstructed image intensity and the unwrapped quantitative phase information. Experimental results based on a microscopic lens array are provided.

Twin removal in digital holography using diffuse illumination.

A method to numerically remove the twin image for inline digital holography, using multiple digital holograms, is discussed. Each individual hologram is recorded by using a statistically independent speckle field to illuminate the object. If the holograms are recorded in this manner and then numerically reconstructed, the twin image appears as a different speckle pattern in each of the reconstructions.

Additional sampling criterion for the linear canonical transform.

The linear canonical transform describes the effect of first-order quadratic phase optical systems on a wave field. Several recent papers have developed sampling rules for the numerical approximation of the transform. However, sampling an analog function according to existing rules will not generally permit the reconstruction of the analog linear canonical transform of that function from its samples.

Introducing secure modes of operation for optical encryption.

We analyze optical encryption systems using the techniques of conventional cryptography. All conventional block encryption algorithms are vulnerable to attack, and often they employ secure modes of operation as one way to increase security. We introduce the concept of conventional secure modes to optical encryption and analyze the results in the context of known conventional and optical attacks.

Numerical sampling rules for paraxial regime pulse diffraction calculations.

Sampling rules for numerically calculating ultrashort pulse fields are discussed. Such pulses are not monochromatic but rather have a finite spectral distribution about some central (temporal) frequency. Accordingly, the diffraction pattern for many spectral components must be considered.

Extended focused imaging for digital holograms of macroscopic three-dimensional objects.

When a digital hologram is reconstructed, only points located at the reconstruction distance are in focus. We have developed a novel technique for creating an in-focus image of the macroscopic objects encoded in a digital hologram. This extended focused image is created by combining numerical reconstructions with depth information extracted by using our depth-from-focus algorithm.