Characterizing colon cancer stages through optical polarimetry-assisted digital staining.

Tissue polarimetry has been gaining importance in extracting useful diagnostic information from the structural attributes of tissues, which vary in response to the tissue health status and hence find great potential in cancer diagnosis. However, the complexities associated with cancer make it challenging to isolate the characteristic changes as the tumor progresses using polarimetry. This study attempts to experimentally characterize the polarimetric behavior in colon cancer associated with various stages of development. Bulk and unstained sections of normal and tumor colon tissue were imaged in the reflection and transmission polarimetry configurations at low and high imaging resolutions using an in-house developed Mueller polarimeter. Through this study, we observed that the information about the major contributors of scattering in colon tissue, manifesting in depolarization and retardance, can be obtained from the bulk tissue and unstained sections. These parameters aid in characterizing the polarimetric changes as the colon tumor progresses. While the unstained colon section best indicated the depolarization contrast between normal and tumor, the contrast through the retardance parameter was more pronounced in the bulk colon tissue. The results suggest that the polarimetric "digitally stained" images obtained by Mueller polarimetry are comparable with the bulk tissue counterparts, making it useful for characterizing colon cancer tissues across different stages of development.

Characterization and classification of ductal carcinoma tissue using four channel based stokes-mueller polarimetry and machine learning.

Interaction of polarized light with healthy and abnormal regions of tissue reveals structural information associated with its pathological condition. Even a slight variation in structural alignment can induce a change in polarization property, which can play a crucial role in the early detection of abnormal tissue morphology. We propose a transmission-based Stokes-Mueller microscope for quantitative analysis of the microstructural properties of the tissue specimen. The Stokes-Mueller based polarization microscopy provides significant structural information of tissue through various polarization parameters such as degree of polarization (DOP), degree of linear polarization (DOLP), and degree of circular polarization (DOCP), anisotropy (r) and Mueller decomposition parameters such as diattenuation, retardance and depolarization. Further, by applying a suitable image processing technique such as Machine learning (ML) output images were analysed effectively. The support vector machine image classification model achieved 95.78% validation accuracy and 94.81% testing accuracy with polarization parameter dataset. The study's findings demonstrate the potential of Stokes-Mueller polarimetry in tissue characterization and diagnosis, providing a valuable tool for biomedical applications.

Polar Decomposition of Jones Matrix and Mueller Matrix of Coherent Rayleigh Backscattering in Single-Mode Fibers.

The Jones matrix and the Mueller matrix of the coherent Rayleigh backscattering (RB) in single-mode fibers (SMFs) have been derived recently. It has been shown that both matrices depict two polarization effects-birefringence and polarization-dependent loss (PDL)-although the SMF under investigation is purely birefringent, having no PDL. In this paper, we aim to perform a theoretical analysis of both matrices using polar decomposition. The derived sub-Jones/Mueller matrices, representing birefringence and PDL, respectively, can be used to investigate the polarization properties of the coherent RB. As an application of the theoretical results, we use the derived formulas to investigate the polarization properties of the optical signals in phase-sensitive optical time-domain reflectometry (φ-OTDR). For the first time, to our knowledge, by using the derived birefringence-Jones matrix, the common optical phase of the optical signal in φ-OTDR is obtained as the function of the forward phase and birefringence distributions. By using the derived PDL-Mueller matrix, the optical intensity of the optical signal in φ-OTDR is obtained as the function of the forward phase and birefringence distributions as well as the input state of polarization (SOP). Further theoretical predictions show that, in φ-OTDR, the common optical phase depends on only the local birefringence in the first half of the fiber section, which is occupied by the sensing pulse, irrelevant of the input SOP. However, the intensity of the φ-OTDR signal is not a local parameter, which depends on the input SOP and the birefringence distribution along the entire fiber section before the optical pulse. Moreover, the PDL measured in φ-OTDR is theoretically proven to be a local parameter, which is determined by the local birefringence and local optical phase distributions.

Possibilities of simulation of coronavirus SARS-CoV-2 by using light scattering approach.

Issues related to human coronavirus (SARS CoV-2) are a burning topic of research in present times. Due to its easily contagious nature, real experimentation under laboratory conditions requires a high level of biosafety. A powerful algorithm serves as a potential tool for the analysis of these particles. We attempted to simulate the light scattering from coronavirus (SARS CoV-2) model. Different images were modelled using a modified version of a Monte Carlo code. The results indicate that spikes on the viruses exhibit a significant scattering profile and that the presence of spikes during modelling contributes to the distinctiveness of the scattering profiles.

Stokes-Mueller polarization-based analysis of model SARS-CoV-2 virions.

Understanding the virology of the coronavirus at the structural level has gained utmost importance to overcome the constant and long-term health complications induced by them. In this work, the light scattering properties of SARS-CoV-2 of size 140 nm were simulated by using discrete dipole approximation (DDA) for two incident wavelengths 200 nm and 350 nm, respectively. Three different 3-dimensional (3D) models of SARS-CoV-2 corresponding to 15, 20, and 40 numbers of spike proteins on the viral capsid surface were constructed as target geometries for the DDA calculations. These models were assessed by employing Stokes-Mueller polarimetry to obtain individual polarization properties such as degree of polarization (DOP), degree of linear polarization (DOLP), and degree of circular polarization (DOCP). Irrespective of its spike numbers, all the coronavirus models were found to display higher DOP and DOCP values and negligibly small DOLP values for circularly polarized incident light, indicating the presence of chiral structures. On the other hand, the lack of understanding about the dependence of the Mueller matrix on its microstructural properties was overcome by transforming 16 Mueller elements into sub-matrices with specific structural and physical properties using Lu-Chipman-based Mueller matrix polar decomposition method. The obtained properties such as retardance, diattenuation, and depolarization were used for investigating the composition and microstructural information. The approach presented in this work has the potential to understand the virology of the coronavirus at the structural level and, therefore, will be beneficial in developing effective detection strategies by exploiting their characteristic electromagnetic scattering signatures.

Polarization Properties of Coherently Superposed Rayleigh Backscattered Light in Single-Mode Fibers.

The properties of the state of polarization (SOP) and the degree of polarization (DOP) of Rayleigh backscattered light (RBL) in single-mode fibers (SMF) are investigated theoretically and experimentally when the incident probe is a perfectly coherent continuous-wave (CW) light. It is concluded that the instantaneous DOP of the coherently superposed RBL is always 100%, and the instantaneous SOP is determined by the distributions of the birefringence and the optical phase along the SMF. Therefore, the instantaneous SOP of the coherently superposed RBL does not have a constant relationship with the SOP of the incident CW probe. Furthermore, the instantaneous SOP varies randomly with time because the optical phase is very sensitive to ambient temperature and vibration even in the lab environment. Further theoretical derivation and experimental verification demonstrate, for the first time, that the temporally averaged SOP of the coherently superposed RBL has a simple constant relationship with the SOP of the incident CW probe, and the temporally averaged DOP is 1/3 in an SMF with low and randomly distributed birefringence. The derived formulas and obtained findings can be used to enhance the modelling and improve the performances of phase-sensitive optical time-domain reflectometry and other Rayleigh backscattering based fiber-optic sensors.

A Dual-Modality Imaging Method Based on Polarimetry and Second Harmonic Generation for Characterization and Evaluation of Skin Tissue Structures.

The characterization and evaluation of skin tissue structures are crucial for dermatological applications. Recently, Mueller matrix polarimetry and second harmonic generation microscopy have been widely used in skin tissue imaging due to their unique advantages. However, the features of layered skin tissue structures are too complicated to use a single imaging modality for achieving a comprehensive evaluation. In this study, we propose a dual-modality imaging method combining Mueller matrix polarimetry and second harmonic generation microscopy for quantitative characterization of skin tissue structures. It is demonstrated that the dual-modality method can well divide the mouse tail skin tissue specimens' images into three layers of stratum corneum, epidermis, and dermis. Then, to quantitatively analyze the structural features of different skin layers, the gray level co-occurrence matrix is adopted to provide various evaluating parameters after the image segmentations. Finally, to quantitatively measure the structural differences between damaged and normal skin areas, an index named Q-Health is defined based on cosine similarity and the gray-level co-occurrence matrix parameters of imaging results. The experiments confirm the effectiveness of the dual-modality imaging parameters for skin tissue structure discrimination and assessment. It shows the potential of the proposed method for dermatological practices and lays the foundation for further, in-depth evaluation of the health status of human skin.

Mueller Matrix Polarimetry on Cyanine Dye J-Aggregates.

Cyanine dyes are known to form H- and J-aggregates in aqueous solutions. Here we show that the cyanine dye, S0271, assembles in water into vortex induced chiral J-aggregates. The chirality of the J-aggregates depends on the directionality of the vortex. This study utilised both conventional benchtop CD spectropolarimeters and Mueller matrix polarimetry. It was found that J-aggregates have real chirality alongside linear dichroism and linear and circular birefringence. We identify the factors that are key to the formation of metastable chiral J-aggregates and propose a mechanism for their assembly.

Stokes Dynamic Polarimeter for Non-Organic and Organic Samples Characterization.

The light polarization properties provide relevant information about linear-optical media quality and condition. The Stokes-Mueller formalism is commonly used to represent the polarization properties of the incident light over sample tests. Currently, different Stokes Polarimeters are mainly defined by resolution, acquisition rate, and light to carry out accurate and fast measurements. This work presents the implementation of an automatic Stokes dynamic polarimeter to characterize non-biological and biological material samples. The proposed system is configured to work in the He-Ne laser beam's reflection or transmission mode to calculate the Mueller matrix. The instrumentation stage includes two asynchronous photoelastic modulators, two nano-stepper motors, and an acquisition data card at 2% of accuracy. The Mueller matrix is numerically calculated by software using the 36 measures method without requiring image processing. Experiments show the efficiency of the proposed optical array to calculate the Mueller matrix in reflection and transmission mode for different samples. The mean squared error is calculated for each element of the obtained matrix using referenced values of the air and a mirror. A comparison with similar works in the literature validates the proposed optical array.

Discriminating between Absorption and Scattering Effects in Complex Turbid Media by Coupling Polarized Light Spectroscopy with the Mueller Matrix Concept.

The separation of the combined effects of absorption and scattering in complex media is a major issue for better characterization and prediction of media properties. In this study, an approach coupling polarized light spectroscopy and the Mueller matrix concept were evaluated to address this issue. A set of 50 turbid liquid optical phantoms with different levels of scattering and absorption properties were made and measured at various orientations of polarizers and analyzers to obtain the 16 elements of the complete Mueller matrix in the VIS-NIR region. Partial least square (PLS) was performed to build calibration models from diffuse reflectance spectra in order to evaluate the potential of polarization spectroscopy through the elements of the Mueller matrix to predict physical and chemical parameters and hence, to discriminate scattering and absorption effects, respectively. In particular, it was demonstrated that absorption and scattering effects can be distinguished in the Rayleigh regime with linear and circular polarization from the M22 and M44 elements of the Mueller matrix, correspondingly.

Generation of circular dichroism from superposed porphyrin films.

Circular dichroism (CD) was observed from the superposed porphyrin deposited glass plates, which were prepared by the vapor deposition of achiral porphyrin molecules and oriented to one direction by rubbing parallel to the surface of plate. The CD spectra depended on the twisted angle between the plates and the number of plates superposed. The observed CD spectra agreed with the simulated ones by the Mueller matrices superposition calculation using the observed linear dichroism spectra and linear birefringence spectra of each plate.

Dual-Retarder Mueller Polarimetry System for Extraction of Optical Properties of Serum Albumin Protein Media.

A dual liquid-crystal variable retarder Mueller polarimetry system incorporating a gold-based surface plasmon resonance prism coupler was proposed for extracting the optical properties of serum albumin protein media in the reflectance configuration. The feasibility of the proposed system was demonstrated by measuring the circular dichroism and circular birefringence properties of glucose tissue phantom solutions with different albumin concentrations. The results showed that the circular dichroism increased with albumin concentration, while the optical rotation angle increased with glucose concentration. Both properties reduced over time as a result of the protein glycation effect, which led to a gradual reduction in the glucose content of the sample.

Polymorphic chiral squaraine crystallites in textured thin films.

An enantiomerically pure (R)-2-methylpyrrolidine-based anilino squaraine crystallizes in two chiral polymorphs adopting a monoclinic C2 and an orthorhombic P21 21 21 structure, respectively. By various thin-film preparation techniques, a control of the polymorph formation is targeted. The local texture of the resulting textured thin films is connected to the corresponding optical properties. Special attention is paid to an unusual Davydov splitting, the anisotropic chiroptical response arising from preferred out-of-plane orientation of the crystallites, and the impact of the polymorph specific excitonic coupling.

Differential Mueller matrix imaging of partially depolarizing optically anisotropic biological tissues.

Since recently, a number of innovative polarization-based optical imaging modalities have been introduced and extensively used in various biomedical applications, with an ultimate aim to attain the practical tool for the optical biopsy and functional characterization of biological tissues. The techniques utilize polarization properties of light and Mueller matrix mapping of microscopic images of histological sections of biological tissues or polycrystalline films of biological fluids. The main drawback of currently developed laser polarimetry approaches and Mueller matrix mapping techniques is poor reproducibility of experimental data. This is due to azimuthal dependence of polarization and ellipticity values of most matrix elements to sample orientation in respect to incidence light polarization. Current study aims to generalize the methods of laser polarimetry for diagnosis of partially depolarizing optically anisotropic biological tissues. A method of differential Mueller matrix mapping for reconstruction of linear and circular birefringence and dichroism parameter distributions of partially depolarizing layers of biological tissues of different morphological structure is introduced and practically implemented. The coordinate distributions of the value of the first-order differential matrix elements of histological sections of brain tissue with spatially structured, optically anisotropic fibrillar network, as well as of parenchymatous tissue of the rectum wall with an "islet" polycrystalline structure are determined. Within the statistical analysis of polarization reproduced distributions of the averaged parameters of phase and amplitude anisotropy, the significant sensitivity of the statistical moments of the third and fourth orders to changes in the polycrystalline structure of partially depolarizing layers of biological tissue is observed. The differentiation of female reproductive sphere connective tissue is realized with excellent accuracy. The differential Mueller matrix mapping method for reconstruction of distributions of linear and circular birefringence and dichroism parameters of partially depolarizing layers of biological tissues of different morphological structures is proposed and substantiated. Differential diagnostics of changes in the phase (good balanced accuracy) and amplitude (excellent balanced accuracy) of the anisotropy of the partially depolarizing layers of the vagina wall tissue with prolapse of the genitals is realized. The maximum diagnostic efficiency of the first-order differential matrix method was demonstrated in comparison with the traditional methods of polarization and Mueller matrix mapping of histological sections of light-scattering biological tissues.

Measurement of Circular Dichroism Spectra without Control of a Phase Modulator using Retardation Domain Analysis.

This study investigated the measurement of circular dichroism (CD) spectra without controlling a phase modulator. In a conventional CD system, the peak retardation of the phase modulator must remain constant over the observed wavelength range. Thus, the phase modulator must be controlled to maintain an appropriate modulation degree at an observed wavelength. In contrast, CD obtained using retardation domain analysis is not affected by peak retardation. Consequently, CD spectra can be measured without control of the phase modulator, which was experimentally demonstrated in this study. Additionally, linear dichroism spectra were obtained using retardation domain analysis.

Imaging linear and circular polarization features in leaves with complete Mueller matrix polarimetry.

Spectropolarimetry of intact plant leaves allows to probe the molecular architecture of vegetation photosynthesis in a non-invasive and non-destructive way and, as such, can offer a wealth of physiological information. In addition to the molecular signals due to the photosynthetic machinery, the cell structure and its arrangement within a leaf can create and modify polarization signals. Using Mueller matrix polarimetry with rotating retarder modulation, we have visualized spatial variations in polarization in transmission around the chlorophyll a absorbance band from 650 nm to 710 nm. We show linear and circular polarization measurements of maple leaves and cultivated maize leaves and discuss the corresponding Mueller matrices and the Mueller matrix decompositions, which show distinct features in diattenuation, polarizance, retardance and depolarization. Importantly, while normal leaf tissue shows a typical split signal with both a negative and a positive peak in the induced fractional circular polarization and circular dichroism, the signals close to the veins only display a negative band. The results are similar to the negative band as reported earlier for single macrodomains. We discuss the possible role of the chloroplast orientation around the veins as a cause of this phenomenon. Systematic artefacts are ruled out as three independent measurements by different instruments gave similar results. These results provide better insight into circular polarization measurements on whole leaves and options for vegetation remote sensing using circular polarization.

On the chiroptical properties of racemic crystals.

In a recent letter on the "Optical activity from racemates", discussed at the 16th International Conference on Chiroptical Spectroscopy in Rennes (June 2017), scientists claimed to have measured the circular dichroism of colored, racemic crystals of two transition metal complexes, observations that "serve to correct a clear deficit in our understanding of the optical properties of racemates." In fact, there is no deficit in our understanding of the optical properties of racemates. Moreover, the measurements presented are unconvincing as evidence of circular dichroism measured in anisotropic crystals and therefore do not inform our understanding of the specific crystals investigated, or racemates generally speaking.

Revisiting polarimetry near the isotropic point of an optically active, non-enantiomorphous, molecular crystal.

Accurate polarimetric measurements of the optical activity of crystals along low symmetry directions are facilitated by isotropic points, frequencies where dispersion curves of eigenrays cross and the linear birefringence disappears. We report here the optical properties and structure of achiral, uniaxial (point group D2d ) potassium trihydrogen di-(cis-4-cyclohexene-1,2-dicarboxylate) dihydrate, whose isotropic point was previously detected (S. A. Kim, C. Grieswatch, H. Küppers, Zeit. Krist. 1993; 208:219-222) and exploited for a singular measurement of optical activity normal to the optic axis. The crystal structure associated with the aforementioned study was never published. We report it here, confirming the space group assignment I 4¯c2, along with the frequency dependence of the fundamental optical properties and the constitutive tensors by fitting optical dispersion relations to measured Mueller matrix spectra. k-Space maps of circular birefringence and of the Mueller matrix near the isotropic wavelength are measured and simulated. The signs of optical rotation are correlated with the absolute crystallographic directions.

Noninvasive assessment of cutaneous alterations in mice exposed to whole body gamma irradiation using optical imaging techniques.

We report the results of a study carried out to investigate the potential of optical techniques such as optical coherence tomography, Mueller matrix spectroscopy, and cross-polarization imaging for noninvasive monitoring of the ionizing radiation exposure-induced alterations in cutaneous tissue of mice. Radiation dose-dependent changes were observed in tissue microvasculature and tissue optical parameters like retardance and depolarization as early as 1 h post radiation exposure. Results suggest that these optical techniques may allow early detection of radiation dose-dependent alterations which could help in screening of population exposed to radiation.

Characterizing the Effects of Washing by Different Detergents on the Wavelength-Scale Microstructures of Silk Samples Using Mueller Matrix Polarimetry.

Silk fibers suffer from microstructural changes due to various external environmental conditions including daily washings. In this paper, we take the backscattering Mueller matrix images of silk samples for non-destructive and real-time quantitative characterization of the wavelength-scale microstructure and examination of the effects of washing by different detergents. The 2D images of the 16 Mueller matrix elements are reduced to the frequency distribution histograms (FDHs) whose central moments reveal the dominant structural features of the silk fibers. A group of new parameters are also proposed to characterize the wavelength-scale microstructural changes of the silk samples during the washing processes. Monte Carlo (MC) simulations are carried out to better understand how the Mueller matrix parameters are related to the wavelength-scale microstructure of silk fibers. The good agreement between experiments and simulations indicates that the Mueller matrix polarimetry and FDH based parameters can be used to quantitatively detect the wavelength-scale microstructural features of silk fibers. Mueller matrix polarimetry may be used as a powerful tool for non-destructive and in situ characterization of the wavelength-scale microstructures of silk based materials.