Biology subjects

Barzda, V.

Publications and source records attributed to Barzda, V..

5 recordsLinked to original sources

bioRxiv2022

Digital polarimetric second harmonic generation microscopy of partially oriented fiber structures

Second harmonic generation (SHG) in biological tissue originates predominantly from noncentrosymmetric fibrillar structures partially oriented within the focal volume (voxel) of a multiphoton excitation microscope. The study is aimed to elucidate fibrillar organization factors influencing SHG intensity, as well as achiral, R, and chiral, C, nonlinear susceptibility tensor component ratios. SHG response is calculated for various configurations of fibrils in a voxel using digital nonlinear microscope. The R and C ratios are calculated using linear incident and outgoing polarization states that simulate polarization-in polarization-out (PIPO) polarimetric measurements. The investigation shows strong SHG intensity dependence on parallel/antiparallel fiber organization. The R and C ratio is strongly influenced by the fiber chirality, tilting of the fibers out of image plane and crossing of the fibers. The study facilitates interpretation of polarimetric SHG microscopy images in terms of ultrastructural organization of fibers in the imaged structures. Statement of SignificanceSecond harmonic generation microscopy is widely used for imaging non-centrosymmetric biological structures such as collagen. The ultrastructure of collagen can be determined with polarimetric SHG microscopy. The coherent nonlinear response of biological structures depends on the 3D orientations and positions of the collagen fibers in the focal volume of the microscope. Here, we show how different fiber organizations and 3D orientations in the focal volume can affect the polarimetric SHG responses. The results are important for understanding and interpreting images obtained with polarimetric SHG microscopy.

biophysics↗

bioRxiv2022

Unsupervised determination of lung tumor margin with widefield polarimetric second-harmonic generation microscopy

The extracellular matrix (ECM) is amongst many tissue components affected by cancer, however, morphological changes of the ECM are not well-understood and thus, often omitted from diagnostic considerations. Polarimetric second-harmonic generation (P-SHG) microscopy allows for visualization and characterization of collagen ultrastructure in the ECM, aiding in better understanding of the changes induced by cancer throughout the tissue. In this paper, a large region of hematoxylin and eosin-stained human lung section, encompassing a tumor margin, connecting a significant tumor portion to normal tissue was imaged with P-SHG microscopy. The resulting polarimetric parameters were utilized in principal components analysis and unsupervised k-means clustering to separate normal- and tumor-like tissue. Consequently, a pseudo-color map of the clustered tissue regions is generated to highlight the irregularity of the ECM collagen structure throughout the region of interest and to identify the tumor margin.

pathology↗

bioRxiv2022

Wide-Field Stokes Polarimetric Microscopy for Second Harmonic Generation Imaging

We employ wide-field second harmonic generation (SHG) microscopy together with nonlinear Stokes polarimetry for quick ultrastructural investigation of large sample areas (700 m x 700 m) in thin histology sections. The Stokes vector components for SHG are obtained from the polarimetric measurements with incident and outgoing linear and circular polarization states. The Stokes components are used to construct the images of polarimetric parameters and deduce the sample maps of achiral and chiral nonlinear susceptibility tensor components ratios and cylindrical axis orientation in fibrillar materials. The imaged histology sections with polarimetric wide-field SHG microscopy provide large area maps of ultrastructural information about the collagenous tissue, which can be used for rapid histology investigations.

biophysics↗

bioRxiv2022

Wide-Field Multicontrast Nonlinear Microscopy for Histopathology

A multicontrast polarimetric wide-field second harmonic generation (SHG) and multiphoton excitation fluorescence (MPF) microscope is optimized for large area imaging of hematoxylin and eosin (H&E) stained and unstained histology slides. The bleaching kinetics of MPF and SHG are examined with various laser intensities at different pulse repetition rates to determine the optimal wide-filed imaging conditions for H&E stained histology slides. Several polarimetric parameters are used to investigate the organization of extracellular matrix collagen in the histology samples.

biophysics↗

bioRxiv2021

Machine learning-enabled cancer diagnostics with widefield polarimetric second-harmonic generation microscopy

The extracellular matrix (ECM) collagen undergoes major remodeling during tumorigenesis. However, alterations to the ECM are not widely considered in cancer diagnostics, due to mostly uniform appearance of collagen fibers in white light images of hematoxylin and eosin-stained tissue sections. Polarimetric second-harmonic generation (P-SHG) microscopy enables label-free visualization and ultrastructural investigation of non-centrosymmetric molecules, which, when combined with texture analysis, provides multiparameter characterization of tissue collagen. This paper demonstrates whole slide imaging of breast tissue microarrays using high-throughput widefield P-SHG microscopy. The resulting P-SHG parameters are used in classification to differentiate tumor tissue from normal with 94.2% accuracy and F1-score, and 6.3% false discovery rate. Subsequently, the trained classifier is employed to predict tumor tissue with 91.3% accuracy, 90.7% F1-score, and 13.8% false omission rate. As such, we show that widefield P-SHG microscopy reveals collagen ultrastructure over large tissue regions and can be utilized as a sensitive biomarker for cancer diagnostics and prognostics studies.

pathology↗