Cardiac tissue characterization using near-infrared spectroscopy

Cardiac tissue from swine and canine hearts were assessed using diffuse reflectance near-infrared spectroscopy (NIRS) ex vivo. Slope measured between 800-880 nm reflectance was found to reveal differences between epicardial fat and normal myocardium tissue. This parameter was observed to increase monotonically from measurements obtained from the onset of radio frequency ablation (RFA). A sheathe-style fiber optic catheter was then developed to allow real-time sampling of the zone of resistive heating during RFA treatment. A model was developed and used to extract changes in tissue absorption and reduced scattering based on the steady-state diffusion approximation. It was found that key changes in tissue optical properties occur during application of RF energy and can be monitored using NIRS. These results encourage the development of NIRS integrated catheters for real-time guidance of the cardiac ablation treatment

Anisotropic material properties of the human uterus

The mechanical function of the uterus is crucial for the protection of the fetus during a healthy pregnancy. Early contractile activation of uterine tissue can lead to preterm labor and birth (PTB). In 2014, 9.56 percent of pregnancies ended in PTB; it is also the leading cause of death in children under five years of age. Characterizing the material properties of uterine tissue is important for understanding the mechanical failures of the uterus and the causes of PTB. In this study, a workflow of experiments and data processing techniques were employed. 78 uterine specimens were collected from consenting 28 patients who underwent hysterectomy. A four-level ramp-hold indentation test was performed. IFEA was performed to fit four material parameters to the experimental data: Young's Modulus E, Poisson’s ratio v, the fiber stiffness factor ksi, and the fiber angle concentration b. Within each uterus, significant differences in Young’s Modulus E and Poisson’s ratio n were observed at different locations and different layers, indicating the heterogeneity of the human uterine material properties. However, the fitted values for fiber stiffness x and angle concentration b exhibited a wide spread with no significant differences observed across comparison groups. There were also no obvious differences between patients with different parities, as suggested in previous studies

3-D Fiber Orientation Mapping for OCT (MATLAB) version 2

A complete framework for analyzing the 3-D structure of fibrous tissue from OCT image volumes. Code includes a pre-processing pipeline for image enhancement and code to obtain the fiber incline and enface angles as pixel-wise orientation maps

L+S (FC-RPCA) Foreground-Background OCT Segmentation

We present a variant on the robust-principal component analysis (RPCA) algorithm, called frequency constrained RPCA (FC-RPCA), for selectively segmenting dynamic phenomena that exhibit spectra within a user-defined range of frequencies. The algorithm lacks subjective parameter tuning and demonstrates robust segmentation in datasets containing multiple motion sources and high amplitude noise. This algorithm was designed to be used with time-lapse Optical Coherence Tomography (OCT) datasets that capture sub-resolution motion. Specifically demonstrated for cilia

3-D Fiber Orientation Mapping Code for OCT version 1

MATLAB code for mapping and modeling 3-D collagen fibers from uterine tissue blocks imaged with OCT

OCT Volume Stitching & Blending Toolbox

This MATLAB code is used to register and fuse Thorlabs SD-OCT image volumes into a single mosaic volume. When the sample is too large to image with a single acquisition, multiple, overlapping volumes can be acquired and fused into a single fluid dataset. This code was written by Dr. Yu Gan and published in the following manuscript: Yu Gan, Wang Yao, Kristin. M Myers, Joy Y. Vink, Ronald. J. Wapner, and Christine P. Hendon, "Analyzing three-dimensional ultrastructure of human cervical tissue using optical coherence tomography," Biomed. Opt. Express 6, 1090-1108 (2015

Collagen Fiber Orientation and Dispersion in the Upper Cervix of Non-Pregnant and Pregnant Women.

The structural integrity of the cervix in pregnancy is necessary for carrying a pregnancy until term, and the organization of human cervical tissue collagen likely plays an important role in the tissue's structural function. Collagen fibers in the cervical extracellular matrix exhibit preferential directionality, and this collagen network ultrastructure is hypothesized to reorient and remodel during cervical softening and dilation at time of parturition. Within the cervix, the upper half is substantially loaded during pregnancy and is where the premature funneling starts to happen. To characterize the cervical collagen ultrastructure for the upper half of the human cervix, we imaged whole axial tissue slices from non-pregnant and pregnant women undergoing hysterectomy or cesarean hysterectomy respectively using optical coherence tomography (OCT) and implemented a pixel-wise fiber orientation tracking method to measure the distribution of fiber orientation. The collagen fiber orientation maps show that there are two radial zones and the preferential fiber direction is circumferential in a dominant outer radial zone. The OCT data also reveal that there are two anatomic regions with distinct fiber orientation and dispersion properties. These regions are labeled: Region 1-the posterior and anterior quadrants in the outer radial zone and Region 2-the left and right quadrants in the outer radial zone and all quadrants in the inner radial zone. When comparing samples from nulliparous vs multiparous women, no differences in these fiber properties were noted. Pregnant tissue samples exhibit an overall higher fiber dispersion and more heterogeneous fiber properties within the sample than non-pregnant tissue. Collectively, these OCT data suggest that collagen fiber dispersion and directionality may play a role in cervical remodeling during pregnancy, where distinct remodeling properties exist according to anatomical quadrant

Data for: Robust, High-Density Lesion Mapping in the Left Atrium with Near-Infrared Spectroscopy

This dataset provides the open-source data organized, pre-processed and cleaned by the authors for the Journal of Biophotonics article, "Robust, High-Density Lesion Mapping in the Left Atrium with Near-Infrared Spectroscopy". The dataset includes optical parameters extracted from the acquired spectrums of ex-vivo swine left atrium using catheter-based near infrared spectroscopy (NIRS) within blood and phosphate-buffered saline (PBS), respectively. A random forest model was applied and the equivalence of predicted lesion probability maps between PBS and blood were assessed. The work illustrate the robustness of optical parameters in blood and without perpendicular contact, confirming their capability to provide useful feedback in-vivo. Keywords: Near-infrared spectroscopy; Biomedical optics; Cardiac ablation; Cardiac electrophysiolog