Automated image segmentation method to analyse skeletal muscle cross section in exercise-induced regenerating myofibers.

Skeletal muscle is an adaptive tissue with the ability to regenerate in response to exercise training. Cross-sectional area (CSA) quantification, as a main parameter to assess muscle regeneration capability, is highly tedious and time-consuming, necessitating an accurate and automated approach to analysis. Although several excellent programs are available to automate analysis of muscle histology, they fail to efficiently and accurately measure CSA in regenerating myofibers in response to exercise training. Here, we have developed a novel fully-automated image segmentation method based on neutrosophic set algorithms to analyse whole skeletal muscle cross sections in exercise-induced regenerating myofibers, referred as MyoView, designed to obtain accurate fiber size and distribution measurements. MyoView provides relatively efficient, accurate, and reliable measurements for CSA quantification and detecting different myofibers, myonuclei and satellite cells in response to the post-exercise regenerating process. We showed that MyoView is comparable with manual quantification. We also showed that MyoView is more accurate and efficient to measure CSA in post-exercise regenerating myofibers as compared with Open-CSAM, MuscleJ, SMASH and MyoVision. Furthermore, we demonstrated that to obtain an accurate CSA quantification of exercise-induced regenerating myofibers, whole muscle cross-section analysis is an essential part, especially for the measurement of different fiber-types. We present MyoView as a new tool to quantify CSA, myonuclei and satellite cells in skeletal muscle from any experimental condition including exercise-induced regenerating myofibers.

A Framework for Hexagonal Image Processing Using Hexagonal Pixel-Perfect Approximations in Subpixel Resolution.

Image processing in hexagonal lattice has many advantages rather than square lattice. Researchers have addressed benefits of hexagonal structure in applications such as binarization, rotation, scaling and edge detection. Approximately all existing hardwares for capturing and displaying images are based on square lattice. Therefore, the best way for using advantages of hexagonal lattice is to find a proper software approach to convert square pixels to hexagonal ones. This paper presents a hexagonal platform based on interpolation which addresses three existing hexagonal challenges including imperfect hexagonal shape, inaccurate intensity level of hexagonal pixels and lower resolution in hexagonal space. The proposed interpolation is computed by overlaps between square and hexagonal pixels. Overlap types are formulated mathematically in 8 separate cases. Each overlap case is detected automatically and used to compute final gray-level intensity of hexagonal pixels. It is mathematically and experimentally shown that the proposed method satisfies necessary conditions for square-to-hexagonal conversion. The proposed scheme is evaluated on synthetic and real images with 10 different levels of noise in interpolation and edge detection applications. In synthetic images, the proposed method achieves the best figure of merit (FOM) 99.92% and 98.67% in high and low SNRs 100 and 20, respectively. Also, the proposed method outperforms existing state of the art hexagonal lattices with interclass correlation coefficient (ICC) 84.18% and mean rating 7.7 (out of 9) in real images.

Automatic Evaluation of Crown Preparation Using Image Processing Techniques: A Substitute to Faculty Scoring in Dental Education.

BACKGROUND: This study presents a new and innovative experimental method, including software and its prerequisite instruments, to use image processing techniques for crown preparation analysis. METHOD: A platform was designed and constructed to take images from artificial teeth in different angles and directions and to process and analyze them by the proposed method to evaluate the quality and quantity of crown preparation. For each tooth, two series of images were taken from the artificial teeth before and after preparation, and image series were registered by two semi-automated and automated methods to transform them into one coordinate system. Region of interest was segmented by user interaction, and tooth region was segmented by substeps such as transformation to hue, saturation, and value color space, edge detection, morphology operations, and contour extraction. Finally, the amount and angle of crown preparation were computed and compared with standard measures to evaluate the quality of crown preparation. The proposed method was applied to a local dataset collected from Isfahan University of Medical Sciences. RESULTS: Difference between the angle of crown preparation computed by the proposed method and that of the experts showed a mean absolute error of 7.17°. The correlation between the segmented regions by the proposed method and those of the experts was also evaluated by the Intersection over Union (IOU) criterion. The best and worst performances achieved in cases by IOU were 0.94 and 0.76, respectively. Finally, the segmentation results of the proposed method indicated an average IOU of 0.89 in all images. CONCLUSION: Students can use this method as an assessment tool in preclinical tooth preparation to compare their crown work with standard parameters.

RETOUCH: The Retinal OCT Fluid Detection and Segmentation Benchmark and Challenge.

Retinal swelling due to the accumulation of fluid is associated with the most vision-threatening retinal diseases. Optical coherence tomography (OCT) is the current standard of care in assessing the presence and quantity of retinal fluid and image-guided treatment management. Deep learning methods have made their impact across medical imaging, and many retinal OCT analysis methods have been proposed. However, it is currently not clear how successful they are in interpreting the retinal fluid on OCT, which is due to the lack of standardized benchmarks. To address this, we organized a challenge RETOUCH in conjunction with MICCAI 2017, with eight teams participating. The challenge consisted of two tasks: fluid detection and fluid segmentation. It featured for the first time: all three retinal fluid types, with annotated images provided by two clinical centers, which were acquired with the three most common OCT device vendors from patients with two different retinal diseases. The analysis revealed that in the detection task, the performance on the automated fluid detection was within the inter-grader variability. However, in the segmentation task, fusing the automated methods produced segmentations that were superior to all individual methods, indicating the need for further improvements in the segmentation performance.

OCT Fluid Segmentation using Graph Shortest Path and Convolutional Neural Network.

Diagnosis and monitoring of retina diseases related to pathologies such as accumulated fluid can be performed using optical coherence tomography (OCT). OCT acquires a series of 2D slices (Bscans). This work presents a fully-automated method based on graph shortest path algorithms and convolutional neural network (CNN) to segment and detect three types of fluid including sub-retinal fluid (SRF), intra-retinal fluid (IRF) and pigment epithelium detachment (PED) in OCT Bscans of subjects with age-related macular degeneration (AMD) and retinal vein occlusion (RVO) or diabetic retinopathy. The proposed method achieves an average dice coefficient of 76.44%, 92.25% and 82.14% in Cirrus, Spectralis and Topcon datasets, respectively. The effectiveness of the proposed methods was also demonstrated in segmenting fluid in OCT images from the 2017 Retouch challenge.

Fully Automated Segmentation of Fluid/Cyst Regions in Optical Coherence Tomography Images With Diabetic Macular Edema Using Neutrosophic Sets and Graph Algorithms.

This paper presents a fully automated algorithm to segment fluid-associated (fluid-filled) and cyst regions in optical coherence tomography (OCT) retina images of subjects with diabetic macular edema. The OCT image is segmented using a novel neutrosophic transformation and a graph-based shortest path method. In neutrosophic domain, an image is transformed into three sets: (true), (indeterminate) that represents noise, and (false). This paper makes four key contributions. First, a new method is introduced to compute the indeterminacy set , and a new -correction operation is introduced to compute the set in neutrosophic domain. Second, a graph shortest-path method is applied in neutrosophic domain to segment the inner limiting membrane and the retinal pigment epithelium as regions of interest (ROI) and outer plexiform layer and inner segment myeloid as middle layers using a novel definition of the edge weights . Third, a new cost function for cluster-based fluid/cyst segmentation in ROI is presented which also includes a novel approach in estimating the number of clusters in an automated manner. Fourth, the final fluid regions are achieved by ignoring very small regions and the regions between middle layers. The proposed method is evaluated using two publicly available datasets: Duke, Optima, and a third local dataset from the UMN clinic which is available online. The proposed algorithm outperforms the previously proposed Duke algorithm by 8% with respect to the dice coefficient and by 5% with respect to precision on the Duke dataset, while achieving about the same sensitivity. Also, the proposed algorithm outperforms a prior method for Optima dataset by 6%, 22%, and 23% with respect to the dice coefficient, sensitivity, and precision, respectively. Finally, the proposed algorithm also achieves sensitivity of 67.3%, 88.8%, and 76.7%, for the Duke, Optima, and the university of minnesota (UMN) datasets, respectively.

Fully-automated segmentation of fluid regions in exudative age-related macular degeneration subjects: Kernel graph cut in neutrosophic domain.

A fully-automated method based on graph shortest path, graph cut and neutrosophic (NS) sets is presented for fluid segmentation in OCT volumes for exudative age related macular degeneration (EAMD) subjects. The proposed method includes three main steps: 1) The inner limiting membrane (ILM) and the retinal pigment epithelium (RPE) layers are segmented using proposed methods based on graph shortest path in NS domain. A flattened RPE boundary is calculated such that all three types of fluid regions, intra-retinal, sub-retinal and sub-RPE, are located above it. 2) Seed points for fluid (object) and tissue (background) are initialized for graph cut by the proposed automated method. 3) A new cost function is proposed in kernel space, and is minimized with max-flow/min-cut algorithms, leading to a binary segmentation. Important properties of the proposed steps are proven and quantitative performance of each step is analyzed separately. The proposed method is evaluated using a publicly available dataset referred as Optima and a local dataset from the UMN clinic. For fluid segmentation in 2D individual slices, the proposed method outperforms the previously proposed methods by 18%, 21% with respect to the dice coefficient and sensitivity, respectively, on the Optima dataset, and by 16%, 11% and 12% with respect to the dice coefficient, sensitivity and precision, respectively, on the local UMN dataset. Finally, for 3D fluid volume segmentation, the proposed method achieves true positive rate (TPR) and false positive rate (FPR) of 90% and 0.74%, respectively, with a correlation of 95% between automated and expert manual segmentations using linear regression analysis.