An Advanced MRI Multi-Modalities Segmentation Methodology Dedicated to Multiple Sclerosis Lesions Exploration and Differentiation

Image segmentation of mouse eye in vivo with optical coherence tomography based on Bayesian classification

OBJECTIVES

Optical coherence tomography (OCT) is a new imaging technology that uses an optical analog of ultrasound imaging for biological tissues. Image segmentation plays an important role in dealing with quantitative analysis of medical images.

METHODS

We have proposed a novel framework to deal with the low intensity problem, based on the labeled patches and Bayesian classification (LPBC) model. The proposed method includes training and testing phases. During the training phase, firstly, we manually select the sub-images of background and Region of Interest (ROI) from the training image, and then extract features by patches. Finally, we train the Bayesian model with the features. The segmentation threshold of each patch is computed by the learned Bayesian model.

RESULTS

In addition, we have collected a new dataset of mouse eyes in vivo with OCT, named MEVOCT, which can be found at URL https://17861318579.github.io/LPBC. MEVOCT consists of 20 high-resolution images. The resolution of every image is 2048 × 2048 pixels.

CONCLUSIONS

The experimental results demonstrate the effectiveness of the LPBC method on the new MEVOCT dataset. The ROI segmentation is of great importance for the distortion correction.

Triple Clipped Histogram-Based Medical Image Enhancement Using Spatial Frequency

In this paper, a novel triple clipped histogram model-based fusion approach has been proposed to improve the basics features, brightness preservation and contrast of the medical images. This incorporates the features of the equalized image and input image together. In the initial step, the low-contrast medical image is equalized using the triple clipped dynamic histogram equalization technique for which the histogram of the input medical image is split into three sections on the basis of standard deviation with almost equal number of pixels. The clipping process of the histogram is performed on every histogram section and mapped to a new dynamic range using simple calculations. In the second step, the sub-histogram equalization process is performed separately. Approximation and detail coefficients of equalized and input images are separated using discrete wavelet transform (DWT). Thereafter, the approximation coefficients are modified using some basic calculation-based fusion which involves singular value decomposition (SVD) and its inverse. Detail coefficients are fused using spatial frequency features. This yields modified approximation and detail coefficients for an enhanced image. Finally, inverse discrete wavelet transform (IDWT) has been applied to the modified coefficients which result in an enhanced image with improved visual quality. These improvements are analyzed qualitatively and quantitatively.

Radius-optimized efficient template matching for lesion detection from brain images

Computer-aided detection of brain lesions from volumetric magnetic resonance imaging (MRI) is in demand for fast and automatic diagnosis of neural diseases. The template-matching technique can provide satisfactory outcome for automatic localization of brain lesions; however, finding the optimal template size that maximizes similarity of the template and the lesion remains challenging. This increases the complexity of the algorithm and the requirement for computational resources, while processing large MRI volumes with three-dimensional (3D) templates. Hence, reducing the computational complexity of template matching is needed. In this paper, we first propose a mathematical framework for computing the normalized cross-correlation coefficient (NCCC) as the similarity measure between the MRI volume and approximated 3D Gaussian template with linear time complexity, [Formula: see text], as opposed to the conventional fast Fourier transform (FFT) based approach with the complexity [Formula: see text], where [Formula: see text] is the number of voxels in the image and [Formula: see text] is the number of tried template radii. We then propose a mathematical formulation to analytically estimate the optimal template radius for each voxel in the image and compute the NCCC with the location-dependent optimal radius, reducing the complexity to [Formula: see text]. We test our methods on one synthetic and two real multiple-sclerosis databases, and compare their performances in lesion detection with FFT and a state-of-the-art lesion prediction algorithm. We demonstrate through our experiments the efficiency of the proposed methods for brain lesion detection and their comparable performance with existing techniques.

Automatic brain lesion segmentation on standard magnetic resonance images: a scoping review

OBJECTIVES

Medical image analysis practices face challenges that can potentially be addressed with algorithm-based segmentation tools. In this study, we map the field of automatic MR brain lesion segmentation to understand the clinical applicability of prevalent methods and study designs, as well as challenges and limitations in the field.

DESIGN

Scoping review.

SETTING

Three databases (PubMed, IEEE Xplore and Scopus) were searched with tailored queries. Studies were included based on predefined criteria. Emerging themes during consecutive title, abstract, methods and whole-text screening were identified. The full-text analysis focused on materials, preprocessing, performance evaluation and comparison.

RESULTS

Out of 2990 unique articles identified through the search, 441 articles met the eligibility criteria, with an estimated growth rate of 10% per year. We present a general overview and trends in the field with regard to publication sources, segmentation principles used and types of lesions. Algorithms are predominantly evaluated by measuring the agreement of segmentation results with a trusted reference. Few articles describe measures of clinical validity.

CONCLUSIONS

The observed reporting practices leave room for improvement with a view to studying replication, method comparison and clinical applicability. To promote this improvement, we propose a list of recommendations for future studies in the field.

Brain and lesion segmentation in multiple sclerosis using fully convolutional neural networks: A large-scale study

OBJECTIVE

To investigate the performance of deep learning (DL) based on fully convolutional neural network (FCNN) in segmenting brain tissues in a large cohort of multiple sclerosis (MS) patients.

METHODS

We developed a FCNN model to segment brain tissues, including T2-hyperintense MS lesions. The training, validation, and testing of FCNN were based on ~1000 magnetic resonance imaging (MRI) datasets acquired on relapsing-remitting MS patients, as a part of a phase 3 randomized clinical trial. Multimodal MRI data (dual-echo, FLAIR, and T1-weighted images) served as input to the network. Expert validated segmentation was used as the target for training the FCNN. We cross-validated our results using the leave-one-center-out approach.

RESULTS

We observed a high average (95% confidence limits) Dice similarity coefficient for all the segmented tissues: 0.95 (0.92-0.98) for white matter, 0.96 (0.93-0.98) for gray matter, 0.99 (0.98-0.99) for cerebrospinal fluid, and 0.82 (0.63-1.0) for T2 lesions. High correlations between the DL segmented tissue volumes and ground truth were observed (R² > 0.92 for all tissues). The cross validation showed consistent results across the centers for all tissues.

CONCLUSION

The results from this large-scale study suggest that deep FCNN can automatically segment MS brain tissues, including lesions, with high accuracy.