Precision Imaging: more descriptive, predictive and integrative imaging

Medical image analysis has grown into a matured field challenged by progress made across all medical imaging technologies and more recent breakthroughs in biological imaging. The cross-fertilisation between medical image analysis, biomedical imaging physics and technology, and domain knowledge from medicine and biology has spurred a truly interdisciplinary effort that stretched outside the original boundaries of the disciplines that gave birth to this field and created stimulating and enriching synergies. Consideration on how the field has evolved and the experience of the work carried out over the last 15 years in our centre, has led us to envision a future emphasis of medical imaging in Precision Imaging. Precision Imaging is not a new discipline but rather a distinct emphasis in medical imaging borne at the cross-roads between, and unifying the efforts behind mechanistic and phenomenological modelbased imaging. It captures three main directions in the effort to deal with the information deluge in imaging sciences, and thus achieve wisdom from data, information, and knowledge. Precision Imaging is finally characterised by being descriptive, predictive and integrative about the imaged object. This paper provides a brief and personal perspective on how the field has evolved, summarises and formalises our vision of Precision Imaging for Precision Medicine, and highlights some connections with past research and current trends in the field

Multi-class Image Segmentation in Fluorescence Microscopy Using Polytrees

Multi-class segmentation is a crucial step in cell image analysis. This process becomes challenging when little information is available for recognising cells from the background, due to their poor discriminative features. To alleviate this, directed acyclic graphs such as trees have been proposed to model top-down statistical dependencies as a prior for improved image segmentation. However, using trees, modelling the relations between labels of multiple classes becomes difficult. To overcome this limitation, we propose a polytree graphical model that captures label proximity relations more naturally compared to tree based approaches. A novel recursive mechanism based on two-pass message passing is developed to efficiently calculate closed form posteriors of graph nodes on the polytree. The algorithm is evaluated using simulated data, synthetic images and real fluorescence microscopy images. Our method achieves Dice scores of 94.5% and 98% on macrophage and seed classes, respectively, outperforming GMM based classifiers

A Multi-Resolution t-Mixture Model Approach to Robust Group-wise Alignment of Shapes

A novel probabilistic, group-wise rigid registration framework is proposed in this study, to robustly align and establish correspondence across anatomical shapes represented as unstructured point sets. Student’s t-mixture model (TMM) is employed to exploit their inherent robustness to outliers. The primary application for such a framework is the automatic construction of statistical shape models (SSMs) of anatomical structures, from medical images. Tools used for automatic segmentation and landmarking of medical images often result in segmentations with varying proportions of outliers. The proposed approach is able to robustly align shapes and establish valid correspondences in the presence of considerable outliers and large variations in shape. A multi-resolution registration (mrTMM) framework is also formulated, to further improve the performance of the proposed TMM-based registration method. Comparisons with a state-of-the art approach using clinical data show that the mrTMM method in particular, achieves higher alignment accuracy and yields SSMs that generalise better to unseen shapes

Supervised saliency map driven segmentation of lesions in dermoscopic images

Lesion segmentation is the first step in most automatic melanoma recognition systems. Deficiencies and difficulties in dermoscopic images such as color inconstancy, hair occlusion, dark corners, and color charts make lesion segmentation an intricate task. In order to detect the lesion in the presence of these problems, we propose a supervised saliency detection method tailored for dermoscopic images based on the discriminative regional feature integration (DRFI). A DRFI method incorporates multilevel segmentation, regional contrast, property, background descriptors, and a random forest regressor to create saliency scores for each region in the image. In our improved saliency detection method, mDRFI, we have added some new features to regional property descriptors. Also, in order to achieve more robust regional background descriptors, a thresholding algorithm is proposed to obtain a new pseudo-background region. Findings reveal that mDRFI is superior to DRFI in detecting the lesion as the salient object in dermoscopic images. The proposed overall lesion segmentation framework uses detected saliency map to construct an initial mask of the lesion through thresholding and postprocessing operations. The initial mask is then evolving in a level set framework to fit better on the lesion's boundaries. The results of evaluation tests on three public datasets show that our proposed segmentation method outperforms the other conventional state-of-the-art segmentation algorithms and its performance is comparable with most recent approaches that are based on deep convolutional neural networks

Segmentation of Lesions in Dermoscopy Images Using Saliency Map And Contour Propagation

Melanoma is one of the most dangerous types of skin cancer and causes thousands of deaths worldwide each year. Recently dermoscopic imaging systems have been widely used as a diagnostic tool for melanoma detection. The first step in the automatic analysis of dermoscopy images is the lesion segmentation. In this article, a novel method for skin lesion segmentation that could be applied to a variety of images with different properties and deficiencies is proposed. After a multi-step preprocessing phase (hair removal and illumination correction), a supervised saliency map construction method is used to obtain an initial guess of lesion location. The construction of the saliency map is based on a random forest regressor that takes a vector of regional image features and return a saliency score based on them. This regressor is trained in a multi-level manner based on 2000 training data provided in ISIC2017 melanoma recognition challenge. In addition to obtaining an initial contour of lesion, the output saliency map can be used as a speed function alongside with image gradient to derive the initial contour toward the lesion boundary using a propagation model. The proposed algorithm has been tested on the ISIC2017 training, validation and test datasets, and gained high values for evaluation metrics

Vascular Tree Tracking and Bifurcation Points Detection in Retinal Images Using a Hierarchical Probabilistic Model

Background and Objective Retinal vascular tree extraction plays an important role in computer-aided diagnosis and surgical operations. Junction point detection and classification provide useful information about the structure of the vascular network, facilitating objective analysis of retinal diseases. Methods In this study, we present a new machine learning algorithm for joint classification and tracking of retinal blood vessels. Our method is based on a hierarchical probabilistic framework, where the local intensity cross sections are classified as either junction or vessel points. Gaussian basis functions are used for intensity interpolation, and the corresponding linear coefficients are assumed to be samples from class-specific Gamma distributions. Hence, a directed Probabilistic Graphical Model (PGM) is proposed and the hyperparameters are estimated using a Maximum Likelihood (ML) solution based on Laplace approximation. Results The performance of proposed method is evaluated using precision and recall rates on the REVIEW database. Our experiments show the proposed approach reaches promising results in bifurcation point detection and classification, achieving 88.67% precision and 88.67% recall rates. Conclusions This technique results in a classifier with high precision and recall when comparing it with Xu’s method

Semi-supervised assessment of incomplete LV coverage in cardiac MRI using generative adversarial nets

Cardiac magnetic resonance (CMR) images play a growing role in diagnostic imaging of cardiovascular diseases. Ensuring full coverage of the Left Ventricle (LV) is a basic criteria of CMR image quality. Complete LV coverage, from base to apex, precedes accurate cardiac volume and functional assessment. Incomplete coverage of the LV is identified through visual inspection, which is time-consuming and usually done retrospectively in large imaging cohorts. In this paper, we propose a novel semi-supervised method to check the coverage of LV from CMR images by using generative adversarial networks (GAN), we call it Semi-Coupled-GANs (SCGANs). To identify missing basal and apical slices in a CMR volume, a two-stage framework is proposed. First, the SCGANs generate adversarial examples and extract high-level features from the CMR images; then these image attributes are used to detect missing basal and apical slices. We constructed extensive experiments to validate the proposed method on UK Biobank with more than 6000 independent volumetric MR scans, which achieved high accuracy and robust results for missing slice detection, comparable with those of state of the art deep learning methods. The proposed method, in principle, can be adapted to other CMR image data for LV coverage assessment

Fully automatic detection of lung nodules in CT images using a hybrid feature set

Purpose: The aim of this study was to develop a novel technique for lung nodule detection using an optimized feature set. This feature set has been achieved after rigorous experimentation, which has helped in reducing the false positives significantly. Method: The proposed method starts with preprocessing, removing any present noise from input images, followed by lung segmentation using optimal thresholding. Then the image is enhanced using multiscale dot enhancement filtering prior to nodule detection and feature extraction. Finally, classification of lung nodules is achieved using Support Vector Machine (SVM) classifier. The feature set consists of intensity, shape (2D and 3D) and texture features, which have been selected to optimize the sensitivity and reduce false positives. In addition to SVM, some other supervised classifiers like K‐Nearest‐Neighbor (KNN), Decision Tree and Linear Discriminant Analysis (LDA) have also been used for performance comparison. The extracted features have also been compared class‐wise to determine the most relevant features for lung nodule detection. The proposed system has been evaluated using 850 scans from Lung Image Database Consortium (LIDC) dataset and k‐fold cross‐validation scheme. Results: The overall sensitivity has been improved compared to the previous methods and false positives per scan have been reduced significantly. The achieved sensitivities at detection and classification stages are 94.20% and 98.15%, respectively, with only 2.19 false positives per scan. Conclusions: It is very difficult to achieve high performance metrics using only a single feature class therefore hybrid approach in feature selection remains a better choice. Choosing right set of features can improve the overall accuracy of the system by improving the sensitivity and reducing false positives

Group-wise similarity registration of point sets using Student’s t-mixture model for statistical shape models

A probabilistic group-wise similarity registration technique based on Student’s t-mixture model (TMM) and a multi-resolution extension of the same (mr-TMM) are proposed in this study, to robustly align shapes and establish valid correspondences, for the purpose of training statistical shape models (SSMs). Shape analysis across large cohorts requires automatic generation of the requisite training sets. Automated segmentation and landmarking of medical images often result in shapes with varying proportions of outliers and consequently require a robust method of alignment and correspondence estimation. Both TMM and mrTMM are validated by comparison with state-of-the-art registration algorithms based on Gaussian mixture models (GMMs), using both synthetic and clinical data. Four clinical data sets are used for validation: (a) 2D femoral heads ( 1000 samples generated from DXA images of healthy subjects); (b) control-hippocampi ( 50 samples generated from T1-weighted magnetic resonance (MR) images of healthy subjects); (c) MCI-hippocampi ( 28 samples generated from MR images of patients diagnosed with mild cognitive impairment); and (d) heart shapes comprising left and right ventricular endocardium and epicardium ( 30 samples generated from short-axis MR images of: 10 healthy subjects, 10 patients diagnosed with pulmonary hypertension and 10 diagnosed with hypertrophic cardiomyopathy). The proposed methods significantly outperformed the state-of-the-art in terms of registration accuracy in the experiments involving synthetic data, with mrTMM offering significant improvement over TMM. With the clinical data, both methods performed comparably to the state-of-the-art for the hippocampi and heart data sets, which contained few outliers. They outperformed the state-of-the-art for the femur data set, containing large proportions of outliers, in terms of alignment accuracy, and the quality of SSMs trained, quantified in terms of generalization, compactness and specificity

Mixture of Probabilistic Principal Component Analyzers for Shapes from Point Sets

Inferring a probability density function (pdf) for shape from a population of point sets is a challenging problem. The lack of point-to-point correspondences and the non-linearity of the shape spaces undermine the linear models. Methods based on manifolds model the shape variations naturally, however, statistics are often limited to a single geodesic mean and an arbitrary number of variation modes. We relax the manifold assumption and consider a piece-wise linear form, implementing a mixture of distinctive shape classes. The pdf for point sets is defined hierarchically, modeling a mixture of Probabilistic Principal Component Analyzers (PPCA) in higher dimension. A Variational Bayesian approach is designed for unsupervised learning of the posteriors of point set labels, local variation modes, and point correspondences. By maximizing the model evidence, the numbers of clusters, modes of variations, and points on the mean models are automatically selected. Using the predictive distribution, we project a test shape to the spaces spanned by the local PPCA's. The method is applied to point sets from: i) synthetic data, ii) healthy versus pathological heart morphologies, and iii) lumbar vertebrae. The proposed method selects models with expected numbers of clusters and variation modes, achieving lower generalization-specificity errors compared to state-of-the-art