Medical imaging analysis with artificial neural networks

Given that neural networks have been widely reported in the research community of medical imaging, we provide a focused literature survey on recent neural network developments in computer-aided diagnosis, medical image segmentation and edge detection towards visual content analysis, and medical image registration for its pre-processing and post-processing, with the aims of increasing awareness of how neural networks can be applied to these areas and to provide a foundation for further research and practical development. Representative techniques and algorithms are explained in detail to provide inspiring examples illustrating: (i) how a known neural network with fixed structure and training procedure could be applied to resolve a medical imaging problem; (ii) how medical images could be analysed, processed, and characterised by neural networks; and (iii) how neural networks could be expanded further to resolve problems relevant to medical imaging. In the concluding section, a highlight of comparisons among many neural network applications is included to provide a global view on computational intelligence with neural networks in medical imaging

Gait recognition and understanding based on hierarchical temporal memory using 3D gait semantic folding

Gait recognition and understanding systems have shown a wide-ranging application prospect. However, their use of unstructured data from image and video has affected their performance, e.g., they are easily influenced by multi-views, occlusion, clothes, and object carrying conditions. This paper addresses these problems using a realistic 3-dimensional (3D) human structural data and sequential pattern learning framework with top-down attention modulating mechanism based on Hierarchical Temporal Memory (HTM). First, an accurate 2-dimensional (2D) to 3D human body pose and shape semantic parameters estimation method is proposed, which exploits the advantages of an instance-level body parsing model and a virtual dressing method. Second, by using gait semantic folding, the estimated body parameters are encoded using a sparse 2D matrix to construct the structural gait semantic image. In order to achieve time-based gait recognition, an HTM Network is constructed to obtain the sequence-level gait sparse distribution representations (SL-GSDRs). A top-down attention mechanism is introduced to deal with various conditions including multi-views by refining the SL-GSDRs, according to prior knowledge. The proposed gait learning model not only aids gait recognition tasks to overcome the difficulties in real application scenarios but also provides the structured gait semantic images for visual cognition. Experimental analyses on CMU MoBo, CASIA B, TUM-IITKGP, and KY4D datasets show a significant performance gain in terms of accuracy and robustness

Detecting cells and cellular activity from two-photon calcium imaging data

To understand how networks of neurons process information, it is essential to monitor their activity in living tissue. Information is transmitted between neurons by electrochemical impulses called action potentials or spikes. Calcium-sensitive fluorescent probes, which emit a characteristic pulse of fluorescence in response to a spike, are used to visualise spiking activity. Combined with two-photon microscopy, they enable the spiking activity of thousands of neurons to be monitored simultaneously at single-cell and single-spike resolution. In this thesis, we develop signal processing tools for detecting cells and cellular activity from two-photon calcium imaging data. Firstly, we present a method to detect the locations of cells within a video. In our framework, an active contour evolves guided by a model-based cost function to identify a cell boundary. We demonstrate that this method, which includes no assumptions about typical cell shape or temporal activity, is able to detect cells with varied properties from real imaging data. Once the location of a cell has been identified, its spiking activity must be inferred from the fluorescence signal. We present a metric that quantifies the similarity between inferred spikes and the ground truth. The proposed metric assesses the similarity of pulse trains obtained from convolution of the spike trains with a smoothing pulse, whose width is derived from the statistics of the data. We demonstrate that the proposed metric is more sensitive than existing metrics to the temporal and rate precision of inferred spike trains. Finally, we extend an existing framework for spike inference to accommodate a wider class of fluorescence signals. Our method, which is based on finite rate of innovation theory, exploits the known parametric structure of the signal to infer the unknown spike times. On in vitro imaging data, we demonstrate that the updated algorithm outperforms a state of the art approach.Open Acces

A multi-view approach to cDNA micro-array analysis

The official published version can be obtained from the link below.Microarray has emerged as a powerful technology that enables biologists to study thousands of genes simultaneously, therefore, to obtain a better understanding of the gene interaction and regulation mechanisms. This paper is concerned with improving the processes involved in the analysis of microarray image data. The main focus is to clarify an image's feature space in an unsupervised manner. In this paper, the Image Transformation Engine (ITE), combined with different filters, is investigated. The proposed methods are applied to a set of real-world cDNA images. The MatCNN toolbox is used during the segmentation process. Quantitative comparisons between different filters are carried out. It is shown that the CLD filter is the best one to be applied with the ITE.This work was supported in part by the Engineering and Physical Sciences Research Council (EPSRC) of the UK under Grant GR/S27658/01, the National Science Foundation of China under Innovative Grant 70621001, Chinese Academy of Sciences under Innovative Group Overseas Partnership Grant, the BHP Billiton Cooperation of Australia Grant, the International Science and Technology Cooperation Project of China under Grant 2009DFA32050 and the Alexander von Humboldt Foundation of Germany

Understanding Physiological and Degenerative Natural Vision Mechanisms to Define Contrast and Contour Operators

BACKGROUND:Dynamical systems like neural networks based on lateral inhibition have a large field of applications in image processing, robotics and morphogenesis modeling. In this paper, we will propose some examples of dynamical flows used in image contrasting and contouring. METHODOLOGY:First we present the physiological basis of the retina function by showing the role of the lateral inhibition in the optical illusions and pathologic processes generation. Then, based on these biological considerations about the real vision mechanisms, we study an enhancement method for contrasting medical images, using either a discrete neural network approach, or its continuous version, i.e. a non-isotropic diffusion reaction partial differential system. Following this, we introduce other continuous operators based on similar biomimetic approaches: a chemotactic contrasting method, a viability contouring algorithm and an attentional focus operator. Then, we introduce the new notion of mixed potential Hamiltonian flows; we compare it with the watershed method and we use it for contouring. CONCLUSIONS:We conclude by showing the utility of these biomimetic methods with some examples of application in medical imaging and computed assisted surgery

Rigidity and flexibility of biological networks

The network approach became a widely used tool to understand the behaviour of complex systems in the last decade. We start from a short description of structural rigidity theory. A detailed account on the combinatorial rigidity analysis of protein structures, as well as local flexibility measures of proteins and their applications in explaining allostery and thermostability is given. We also briefly discuss the network aspects of cytoskeletal tensegrity. Finally, we show the importance of the balance between functional flexibility and rigidity in protein-protein interaction, metabolic, gene regulatory and neuronal networks. Our summary raises the possibility that the concepts of flexibility and rigidity can be generalized to all networks.Comment: 21 pages, 4 figures, 1 tabl

Tectonic modeling of Konya-Beysehir Region (Turkey) using cellular neural networks

In this paper, to separate regional-residual anomaly maps and to detect borders of buried geological bodies, we applied the Cellular Neural Network (CNN) approach to gravity and magnetic anomaly maps. CNN is a stochastic image processing technique, based optimization of templates, which imply relationships of neighborhood pixels in 2-Dimensional (2D) potential anomalies. Here, CNN performance in geophysics, tested by various synthetic examples and the results are compared to classical methods such as boundary analysis and second vertical derivatives. After we obtained satisfactory results in synthetic models, we applied CNN to Bouguer anomaly map of Konya-Beysehir Region, which has complex tectonic structure with various fault combinations. We evaluated CNN outputs and 2D/3D models, which are constructed using forward and inversion methods. Then we presented a new tectonic structure of Konya-Beysehir Region. We have denoted (F1, F2, …, F7) and (Konya1, Konya2) faults according to our evaluations of CNN outputs. Thus, we have concluded that CNN is a compromising stochastic image processing technique in geophysics