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

Second-order neural core for bioinspired focal-plane dynamic image processing in CMOS

Based on studies of the mammalian retina, a bioinspired model for mixed-signal array processing has been implemented on silicon. This model mimics the way in which images are processed at the front-end of natural visual pathways, by means of programmable complex spatio-temporal dynamic. When embedded into a focal-plane processing chip, such a model allows for online parallel filtering of the captured image; the outcome of such processing can be used to develop control feedback actions to adapt the response of photoreceptors to local image features. Beyond simple resistive grid filtering, it is possible to program other spatio-temporal processing operators into the model core, such as nonlinear and anisotropic diffusion, among others. This paper presents analog and mixed-signal very large-scale integration building blocks to implement this model, and illustrates their operation through experimental results taken from a prototype chip fabricated in a 0.5-μm CMOS technology.European Union IST 2001 38097Ministerio de Ciencia y Tecnología TIC 2003 09817 C02 01Office of Naval Research (USA) N00014021088

Computational methods to predict and enhance decision-making with biomedical data.

The proposed research applies machine learning techniques to healthcare applications. The core ideas were using intelligent techniques to find automatic methods to analyze healthcare applications. Different classification and feature extraction techniques on various clinical datasets are applied. The datasets include: brain MR images, breathing curves from vessels around tumor cells during in time, breathing curves extracted from patients with successful or rejected lung transplants, and lung cancer patients diagnosed in US from in 2004-2009 extracted from SEER database. The novel idea on brain MR images segmentation is to develop a multi-scale technique to segment blood vessel tissues from similar tissues in the brain. By analyzing the vascularization of the cancer tissue during time and the behavior of vessels (arteries and veins provided in time), a new feature extraction technique developed and classification techniques was used to rank the vascularization of each tumor type. Lung transplantation is a critical surgery for which predicting the acceptance or rejection of the transplant would be very important. A review of classification techniques on the SEER database was developed to analyze the survival rates of lung cancer patients, and the best feature vector that can be used to predict the most similar patients are analyzed

Optical control of spatially localized red blood cell activity by holographic tweezing

Red blood cells possess unique biomechanical ability to squeeze through capillaries smaller than their size to enable gas and ion exchange. A key signature of their active biomechanics is the out-of-equilibrium fluctuation of the plasma membrane, also known as flickering motion. This active flickering is driven by motor proteins that connect the forces between the spectrin skeleton and the lipid bilayer. However, studying flickering motions in living red blood cells is challenging without altering their physical properties. Here, we implemented a holographic optical tweezer that sculpted a laser beam to create a force field distributed directly along the membrane equatorial contour. We show heterogeneous membrane flickering activity driven by membrane kickers in free-standing cells. Then we inhibited the active kickers by optical forces under minimal invasion, thus benchmarking the active motion against thermal fluctuations. Our work paves the way for optical control of biophysical forces, providing touchless strategies for mechanotransduction in living cells.Comment: 6 figure

Extracting the Structure and Conformations of Biological Entities from Large Datasets

In biology, structure determines function, which often proceeds via changes in conformation. Efficient means for determining structure exist, but mapping conformations continue to present a serious challenge. Single-particles approaches, such as cryogenic electron microscopy (cryo-EM) and emerging diffract & destroy X-ray techniques are, in principle, ideally positioned to overcome these challenges. But the algorithmic ability to extract information from large heterogeneous datasets consisting of unsorted snapshots - each emanating from an unknown orientation of an object in an unknown conformation - remains elusive. It is the objective of this thesis to describe and validate a powerful suite of manifold-based algorithms able to extract structural and conformational information from large datasets. These computationally efficient algorithms offer a new approach to determining the structure and conformations of viruses and macromolecules. After an introduction, we demonstrate a distributed, exact k-Nearest Neighbor Graph (k-NNG) construction method, in order to establish a firm algorithmic basis for manifold-based analysis. The proposed algorithm uses Graphics Processing Units (GPUs) and exploits multiple levels of parallelism in distributed computational environment and it is scalable for different cluster sizes, with each compute node in the cluster containing multiple GPUs. Next, we present applications of manifold-based analysis in determining structure and conformational variability. Using the Diffusion Map algorithm, a new approach is presented, which is capable of determining structure of symmetric objects, such as viruses, to 1/100th of the object diameter, using low-signal diffraction snapshots. This is demonstrated by means of a successful 3D reconstruction of the Satellite Tobacco Necrosis Virus (STNV) to atomic resolution from simulated diffraction snapshots with and without noise. We next present a new approach for determining discrete conformational changes of the enzyme Adenylate kinase (ADK) from very large datasets of up to 20 million snapshots, each with ~104 pixels. This exceeds by an order of magnitude the largest dataset previously analyzed. Finally, we present a theoretical framework and an algorithmic pipeline for capturing continuous conformational changes of the ribosome from ultralow-signal (-12dB) experimental cryo-EM. Our analysis shows a smooth, concerted change in molecular structure in two-dimensional projection, which might be indicative of the way the ribosome functions as a molecular machine. The thesis ends with a summary and future prospects

Weighted Mean Curvature

In image processing tasks, spatial priors are essential for robust computations, regularization, algorithmic design and Bayesian inference. In this paper, we introduce weighted mean curvature (WMC) as a novel image prior and present an efficient computation scheme for its discretization in practical image processing applications. We first demonstrate the favorable properties of WMC, such as sampling invariance, scale invariance, and contrast invariance with Gaussian noise model; and we show the relation of WMC to area regularization. We further propose an efficient computation scheme for discretized WMC, which is demonstrated herein to process over 33.2 giga-pixels/second on GPU. This scheme yields itself to a convolutional neural network representation. Finally, WMC is evaluated on synthetic and real images, showing its superiority quantitatively to total-variation and mean curvature.Comment: 12 page