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Particle Swarm Optimization and Differential Evolution for model-based object detection

Automatically detecting objects in images or video sequences is one of the most relevant and frequently tackled tasks in computer vision and pattern recognition. The starting point for this work is a very general model-based approach to object detection. The problem is turned into a global continuous optimization one: given a parametric model of the object to be detected within an image, a function is maximized, which represents the similarity between the model and a region of the image under investigation. In particular, in this work, the optimization problem is tackled using Particle Swarm Optimization (PSO) and Differential Evolution (DE). We compare the performances of these optimization techniques on two real-world paradigmatic problems, onto which many other real-world object detection problems can be mapped: hippocampus localization in histological images and human body pose estimation in video sequences. In the former, a 2D deformable model of a section of the hippocampus is fit to the corresponding region of a histological image, to accurately localize such a structure and analyze gene expression in specific sub-regions. In the latter, an articulated 3D model of a human body is matched against a set of images of a human performing some action, taken from different perspectives, to estimate the subjects posture in space. Given the significant computational burden imposed by this approach, we implemented PSO and DE as parallel algorithms within the nVIDIA(TM) CUDA computing architecture.

Biomedical image segmentation using geometric deformable models and metaheuristics

This paper describes a hybrid level set approach for medical image segmentation. This new geometric deformable model combines region- and edge-based information with the prior shape knowledge introduced using deformable registration. Our proposal consists of two phases: training and test. The former implies the learning of the level set parameters by means of a Genetic Algorithm, while the latter is the proper segmentation, where another metaheuristic, in this case Scatter Search, derives the shape prior. In an experimental comparison, this approach has shown a better performance than a number of state-of-the-art methods when segmenting anatomical structures from different biomedical image modalities.

Automatic hippocampus localization in histological images using Differential Evolution-based deformable models

In this paper, the localization of structures in biomedical images is considered as a multimodal global continuous optimization problem and solved by means of soft computing techniques. We have developed an automatic method aimed at localizing the hippocampus in histological images, after discoveries indicating the relevance of structural changes of this region as early biomarkers for Alzheimers disease and epilepsy. The localization is achieved by searching the parameters of an empirically-derived deformable model of the hippocampus which maximize its overlap with the corresponding anatomical structure in histological brain images. The comparison between six real-parameter optimization techniques (Levenberg-Marquardt, Differential Evolution, Simulated Annealing, Genetic Algorithms, Particle Swarm Optimization and Scatter Search) shows that Differential Evolution significantly outperforms the other techniques in this task, providing successful localizations in 90.9% and 93.0% of two test sets of real and synthetic images, respectively.

libCudaOptimize: an open source library of GPU-based metaheuristics

Evolutionary Computation techniques and other metaheuristics have been increasingly used in the last years for solving many real-world tasks that can be formulated as optimization problems. Among their numerous strengths, a major one is their natural predisposition to parallelization. In this paper, we introduce libCudaOptimize, an open source library which implements some metaheuristics for continuous optimization: presently Particle Swarm Optimization, Differential Evolution, Scatter Search, and Solis&Wets local search. This library allows users either to apply these metaheuristics directly to their own fitness function or to extend it by implementing their own parallel optimization techniques. The library is written in CUDA-C to make extensive use of parallelization, as allowed by Graphics Processing Units. After describing the library, we consider two practical case studies: the optimization of a fitness function for the automatic localization of anatomical brain structures in histological images, and the parallel implementation of Simulated Annealing as a new module, which extends the library while keeping code compatibility with it, so that the new method can be readily available for future use within the library as an alternative optimization technique.

A comparative study of three GPU-based metaheuristics

In this paper we compare GPU-based implementations of three metaheuristics: Particle Swarm Optimization, Differential Evolution, and Scatter Search. A GPU-based implementation, obviously, does not change the general properties of the algorithms. As well, we give for granted that GPU-based implementation of both algorithm and fitness function produces a significant speed-up with respect to a sequential implementation. Accordingly, the main goal of this work has been to fairly assess the efficiency of the GPU-based implementations of the three metaheuristics, based on the statistical analysis of the results they obtain in optimizing a benchmark of twenty functions within a prefixed limited time.

Automatic segmentation of hippocampus in histological images of mouse brains using deformable models and random forest

We perform a two-step segmentation of the hippocampus in histological images. First, we maximize the overlap of an empirically-derived parametric Deformable Model with two crucial landmark sub-structures in the brain image using Differential Evolution. Then, the points located in the previous step determine the region where a thresholding technique based on Otsus method is to be applied. Finally, the segmentation is expanded employing Random Forest in the regions not covered by the model. Our approach showed an average segmentation accuracy of the 92.25% and 92.11% on test sets comprising 15 real and 15 synthetic images, respectively.

Visual Search of Neuropil-Enriched RNAs from Brain In Situ Hybridization Data through the Image Analysis Pipeline Hippo-ATESC

Motivation RNA molecules specifically enriched in the neuropil of neuronal cells and in particular in dendritic spines are of great interest for neurobiology in virtue of their involvement in synaptic structure and plasticity. The systematic recognition of such molecules is therefore a very important task. High resolution images of RNA in situ hybridization experiments contained in the Allen Brain Atlas (ABA) represent a very rich resource to identify them and have been so far exploited for this task through human-expert analysis. However, software tools that may automatically address the same objective are not very well developed. Results In this study we describe an automatic method for exploring in situ hybridization data and discover neuropil-enriched RNAs in the mouse hippocampus. We called it Hippo-ATESC (Automatic Texture Extraction from the Hippocampal region using Soft Computing). Bioinformatic validation showed that the Hippo-ATESC is very efficient in the recognition of RNAs which are manually identified by expert curators as neuropil-enriched on the same image series. Moreover, we show that our method can also highlight genes revealed by microdissection-based methods but missed by human visual inspection. We experimentally validated our approach by identifying a non-coding transcript enriched in mouse synaptosomes. The code is freely available on the web at http://ibislab.ce.unipr.it/software/hippo/.

Segmentation of histological images using a metaheuristic-based level set approach

This paper presents a two-phase method to segment the hippocampus in histological images. The first phase represents a training stage where, from a training set of manually labelled images, the hippocampus representative shape and texture are derived. The second one, the proper segmentation, uses a metaheuristic to evolve the contour of a geometric deformable model using region and texture information. Three different metaheuristics (real-coded GA, Particle Swarm Optimization and Differential Evolution) and two classical segmentation algorithms (Chan & Vese model and Geodesic Active Contours) were compared over a test set of 10 histological images. The best results were attained by the real-coded GA, achieving an average and median Dice Coefficient of 0.72 and 0.77, respectively.

Automatic evolutionary medical image segmentation using deformable models

This paper describes a hybrid level set approach to medical image segmentation. The method combines region-and edge-based information with the prior shape knowledge introduced using deformable registration. A parameter tuning mechanism, based on Genetic Algorithms, provides the ability to automatically adapt the level set to different segmentation tasks. Provided with a set of examples, the GA learns the correct weights for each image feature used in the segmentation. The algorithm has been tested over four different medical datasets across three image modalities. Our approach has shown significantly more accurate results in comparison with six state-of-the-art segmentation methods. The contributions of both the image registration and the parameter learning steps to the overall performance of the method have also been analyzed.

First results and future developments of the MIBISOC Project in the IBISlab of the university of parma

Medical Imaging using Bio-Inspired and Soft Computing (MIBISOC) is a Marie Curie Initial Training Network (ITN) within the EU Seventh Framework Programme. MIBISOC is a training programme in which sixteen Early-Stage Researchers (ESRs) are exposed to a wide variety of Soft Computing (SC) and Bio-Inspired Computing (BC) techniques, and face the challenge of applying them to the different situations and problems which characterize medical image processing tasks. Hence, the main goal of the project is to generate new methods and solutions from the combination of the ideas of experts from the area of Medical Imaging (MI) with those working on BC and SC applications. The Intelligent Bio-Inpired Systems laboratory (IBISlab) in the University of Parma is one of the partners of this ITN. In this paper, we describe the work which is being developed in the IBISlab, as well as its future developments and main objectives, within the framework of this ITN.