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Sergio Escalera, Ana Puig, Oscar Amoros, & Maria Salamo. (2011). Intelligent GPGPU Classification in Volume Visualization: a framework based on Error-Correcting Output Codes. CGF - Computer Graphics Forum, 30(7), 2107–2115.
Abstract: IF JCR 1.455 2010 25/99
In volume visualization, the definition of the regions of interest is inherently an iterative trial-and-error process finding out the best parameters to classify and render the final image. Generally, the user requires a lot of expertise to analyze and edit these parameters through multi-dimensional transfer functions. In this paper, we present a framework of intelligent methods to label on-demand multiple regions of interest. These methods can be split into a two-level GPU-based labelling algorithm that computes in time of rendering a set of labelled structures using the Machine Learning Error-Correcting Output Codes (ECOC) framework. In a pre-processing step, ECOC trains a set of Adaboost binary classifiers from a reduced pre-labelled data set. Then, at the testing stage, each classifier is independently applied on the features of a set of unlabelled samples and combined to perform multi-class labelling. We also propose an alternative representation of these classifiers that allows to highly parallelize the testing stage. To exploit that parallelism we implemented the testing stage in GPU-OpenCL. The empirical results on different data sets for several volume structures shows high computational performance and classification accuracy.
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Laura Igual, Joan Carles Soliva, Antonio Hernandez, Sergio Escalera, Xavier Jimenez, Oscar Vilarroya, et al. (2011). A fully-automatic caudate nucleus segmentation of brain MRI: Application in volumetric analysis of pediatric attention-deficit/hyperactivity disorder. BEO - BioMedical Engineering Online, 10(105), 1–23.
Abstract: Background
Accurate automatic segmentation of the caudate nucleus in magnetic resonance images (MRI) of the brain is of great interest in the analysis of developmental disorders. Segmentation methods based on a single atlas or on multiple atlases have been shown to suitably localize caudate structure. However, the atlas prior information may not represent the structure of interest correctly. It may therefore be useful to introduce a more flexible technique for accurate segmentations.
Method
We present Cau-dateCut: a new fully-automatic method of segmenting the caudate nucleus in MRI. CaudateCut combines an atlas-based segmentation strategy with the Graph Cut energy-minimization framework. We adapt the Graph Cut model to make it suitable for segmenting small, low-contrast structures, such as the caudate nucleus, by defining new energy function data and boundary potentials. In particular, we exploit information concerning the intensity and geometry, and we add supervised energies based on contextual brain structures. Furthermore, we reinforce boundary detection using a new multi-scale edgeness measure.
Results
We apply the novel CaudateCut method to the segmentation of the caudate nucleus to a new set of 39 pediatric attention-deficit/hyperactivity disorder (ADHD) patients and 40 control children, as well as to a public database of 18 subjects. We evaluate the quality of the segmentation using several volumetric and voxel by voxel measures. Our results show improved performance in terms of segmentation compared to state-of-the-art approaches, obtaining a mean overlap of 80.75%. Moreover, we present a quantitative volumetric analysis of caudate abnormalities in pediatric ADHD, the results of which show strong correlation with expert manual analysis.
Conclusion
CaudateCut generates segmentation results that are comparable to gold-standard segmentations and which are reliable in the analysis of differentiating neuroanatomical abnormalities between healthy controls and pediatric ADHD.
Keywords: Brain caudate nucleus; segmentation; MRI; atlas-based strategy; Graph Cut framework
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Laura Igual, Xavier Perez Sala, Sergio Escalera, Cecilio Angulo, & Fernando De la Torre. (2014). Continuous Generalized Procrustes Analysis. PR - Pattern Recognition, 47(2), 659–671.
Abstract: PR4883, PII: S0031-3203(13)00327-0
Two-dimensional shape models have been successfully applied to solve many problems in computer vision, such as object tracking, recognition, and segmentation. Typically, 2D shape models are learned from a discrete set of image landmarks (corresponding to projection of 3D points of an object), after applying Generalized Procustes Analysis (GPA) to remove 2D rigid transformations. However, the
standard GPA process suffers from three main limitations. Firstly, the 2D training samples do not necessarily cover a uniform sampling of all the 3D transformations of an object. This can bias the estimate of the shape model. Secondly, it can be computationally expensive to learn the shape model by sampling 3D transformations. Thirdly, standard GPA methods use only one reference shape, which can might be insufficient to capture large structural variability of some objects.
To address these drawbacks, this paper proposes continuous generalized Procrustes analysis (CGPA).
CGPA uses a continuous formulation that avoids the need to generate 2D projections from all the rigid 3D transformations. It builds an efficient (in space and time) non-biased 2D shape model from a set of 3D model of objects. A major challenge in CGPA is the need to integrate over the space of 3D rotations, especially when the rotations are parameterized with Euler angles. To address this problem, we introduce the use of the Haar measure. Finally, we extended CGPA to incorporate several reference shapes. Experimental results on synthetic and real experiments show the benefits of CGPA over GPA.
Keywords: Procrustes analysis; 2D shape model; Continuous approach
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Francesco Ciompi, Oriol Pujol, Carlo Gatta, Marina Alberti, Simone Balocco, Xavier Carrillo, et al. (2012). HoliMab: A Holistic Approach for Media-Adventitia Border Detection in Intravascular Ultrasound. MIA - Medical Image Analysis, 16(6), 1085–1100.
Abstract: We present a fully automatic methodology for the detection of the Media-Adventitia border (MAb) in human coronary artery in Intravascular Ultrasound (IVUS) images. A robust border detection is achieved by means of a holistic interpretation of the detection problem where the target object, i.e. the media layer, is considered as part of the whole vessel in the image and all the relationships between tissues are learnt. A fairly general framework exploiting multi-class tissue characterization as well as contextual information on the morphology and the appearance of the tissues is presented. The methodology is (i) validated through an exhaustive comparison with both Inter-observer variability on two challenging databases and (ii) compared with state-of-the-art methods for the detection of the MAb in IVUS. The obtained averaged values for the mean radial distance and the percentage of area difference are 0.211 mm and 10.1%, respectively. The applicability of the proposed methodology to clinical practice is also discussed.
Keywords: Media–Adventitia border detection; Intravascular ultrasound; Multi-Scale Stacked Sequential Learning; Error-correcting output codes; Holistic segmentation
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Marina Alberti, Simone Balocco, Carlo Gatta, Francesco Ciompi, Oriol Pujol, Joana Silva, et al. (2012). Automatic Bifurcation Detection in Coronary IVUS Sequences. TBME - IEEE Transactions on Biomedical Engineering, 59(4), 1022–2031.
Abstract: In this paper, we present a fully automatic method which identifies every bifurcation in an intravascular ultrasound (IVUS) sequence, the corresponding frames, the angular orientation with respect to the IVUS acquisition, and the extension. This goal is reached using a two-level classification scheme: first, a classifier is applied to a set of textural features extracted from each image of a sequence. A comparison among three state-of-the-art discriminative classifiers (AdaBoost, random forest, and support vector machine) is performed to identify the most suitable method for the branching detection task. Second, the results are improved by exploiting contextual information using a multiscale stacked sequential learning scheme. The results are then successively refined using a-priori information about branching dimensions and geometry. The proposed approach provides a robust tool for the quick review of pullback sequences, facilitating the evaluation of the lesion at bifurcation sites. The proposed method reaches an F-Measure score of 86.35%, while the F-Measure scores for inter- and intraobserver variability are 71.63% and 76.18%, respectively. The obtained results are positive. Especially, considering the branching detection task is very challenging, due to high variability in bifurcation dimensions and appearance.
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