Genomic signal processing methods for computation of alignment-free distances from DNA sequences.

Genomic signal processing (GSP) refers to the use of digital signal processing (DSP) tools for analyzing genomic data such as DNA sequences. A possible application of GSP that has not been fully explored is the computation of the distance between a pair of sequences. In this work we present GAFD, a novel GSP alignment-free distance computation method. We introduce a DNA sequence-to-signal mapping function based on the employment of doublet values, which increases the number of possible amplitude values for the generated signal. Additionally, we explore the use of three DSP distance metrics as descriptors for categorizing DNA signal fragments. Our results indicate the feasibility of employing GAFD for computing sequence distances and the use of descriptors for characterizing DNA fragments.

Standardized evaluation methodology and reference database for evaluating IVUS image segmentation.

This paper describes an evaluation framework that allows a standardized and quantitative comparison of IVUS lumen and media segmentation algorithms. This framework has been introduced at the MICCAI 2011 Computing and Visualization for (Intra)Vascular Imaging (CVII) workshop, comparing the results of eight teams that participated. We describe the available data-base comprising of multi-center, multi-vendor and multi-frequency IVUS datasets, their acquisition, the creation of the reference standard and the evaluation measures. The approaches address segmentation of the lumen, the media, or both borders; semi- or fully-automatic operation; and 2-D vs. 3-D methodology. Three performance measures for quantitative analysis have been proposed. The results of the evaluation indicate that segmentation of the vessel lumen and media is possible with an accuracy that is comparable to manual annotation when semi-automatic methods are used, as well as encouraging results can be obtained also in case of fully-automatic segmentation. The analysis performed in this paper also highlights the challenges in IVUS segmentation that remains to be solved.

Segmentation of the luminal border in intravascular ultrasound B-mode images using a probabilistic approach.

Intravascular ultrasound (IVUS) is a catheter-based medical imaging technique that produces cross-sectional images of blood vessels and is particularly useful for studying atherosclerosis. In this paper, we present a computational method for the delineation of the luminal border in IVUS B-mode images. The method is based in the minimization of a probabilistic cost function (that deforms a parametric curve) which defines a probability field that is regularized with respect to the given likelihoods of the pixels belonging to blood and non-blood. These likelihoods are obtained by a Support Vector Machine classifier trained using samples of the lumen and non-lumen regions provided by the user in the first frame of the sequence to be segmented. In addition, an optimization strategy is introduced in which the direction of the steepest descent and Broyden-Fletcher-Goldfarb-Shanno optimization methods are linearly combined to improve convergence. Our proposed method (MRK) is capable of segmenting IVUS B-mode images from different systems and transducer frequencies without the need of any parameter tuning, and it is robust with respect to changes of the B-mode reconstruction parameters which are subjectively adjusted by the interventionist. We validated the proposed method on six 20MHz and six 40MHz IVUS stationary sequences corresponding to regions with different degrees of stenosis, and evaluated its performance by comparing the segmentation results with manual segmentation by two observers. Furthermore, we compared our method with the segmentation results on the same sequences as provided by the authors of three other segmentation methods available in the literature. The performance of all methods was quantified using Dice and Jaccard similarity indexes, Hausdorff distance, linear regression and Bland-Altman analysis. The results indicate the advantages of our method for the segmentation of the lumen contour.

Probabilistic segmentation of the lumen from intravascular ultrasound radio frequency data.

Intravascular ultrasound (IVUS) is a catheter-based medical imaging technique that produces cross-sectional images of blood vessels. In this paper, we present a method for the segmentation of the luminal border using IVUS radio frequency (RF) data. Specifically, we parameterize the lumen contour using Fourier series. This contour is deformed by minimizing a cost function that is formulated using a probabilistic approach in which the a priori term is obtained using the prediction confidence of a Support Vector Machine classifier using features extracted from the RF signal. We evaluated the performance of our method by comparing our results with manual segmentations from two expert observers on 280 frames from eight 40 MHz IVUS sequences from rabbits and pigs. The performance was evaluated using the Dice similarity coefficient, coefficient of determination, and linear regressions of the lumen area for each frame. Our results indicate the feasibility of our method for the segmentation of the lumen from IVUS RF data.

Towards extra-luminal blood detection from intravascular ultrasound radio frequency data.

Recent evidence has suggested that the presence and proliferation of vasa vasorum (VV) in the plaque is correlated to an increase in plaque inflammation and destabilization, leading to acute coronary events (e.g., heart attacks). Therefore, the detection and quantification of VV in plaque (i.e., extra luminal blood perfusion) is an important problem since it may enable the development of an index of plaque vulnerability. In this paper, we explore the feasibility of a method that employs a physics-based model of the scattered intravascular ultrasound (IVUS) radio frequency signal for the detection of blood. We evaluate our method using synthetic data and validate it using six 40 MHz pullback sequences acquired with three different IVUS systems from different arteries of rabbits and swines. Our experimental results are very promising and indicate the feasibility of our method for the computation of a feature that leads to automatic extra-luminal blood detection which may be an indication of plaque inflammation.

An inverse scattering algorithm for the segmentation of the luminal border on intravascular ultrasound data.

Intravascular ultrasound (IVUS) is a catheter-based medical imaging technique that produces cross-sectional images of blood vessels and is particularly useful for studying atherosclerosis. In this paper, we present a novel method for segmentation of the luminal border on IVUS images using the radio frequency (RF) raw signal based on a scattering model and an inversion scheme. The scattering model is based on a random distribution of point scatterers in the vessel. The per-scatterer signal uses a differential backscatter cross-section coefficient (DBC) that depends on the tissue type. Segmentation requires two inversions: a calibration inversion and a reconstruction inversion. In the calibration step, we use a single manually segmented frame and then solve an inverse problem to recover the DBC for the lumen and vessel wall (kappa(l) and kappa(w), respectively) and the width of the impulse signal theta. In the reconstruction step, we use the parameters from the calibration step to solve a new inverse problem: for each angle theta(i) of the IVUS data, we reconstruct the lumen-vessel wall interface. We evaluated our method using three 40MHz IVUS sequences by comparing with manual segmentations. Our preliminary results indicate that it is possible to segment the luminal border by solving an inverse problem using the IVUS RF raw signal with the scatterer model.