Level set segmentation of bovine corpora lutea in ex situ ovarian ultrasound images

<p>Abstract</p> <p>Background</p> <p>The objective of this study was to investigate the viability of level set image segmentation methods for the detection of corpora lutea (corpus luteum, CL) boundaries in ultrasonographic ovarian images. It was hypothesized that bovine CL boundaries could be located within 1–2 mm by a level set image segmentation methodology.</p> <p>Methods</p> <p>Level set methods embed a 2D contour in a 3D surface and evolve that surface over time according to an image-dependent speed function. A speed function suitable for segmentation of CL's in ovarian ultrasound images was developed. An initial contour was manually placed and contour evolution was allowed to proceed until the rate of change of the area was sufficiently small. The method was tested on ovarian ultrasonographic images (<it>n </it>= 8) obtained <it>ex situ</it>. A expert in ovarian ultrasound interpretation delineated CL boundaries manually to serve as a "ground truth". Accuracy of the level set segmentation algorithm was determined by comparing semi-automatically determined contours with ground truth contours using the mean absolute difference (MAD), root mean squared difference (RMSD), Hausdorff distance (HD), sensitivity, and specificity metrics.</p> <p>Results and discussion</p> <p>The mean MAD was 0.87 mm (sigma = 0.36 mm), RMSD was 1.1 mm (sigma = 0.47 mm), and HD was 3.4 mm (sigma = 2.0 mm) indicating that, on average, boundaries were accurate within 1–2 mm, however, deviations in excess of 3 mm from the ground truth were observed indicating under- or over-expansion of the contour. Mean sensitivity and specificity were 0.814 (sigma = 0.171) and 0.990 (sigma = 0.00786), respectively, indicating that CLs were consistently undersegmented but rarely did the contour interior include pixels that were judged by the human expert not to be part of the CL. It was observed that in localities where gradient magnitudes within the CL were strong due to high contrast speckle, contour expansion stopped too early.</p> <p>Conclusion</p> <p>The hypothesis that level set segmentation can be accurate to within 1–2 mm on average was supported, although there can be some greater deviation. The method was robust to boundary leakage as evidenced by the high specificity. It was concluded that the technique is promising and that a suitable data set of human ovarian images should be obtained to conduct further studies.</p

Automatic Prostate Segmentation in Ultrasound Images using Gradient Vector Flow Active Contour

ABSTRACT: Prostate cancer is one of the leading causes of death by cancer among men in the world. Ultrasonography is said to be the safest technique in medical imaging so it is used extensively in prostate cancer detection. On the other hand, determining of prostate&apos;s boundary in TRUS (Transrectal Ultrasound) images is very necessary in lots of treatment methods prostate cancer. So the first and essential step for computer aided diagnosis (CAD) is the automatic prostate segmentation that is an open problem yet. But the low SNR, presence of strong speckle noise, Weak edges and shadow artifacts in these kinds of images limit the effectiveness of classical segmentation schemes. The classical segmentation methods fail completely or require post processing step to remove invalid object boundaries in the segmentation results. This paper has proposed a fully automatic algorithm for prostate segmentation in TRUS images that overcomes the explained problems completely. The presented algorithm contains three main stages. First, morphological smoothing and stick&apos;s filter are used for noise removing. A neural network is employed in the second step to find a point in prostate region. Finally in the last step, the prostate boundaries are extracted by GVF active contour. Some experiments for the performance validity of the presented method, compared with the extracted prostate by the proposed algorithm with manually-delineated boundaries by radiologist. The results show that our method extracts prostate boundaries with mean square area error lower than 4.4%

Structure boundary-preserving U-Net for prostate ultrasound image segmentation

Prostate cancer diagnosis is performed under ultrasound-guided puncture for pathological cell extraction. However, determining accurate prostate location remains a challenge from two aspects: (1) prostate boundary in ultrasound images is always ambiguous; (2) the delineation of radiologists always occupies multiple pixels, leading to many disturbing points around the actual contour. We proposed a boundary structure-preserving U-Net (BSP U-Net) in this paper to achieve precise prostate contour. BSP U-Net incorporates prostate shape prior to traditional U-Net. The prior shape is built by the key point selection module, which is an active shape model-based method. Then, the module plugs into the traditional U-Net structure network to achieve prostate segmentation. The experiments were conducted on two datasets: PH2 + ISBI 2016 challenge and our private prostate ultrasound dataset. The results on PH2 + ISBI 2016 challenge achieved a Dice similarity coefficient (DSC) of 95.94% and a Jaccard coefficient (JC) of 88.58%. The results of prostate contour based on our method achieved a higher pixel accuracy of 97.05%, a mean intersection over union of 93.65%, a DSC of 92.54%, and a JC of 93.16%. The experimental results show that the proposed BSP U-Net has good performance on PH2 + ISBI 2016 challenge and prostate ultrasound image segmentation and outperforms other state-of-the-art methods

Characterising pattern asymmetry in pigmented skin lesions

Abstract. In clinical diagnosis of pigmented skin lesions asymmetric pigmentation is often indicative of melanoma. This paper describes a method and measures for characterizing lesion symmetry. The estimate of mirror symmetry is computed first for a number of axes at different degrees of rotation with respect to the lesion centre. The statistics of these estimates are the used to assess the overall symmetry. The method is applied to three different lesion representations showing the overall pigmentation, the pigmentation pattern, and the pattern of dermal melanin. The best measure is a 100% sensitive and 96% specific indicator of melanoma on a test set of 33 lesions, with a separate training set consisting of 66 lesions

A novel NMF-based DWI CAD framework for prostate cancer.

In this thesis, a computer aided diagnostic (CAD) framework for detecting prostate cancer in DWI data is proposed. The proposed CAD method consists of two frameworks that use nonnegative matrix factorization (NMF) to learn meaningful features from sets of high-dimensional data. The first technique, is a three dimensional (3D) level-set DWI prostate segmentation algorithm guided by a novel probabilistic speed function. This speed function is driven by the features learned by NMF from 3D appearance, shape, and spatial data. The second technique, is a probabilistic classifier that seeks to label a prostate segmented from DWI data as either alignat, contain cancer, or benign, containing no cancer. This approach uses a NMF-based feature fusion to create a feature space where data classes are clustered. In addition, using DWI data acquired at a wide range of b-values (i.e. magnetic field strengths) is investigated. Experimental analysis indicates that for both of these frameworks, using NMF producing more accurate segmentation and classification results, respectively, and that combining the information from DWI data at several b-values can assist in detecting prostate cancer

Lung nodule modeling and detection for computerized image analysis of low dose CT imaging of the chest.

From a computerized image analysis prospective, early diagnosis of lung cancer involves detection of doubtful nodules and classification into different pathologies. The detection stage involves a detection approach, usually by template matching, and an authentication step to reduce false positives, usually conducted by a classifier of one form or another; statistical, fuzzy logic, support vector machines approaches have been tried. The classification stage matches, according to a particular approach, the characteristics (e.g., shape, texture and spatial distribution) of the detected nodules to common characteristics (again, shape, texture and spatial distribution) of nodules with known pathologies (confirmed by biopsies). This thesis focuses on the first step; i.e., nodule detection. Specifically, the thesis addresses three issues: a) understanding the CT data of typical low dose CT (LDCT) scanning of the chest, and devising an image processing approach to reduce the inherent artifacts in the scans; b) devising an image segmentation approach to isolate the lung tissues from the rest of the chest and thoracic regions in the CT scans; and c) devising a nodule modeling methodology to enhance the detection rate and lend benefits for the ultimate step in computerized image analysis of LDCT of the lungs, namely associating a pathology to the detected nodule. The methodology for reducing the noise artifacts is based on noise analysis and examination of typical LDCT scans that may be gathered on a repetitive fashion; since, a reduction in the resolution is inevitable to avoid excessive radiation. Two optimal filtering methods are tested on samples of the ELCAP screening data; the Weiner and the Anisotropic Diffusion Filters. Preference is given to the Anisotropic Diffusion Filter, which can be implemented on 7x7 blocks/windows of the CT data. The methodology for lung segmentation is based on the inherent characteristics of the LDCT scans, shown as distinct bi-modal gray scale histogram. A linear model is used to describe the histogram (the joint probability density function of the lungs and non-lungs tissues) by a linear combination of weighted kernels. The Gaussian kernels were chosen, and the classic Expectation-Maximization (EM) algorithm was employed to estimate the marginal probability densities of the lungs and non-lungs tissues, and select an optimal segmentation threshold. The segmentation is further enhanced using standard shape analysis based on mathematical morphology, which improves the continuity of the outer and inner borders of the lung tissues. This approach (a preliminary version of it appeared in [14]) is found to be adequate for lung segmentation as compared to more sophisticated approaches developed at the CVIP Lab (e.g., [15][16]) and elsewhere. The methodology developed for nodule modeling is based on understanding the physical characteristics of the nodules in LDCT scans, as identified by human experts. An empirical model is introduced for the probability density of the image intensity (or Hounsfield units) versus the radial distance measured from the centroid – center of mass - of typical nodules. This probability density showed that the nodule spatial support is within a circle/square of size 10 pixels; i.e., limited to 5 mm in length; which is within the range that the radiologist specify to be of concern. This probability density is used to fill in the intensity (or Hounsfield units) of parametric nodule models. For these models (e.g., circles or semi-circles), given a certain radius, we calculate the intensity (or Hounsfield units) using an exponential expression for the radial distance with parameters specified from the histogram of an ensemble of typical nodules. This work is similar in spirit to the earlier work of Farag et al., 2004 and 2005 [18][19], except that the empirical density of the radial distance and the histogram of typical nodules provide a data-driven guide for estimating the intensity (or Hounsfield units) of the nodule models. We examined the sensitivity and specificity of parametric nodules in a template-matching framework for nodule detection. We show that false positives are inevitable problems with typical machine learning methods of automatic lung nodule detection, which invites further efforts and perhaps fresh thinking into automatic nodule detection. A new approach for nodule modeling is introduced in Chapter 5 of this thesis, which brings high promise in both the detection, and the classification of nodules. Using the ELCAP study, we created an ensemble of four types of nodules and generated a nodule model for each type based on optimal data reduction methods. The resulting nodule model, for each type, has lead to drastic improvements in the sensitivity and specificity of nodule detection. This approach may be used as well for classification. In conclusion, the methodologies in this thesis are based on understanding the LDCT scans and what is to be expected in terms of image quality. Noise reduction and image segmentation are standard. The thesis illustrates that proper nodule models are possible and indeed a computerized approach for image analysis to detect and classify lung nodules is feasible. Extensions to the results in this thesis are immediate and the CVIP Lab has devised plans to pursue subsequent steps using clinical data

Prostate Segmentation and Regions of Interest Detection in Transrectal Ultrasound Images

The early detection of prostate cancer plays a significant role in the success of treatment and outcome. To detect prostate cancer, imaging modalities such as TransRectal UltraSound (TRUS) and Magnetic Resonance Imaging (MRI) are relied on. MRI images are more comprehensible than TRUS images which are corrupted by noise such as speckles and shadowing. However, MRI screening is costly, often unavailable in many community hospitals, time consuming, and requires more patient preparation time. Therefore, TRUS is more popular for screening and biopsy guidance for prostate cancer. For these reasons, TRUS images are chosen in this research. Radiologists first segment the prostate image from ultrasound image and then identify the hypoechoic regions which are more likely to exhibit cancer and should be considered for biopsy. In this thesis, the focus is on prostate segmentation and on Regions of Interest (ROI)segmentation. First, the extraneous tissues surrounding the prostate gland are eliminated. Consequently, the process of detecting the cancerous regions is focused on the prostate gland only. Thus, the diagnosing process is significantly shortened. Also, segmentation techniques such as thresholding, region growing, classification, clustering, Markov random field models, artificial neural networks (ANNs), atlas-guided, and deformable models are investigated. In this dissertation, the deformable model technique is selected because it is capable of segmenting difficult images such as ultrasound images. Deformable models are classified as either parametric or geometric deformable models. For the prostate segmentation, one of the parametric deformable models, Gradient Vector Flow (GVF) deformable contour, is adopted because it is capable of segmenting the prostate gland, even if the initial contour is not close to the prostate boundary. The manual segmentation of ultrasound images not only consumes much time and effort, but also leads to operator-dependent results. Therefore, a fully automatic prostate segmentation algorithm is proposed based on knowledge-based rules. The new algorithm results are evaluated with respect to their manual outlining by using distance-based and area-based metrics. Also, the novel technique is compared with two well-known semi-automatic algorithms to illustrate its superiority. With hypothesis testing, the proposed algorithm is statistically superior to the other two algorithms. The newly developed algorithm is operator-independent and capable of accurately segmenting a prostate gland with any shape and orientation from the ultrasound image. The focus of the second part of the research is to locate the regions which are more prone to cancer. Although the parametric dynamic contour technique can readily segment a single region, it is not conducive for segmenting multiple regions, as required in the regions of interest (ROI) segmentation part. Since the number of regions is not known beforehand, the problem is stated as 3D one by using level set approach to handle the topology changes such as splitting and merging the contours. For the proposed ROI segmentation algorithm, one of the geometric deformable models, active contours without edges, is used. This technique is capable of segmenting the regions with either weak edges, or even, no edges at all. The results of the proposed ROI segmentation algorithm are compared with those of the two experts' manual marking. The results are also compared with the common regions manually marked by both experts and with the total regions marked by either expert. The proposed ROI segmentation algorithm is also evaluated by using region-based and pixel-based strategies. The evaluation results indicate that the proposed algorithm produces similar results to those of the experts' manual markings, but with the added advantages of being fast and reliable. This novel algorithm also detects some regions that have been missed by one expert but confirmed by the other. In conclusion, the two newly devised algorithms can assist experts in segmenting the prostate image and detecting the suspicious abnormal regions that should be considered for biopsy. This leads to the reduction the number of biopsies, early detection of the diseased regions, proper management, and possible reduction of death related to prostate cancer