Unsupervised supervoxel-based lung tumor segmentation across patient scans in hybrid PET/MRI

Tumor segmentation is a crucial but difficult task in treatment planning and follow-up of cancerous patients. The challenge of automating the tumor segmentation has recently received a lot of attention, but the potential of utilizing hybrid positron emission tomography (PET)/magnetic resonance imaging (MRI), a novel and promising imaging modality in oncology, is still under-explored. Recent approaches have either relied on manual user input and/or performed the segmentation patient-by-patient, whereas a fully unsupervised segmentation framework that exploits the available information from all patients is still lacking. We present an unsupervised across-patients supervoxel-based clustering framework for lung tumor segmentation in hybrid PET/MRI. The method consists of two steps: First, each patient is represented by a set of PET/ MRI supervoxel-features. Then the data points from all patients are transformed and clustered on a population level into tumor and non-tumor supervoxels. The proposed framework is tested on the scans of 18 non-small cell lung cancer patients with a total of 19 tumors and evaluated with respect to manual delineations provided by clinicians. Experiments study the performance of several commonly used clustering algorithms within the framework and provide analysis of (i) the effect of tumor size, (ii) the segmentation errors, (iii) the benefit of across-patient clustering, and (iv) the noise robustness. The proposed framework detected 15 out of 19 tumors in an unsupervised manner. Moreover, performance increased considerably by segmenting across patients, with the mean dice score increasing from 0.169 ± 0.295 (patient-by-patient) to 0.470 ± 0.308 (across-patients). Results demonstrate that both spectral clustering and Manhattan hierarchical clustering have the potential to segment tumors in PET/MRI with a low number of missed tumors and a low number of false-positives, but that spectral clustering seems to be more robust to noise

Fuzzy Image Segmentation based upon Hierarchical Clustering

In this paper we introduce the concept of Fuzzy Image Segmentation, providing an algorithm to build fuzzy boundaries based on the existing relations between the fuzzy boundary set problem and the (crisp) hierarchical image segmentation problem. In particular, since a crisp image segmentation can be characterized in terms of the set of edges that separates the adjacent regions of the segmentation, from these edges we introduce the concept of fuzzy image segmentation. Hence,each fuzzy image segmentation is characterized by means of a fuzzy set over the set of edges, which can be then understood as the fuzzy boundary of the image. Some computational experiences are included in order to show the obtained fuzzy boundaries of some digital images

Neutro-Connectedness Theory, Algorithms and Applications

Connectedness is an important topological property and has been widely studied in digital topology. However, three main challenges exist in applying connectedness to solve real world problems: (1) the definitions of connectedness based on the classic and fuzzy logic cannot model the “hidden factors” that could influence our decision-making; (2) these definitions are too general to be applied to solve complex problem; and (4) many measurements of connectedness are heavily dependent on the shape (spatial distribution of vertices) of the graph and violate the intuitive idea of connectedness. This research focused on solving these challenges by redesigning the connectedness theory, developing fast algorithms for connectedness computation, and applying the newly proposed theory and algorithms to solve challenges in real problems. The newly proposed Neutro-Connectedness (NC) generalizes the conventional definitions of connectedness and can model uncertainty and describe the part and the whole relationship. By applying the dynamic programming strategy, a fast algorithm was proposed to calculate NC for general dataset. It is not just calculating NC map, and the output NC forest can discover a dataset’s topological structure regarding connectedness. In the first application, interactive image segmentation, two approaches were proposed to solve the two most difficult challenges: user interaction-dependence and intense interaction. The first approach, named NC-Cut, models global topologic property among image regions and reduces the dependence of segmentation performance on the appearance models generated by user interactions. It is less sensitive to the initial region of interest (ROI) than four state-of-the-art ROI-based methods. The second approach, named EISeg, provides user with visual clues to guide the interacting process based on NC. It reduces user interaction greatly by guiding user to where interacting can produce the best segmentation results. In the second application, NC was utilized to solve the challenge of weak boundary problem in breast ultrasound image segmentation. The approach can model the indeterminacy resulted from weak boundaries better than fuzzy connectedness, and achieved more accurate and robust result on our dataset with 131 breast tumor cases

Clustering Algorithms: Their Application to Gene Expression Data

Gene expression data hide vital information required to understand the biological process that takes place in a particular organism in relation to its environment. Deciphering the hidden patterns in gene expression data proffers a prodigious preference to strengthen the understanding of functional genomics. The complexity of biological networks and the volume of genes present increase the challenges of comprehending and interpretation of the resulting mass of data, which consists of millions of measurements; these data also inhibit vagueness, imprecision, and noise. Therefore, the use of clustering techniques is a first step toward addressing these challenges, which is essential in the data mining process to reveal natural structures and iden-tify interesting patterns in the underlying data. The clustering of gene expression data has been proven to be useful in making known the natural structure inherent in gene expression data, understanding gene functions, cellular processes, and subtypes of cells, mining useful information from noisy data, and understanding gene regulation. The other benefit of clustering gene expression data is the identification of homology, which is very important in vaccine design. This review examines the various clustering algorithms applicable to the gene expression data in order to discover and provide useful knowledge of the appropriate clustering technique that will guarantee stability and high degree of accuracy in its analysis procedure