A novel 3-D segmentation algorithm for anatomic liver and tumor volume calculations for liver cancer treatment planning

Three-Dimensional (3-D) imaging is vital in computer-assisted surgical planning including minimal invasive surgery, targeted drug delivery, and tumor resection. Selective Internal Radiation Therapy (SIRT) is a liver directed radiation therapy for the treatment of liver cancer. Accurate calculation of anatomical liver and tumor volumes are essential for the determination of the tumor to normal liver ratio and for the calculation of the dose of Y-90 microspheres that will result in high concentration of the radiation in the tumor region as compared to nearby healthy tissue. Present manual techniques for segmentation of the liver from Computed Tomography (CT) tend to be tedious and greatly dependent on the skill of the technician/doctor performing the task. ^ This dissertation presents the development and implementation of a fully integrated algorithm for 3-D liver and tumor segmentation from tri-phase CT that yield highly accurate estimations of the respective volumes of the liver and tumor(s). The algorithm as designed requires minimal human intervention without compromising the accuracy of the segmentation results. Embedded within this algorithm is an effective method for extracting blood vessels that feed the tumor(s) in order to plan effectively the appropriate treatment. ^ Segmentation of the liver led to an accuracy in excess of 95% in estimating liver volumes in 20 datasets in comparison to the manual gold standard volumes. In a similar comparison, tumor segmentation exhibited an accuracy of 86% in estimating tumor(s) volume(s). Qualitative results of the blood vessel segmentation algorithm demonstrated the effectiveness of the algorithm in extracting and rendering the vasculature structure of the liver. Results of the parallel computing process, using a single workstation, showed a 78% gain. Also, statistical analysis carried out to determine if the manual initialization has any impact on the accuracy showed user initialization independence in the results. ^ The dissertation thus provides a complete 3-D solution towards liver cancer treatment planning with the opportunity to extract, visualize and quantify the needed statistics for liver cancer treatment. Since SIRT requires highly accurate calculation of the liver and tumor volumes, this new method provides an effective and computationally efficient process required of such challenging clinical requirements.^

Positron emission tomography (PET) tumor segmentation and quantification: Development of new algorithms

Tumor functional volume (FV) and its mean activity concentration (mAC) are the quantities derived from positron emission tomography (PET). These quantities are used for estimating radiation dose for a therapy, evaluating the progression of a disease and also use it as a prognostic indicator for predicting outcome. PET images have low resolution, high noise and affected by partial volume effect (PVE). Manually segmenting each tumor is very cumbersome and very hard to reproduce. To solve the above problem I developed an algorithm, called iterative deconvolution thresholding segmentation (IDTS) algorithm; the algorithm segment the tumor, measures the FV, correct for the PVE and calculates mAC. The algorithm corrects for the PVE without the need to estimate camera's point spread function (PSF); also does not require optimizing for a specific camera. My algorithm was tested in physical phantom studies, where hollow spheres (0.5-16 ml) were used to represent tumors with a homogeneous activity distribution. It was also tested on irregular shaped tumors with a heterogeneous activity profile which were acquired using physical and simulated phantom. The physical phantom studies were performed with different signal to background ratios (SBR) and with different acquisition times (1-5 min). The algorithm was applied on ten clinical data where the results were compared with manual segmentation and fixed percentage thresholding method called T50 and T60 in which 50% and 60% of the maximum intensity respectively is used as threshold. The average error in FV and mAC calculation was 30% and -35% for 0.5 ml tumor. The average error FV and mAC calculation were ~5% for 16 ml tumor. The overall FV error was ∼10% for heterogeneous tumors in physical and simulated phantom data. The FV and mAC error for clinical image compared to manual segmentation was around -17% and 15% respectively. In summary my algorithm has potential to be applied on data acquired from different cameras as its not dependent on knowing the camera's PSF. The algorithm can also improve dose estimation and treatment planning.^

Algorithms for efficient transaction management and consistent queries in client -server semantic object-oriented parallel databases

Large read-only or read-write transactions with a large read set and a small write set constitute an important class of transactions used in such applications as data mining, data warehousing, statistical applications, and report generators. Such transactions are best supported with optimistic concurrency, because locking of large amounts of data for extended periods of time is not an acceptable solution. The abort rate in regular optimistic concurrency algorithms increases exponentially with the size of the transaction. The algorithm proposed in this dissertation solves this problem by using a new transaction scheduling technique that allows a large transaction to commit safely with significantly greater probability that can exceed several orders of magnitude versus regular optimistic concurrency algorithms. A performance simulation study and a formal proof of serializability and external consistency of the proposed algorithm are also presented.^ This dissertation also proposes a new query optimization technique (lazy queries). Lazy Queries is an adaptive query execution scheme which optimizes itself as the query runs. Lazy queries can be used to find an intersection of sub-queries in a very efficient way, which does not require full execution of large sub-queries nor does it require any statistical knowledge about the data.^ An efficient optimistic concurrency control algorithm used in a massively parallel B-tree with variable-length keys is introduced. B-trees with variable-length keys can be effectively used in a variety of database types. In particular, we show how such a B-tree was used in our implementation of a semantic object-oriented DBMS. The concurrency control algorithm uses semantically safe optimistic virtual "locks" that achieve very fine granularity in conflict detection. This algorithm ensures serializability and external consistency by using logical clocks and backward validation of transactional queries. A formal proof of correctness of the proposed algorithm is also presented. ^

XML storage and retrieval using the semantic binary object -oriented database system (SEM-ODB)

Over the past five years, XML has been embraced by both the research and industrial community due to its promising prospects as a new data representation and exchange format on the Internet. The widespread popularity of XML creates an increasing need to store XML data in persistent storage systems and to enable sophisticated XML queries over the data. The currently available approaches to addressing the XML storage and retrieval issue have the limitations of either being not mature enough (e.g. native approaches) or causing inflexibility, a lot of fragmentation and excessive join operations (e.g. non-native approaches such as the relational database approach). ^ In this dissertation, I studied the issue of storing and retrieving XML data using the Semantic Binary Object-Oriented Database System (Sem-ODB) to leverage the advanced Sem-ODB technology with the emerging XML data model. First, a meta-schema based approach was implemented to address the data model mismatch issue that is inherent in the non-native approaches. The meta-schema based approach captures the meta-data of both Document Type Definitions (DTDs) and Sem-ODB Semantic Schemas, thus enables a dynamic and flexible mapping scheme. Second, a formal framework was presented to ensure precise and concise mappings. In this framework, both schemas and the conversions between them are formally defined and described. Third, after major features of an XML query language, XQuery, were analyzed, a high-level XQuery to Semantic SQL (Sem-SQL) query translation scheme was described. This translation scheme takes advantage of the navigation-oriented query paradigm of the Sem-SQL, thus avoids the excessive join problem of relational approaches. Finally, the modeling capability of the Semantic Binary Object-Oriented Data Model (Sem-ODM) was explored from the perspective of conceptually modeling an XML Schema using a Semantic Schema. ^ It was revealed that the advanced features of the Sem-ODB, such as multi-valued attributes, surrogates, the navigation-oriented query paradigm, among others, are indeed beneficial in coping with the XML storage and retrieval issue using a non-XML approach. Furthermore, extensions to the Sem-ODB to make it work more effectively with XML data were also proposed. ^

Semantic geographic information system

This thesis research describes the design and implementation of a Semantic Geographic Information System (GIS) and the creation of its spatial database. The database schema is designed and created, and all textual and spatial data are loaded into the database with the help of the Semantic DBMS's Binary Database Interface currently being developed at the FIU's High Performance Database Research Center (HPDRC). A friendly graphical user interface is created together with the other main system's areas: displaying process, data animation, and data retrieval. All these components are tightly integrated to form a novel and practical semantic GIS that has facilitated the interpretation, manipulation, analysis, and display of spatial data like: Ocean Temperature, Ozone(TOMS), and simulated SeaWiFS data. At the same time, this system has played a major role in the testing process of the HPDRC's high performance and efficient parallel Semantic DBMS.

Semantic Categorization in Portuguese-English Bilinguals

The main purpose of this study was to investigate the cross-linguistic interactions in the semantic categorization of late Portuguese-English bilinguals. The lexical items used in this study have a wider range of applications in one language and narrower in the other. Three types of categories were examined: classical, homophones, and radials. Late Portuguese-English bilinguals, as well as Portuguese and English monolinguals, were tested. After hearing a word, participants were asked to choose from a set of images, one that could be labelled as such. Analyses showed that when tested in English, participants performed better when it was the wider language. Participants’ performance was lower on classical categories than on homophone and radial categories.

A Cross-Generational Analysis of Spanish-to-English Lexico-Semantic Phenomena in Emerging Miami English

Sociolinguists have documented the substrate influence of various languages on the formation of dialects in numerous ethnic-regional setting throughout the United States. This literature shows that while phonological and grammatical influences from other languages may be instantiated as durable dialect features, lexical phenomena often fade over time as ethnolinguistic communities assimilate with contiguous dialect groups. In preliminary investigations of emerging Miami Latino English, we have observed that lexical forms based on Spanish lexical forms are not only ubiquitous among the speech of the first generation Cuban Americans but also of the second. Examples, observed in field work, casual observation, and studied formally in an experimental context include the following: “get down from the car,” which derives from the Spanish equivalent, bajar del carro instead of “get out of the car”. The translation task administered to thirty-one participants showed a variety lexical phenomena are still maintained at equal or higher frequencies.

The effects of semantic and syntactic instruction on user performance and satisfaction in search user interface design

The design of interfaces to facilitate user search has become critical for search engines, ecommercesites, and intranets. This study investigated the use of targeted instructional hints to improve search by measuring the quantitative effects of users' performance and satisfaction. The effects of syntactic, semantic and exemplar search hints on user behavior were evaluated in an empirical investigation using naturalistic scenarios. Combining the three search hint components, each with two levels of intensity, in a factorial design generated eight search engine interfaces. Eighty participants participated in the study and each completed six realistic search tasks. Results revealed that the inclusion of search hints improved user effectiveness, efficiency and confidence when using the search interfaces, but with complex interactions that require specific guidelines for search interface designers. These design guidelines will allow search designers to create more effective interfaces for a variety of searchapplications.

A methodology for hierarchical image segmentation evaluation

This paper proposes a method to evaluate hierarchical image segmentation procedures, in order to enable comparisons between different hierarchical algorithms and of these with other (non-hierarchical) segmentation techniques (as well as with edge detectors) to be made. The proposed method builds up on the edge-based segmentation evaluation approach by considering a set of reference human segmentations as a sample drawn from the population of different levels of detail that may be used in segmenting an image. Our main point is that, since a hierarchical sequence of segmentations approximates such population, those segmentations in the sequence that best capture each human segmentation level of detail should provide the basis for the evaluation of the hierarchical sequence as a whole. A small computational experiment is carried out to show the feasibility of our approach.

GraniteNights - A Multi-Agent Visit Scheduler Utilising Semantic Web Technology

Postprint

FEARLUS-G: A Semantic Grid Service for Land-Use Modelling,

Postprint

Assessing the Quality of Semantic Sensor Data

Acknowledgements The research described here is supported by the award made by the RCUK Digital Economy programme to the dot.rural Digital Economy Hub; award reference: EP/G066051/1

Notes on the Floridian Theory of Strongly Semantic Information

Other

An Empirical Investigation of Learning From the Semantic Web

Peer reviewed

Semantic Stream Processing for IoT Devices in the Food Safety Domain

Postprint