Dataset Information

Volume visualization: a technical overview with a focus on medical applications.

ABSTRACT: With the increasing availability of high-resolution isotropic three- or four-dimensional medical datasets from sources such as magnetic resonance imaging, computed tomography, and ultrasound, volumetric image visualization techniques have increased in importance. Over the past two decades, a number of new algorithms and improvements have been developed for practical clinical image display. More recently, further efficiencies have been attained by designing and implementing volume-rendering algorithms on graphics processing units (GPUs). In this paper, we review volumetric image visualization pipelines, algorithms, and medical applications. We also illustrate our algorithm implementation and evaluation results, and address the advantages and drawbacks of each algorithm in terms of image quality and efficiency. Within the outlined literature review, we have integrated our research results relating to new visualization, classification, enhancement, and multimodal data dynamic rendering. Finally, we illustrate issues related to modern GPU working pipelines, and their applications in volume visualization domain.

SUBMITTER: Zhang Q

PROVIDER: S-EPMC3138940 | biostudies-literature | 2011 Aug

REPOSITORIES: biostudies-literature

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Volume visualization: a technical overview with a focus on medical applications.

Zhang Qi Q Eagleson Roy R Peters Terry M TM

Journal of digital imaging 20110801 4

With the increasing availability of high-resolution isotropic three- or four-dimensional medical datasets from sources such as magnetic resonance imaging, computed tomography, and ultrasound, volumetric image visualization techniques have increased in importance. Over the past two decades, a number of new algorithms and improvements have been developed for practical clinical image display. More recently, further efficiencies have been attained by designing and implementing volume-rendering algor ...[more]

PMID: 20714917

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Project description:BackgroundChatbots are applications that can conduct natural language conversations with users. In the medical field, chatbots have been developed and used to serve different purposes. They provide patients with timely information that can be critical in some scenarios, such as access to mental health resources. Since the development of the first chatbot, ELIZA, in the late 1960s, much effort has followed to produce chatbots for various health purposes developed in different ways.ObjectiveThis study aimed to explore the technical aspects and development methodologies associated with chatbots used in the medical field to explain the best methods of development and support chatbot development researchers on their future work.MethodsWe searched for relevant articles in 8 literature databases (IEEE, ACM, Springer, ScienceDirect, Embase, MEDLINE, PsycINFO, and Google Scholar). We also performed forward and backward reference checking of the selected articles. Study selection was performed by one reviewer, and 50% of the selected studies were randomly checked by a second reviewer. A narrative approach was used for result synthesis. Chatbots were classified based on the different technical aspects of their development. The main chatbot components were identified in addition to the different techniques for implementing each module.ResultsThe original search returned 2481 publications, of which we identified 45 studies that matched our inclusion and exclusion criteria. The most common language of communication between users and chatbots was English (n=23). We identified 4 main modules: text understanding module, dialog management module, database layer, and text generation module. The most common technique for developing text understanding and dialogue management is the pattern matching method (n=18 and n=25, respectively). The most common text generation is fixed output (n=36). Very few studies relied on generating original output. Most studies kept a medical knowledge base to be used by the chatbot for different purposes throughout the conversations. A few studies kept conversation scripts and collected user data and previous conversations.ConclusionsMany chatbots have been developed for medical use, at an increasing rate. There is a recent, apparent shift in adopting machine learning-based approaches for developing chatbot systems. Further research can be conducted to link clinical outcomes to different chatbot development techniques and technical characteristics.

Project description:BackgroundAs whole exome sequencing (WES) and whole genome sequencing (WGS) transition from research tools to clinical diagnostic tests, it is increasingly critical for sequencing methods and analysis pipelines to be technically accurate. The Genome in a Bottle Consortium has recently published a set of benchmark SNV, indel, and homozygous reference genotypes for the pilot whole genome NIST Reference Material based on the NA12878 genome.MethodsWe examine the relationship between human genome complexity and genes/variants reported to be associated with human disease. Specifically, we map regions of medical relevance to benchmark regions of high or low confidence. We use benchmark data to assess the sensitivity and positive predictive value of two representative sequencing pipelines for specific classes of variation.ResultsWe observe that the accuracy of a variant call depends on the genomic region, variant type, and read depth, and varies by analytical pipeline. We find that most false negative WGS calls result from filtering while most false negative WES variants relate to poor coverage. We find that only 74.6% of the exonic bases in ClinVar and OMIM genes and 82.1% of the exonic bases in ACMG-reportable genes are found in high-confidence regions. Only 990 genes in the genome are found entirely within high-confidence regions while 593 of 3,300 ClinVar/OMIM genes have less than 50% of their total exonic base pairs in high-confidence regions. We find greater than 77 % of the pathogenic or likely pathogenic SNVs currently in ClinVar fall within high-confidence regions. We identify sites that are prone to sequencing errors, including thousands present in publicly available variant databases. Finally, we examine the clinical impact of mandatory reporting of secondary findings, highlighting a false positive variant found in BRCA2.ConclusionsTogether, these data illustrate the importance of appropriate use and continued improvement of technical benchmarks to ensure accurate and judicious interpretation of next-generation DNA sequencing results in the clinical setting.

Dataset Information

Volume visualization: a technical overview with a focus on medical applications.

Publications

Volume visualization: a technical overview with a focus on medical applications.

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