Browsing by Author "Sensen, Christoph W."
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Item Open Access Bluejay 1.0: genome browsing and comparison with rich customization provision and dynamic resource linking(BioMed Central, 2008) Soh, Jung; Gordon, Paul M. K.; Taschuk, Morgan L.; Dong, Anguo; Ah-Seng, Andrew C.; Turinsky, Andrei L; Sensen, Christoph W.Item Open Access Building generic anatomical models using virtual model cutting and iterative registration(BioMed Central, 2010-02-08) Xiao, Mei; Soh, Jung; Meruvia-Pastor, Oscar; Schmidt, Eric; Hallgrímsson, Benedikt; Sensen, Christoph W.Item Open Access Estimating Cell Count and Distribution in Labeled Histological Samples Using Incremental Cell Search(2011-05-24) Meruvia-Pastor, Oscar E.; Soh, Jung; Schmidt, Eric J.; Boughner, Julia C.; Xiao, Mei; Jamniczky, Heather A.; Hallgrímsson, Benedikt; Sensen, Christoph W.Cell proliferation is critical to the outgrowth of biological structures including the face and limbs. This cellular process has traditionally been studied via sequential histological sampling of these tissues. The length and tedium of traditional sampling is a major impediment to analyzing the large datasets required to accurately model cellular processes. Computerized cell localization and quantification is critical for high-throughput morphometric analysis of developing embryonic tissues. We have developed the Incremental Cell Search (ICS), a novel software tool that expedites the analysis of relationships between morphological outgrowth and cell proliferation in embryonic tissues. Based on an estimated average cell size and stain color, ICS rapidly indicates the approximate location and amount of cells in histological images of labeled embryonic tissue and provides estimates of cell counts in regions with saturated fluorescence and blurred cell boundaries. This capacity opens the door to high-throughput 3D and 4D quantitative analyses of developmental patterns.Item Open Access Immersive and interactive visualization of volume interiors with a flashlight-based detail-in-context lens tool(2007) Stromer, Julie; Sensen, Christoph W.; Barker, Kenneth E.Item Open Access Micro-computed tomography-based phenotypic approaches in embryology: procedural artifacts on assessments of embryonic craniofacial growth and development(BioMed Central, 2010-02-17) Schmidt, Eric J.; Parsons, Trish E.; Jamniczky, Heather A.; Gitelman, Julian; Trpkov, Cvett; Boughner, Julia C.; Logan, C Cairine.; Sensen, Christoph W.; Hallgrímsson, BenediktItem Open Access Multiple whole genome comparison in bluejay(2008) Dong, Anguo; Sensen, Christoph W.Item Open Access A Pilot Study into the Usability of a Scientific Workflow Construction Tool(2007-07-24) Gordon, Paul M. K.; Sensen, Christoph W.We describe a recent pilot study into the usability of the scientific workflow creation and enactment tool called Taverna. Both programmers and non-programmers were used as subjects for a defined programming task. We used a combination of user observation and questionnaires to determine programming efficiency roadblocks in the tool. More generally, differences between the roadblocks encountered by programmers and nonprogrammers suggest that pilot studies are crucial to inform the proper evaluation of novice programming tools. The study also suggests that there is a high demand for reusable Life Sciences workflows, due to both their ability to facilitate human-human communication about data analysis, and their ability to simplify repetitive operations used by bench scientists. Most roadblocks to Taverna programming are interface related, but a more fundamental issue is related to data input and type enforcement. Despite UI issues, we discovered users willingness to re-use and modify workflows, which leads us to suggest that programs first be created in simpler tools as a stepping stone in end-user development for the Life Sciences.Item Open Access Spatiotemporal integration of molecular and anatomical data in virtual reality using semantic mapping(Dove Medical Press, 2009-04-01) Soh, Jung; Turinsky, Andrei L.; Trinh, Quang M.; Chang, Jasmine; Sabhaney, Ajay; Dong, Xiaoli; Gordon, Paul M. K.; Janzen, Ryan P. W.; Hau, David; Xia, Jianguo; Wishart, David S.; Sensen, Christoph W.Item Open Access Tool support for automatic performance testing of Java3d graphics applications(2007) Shu, Xueling; Maurer, Frank Oliver; Sensen, Christoph W.