FY2010 - Oak Ridge National Laboratory

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Seed Money Fund— Measurement Science and Systems Engineering Division of development, ranging from postnatal day 1 to postnatal day 13. Three individual cells were manually cropped from each volume, resulting in a total of 285 single-cell volumes in addition to the original whole-field volumes. We developed new algorithms to automatically detect and segment the soma (cell body) and dendrites of each neuron in the single-cell volumes. For the somas, we detected the center of the soma using morphological grayscale erosion, and we segmented the soma using a level-set segmentation technique. For the dendrites, we developed a technique for finding an appropriate threshold that separates the fluorescent cell material from the background to create a binary volume. We developed an intensity-based three-dimensional skeletonization technique to thin the resulting binary volume and localize the centerlines of the dendrites while preserving their structure and topology. We compared a small subset of our detected dendritic centerlines to those generated manually on the same cells by our collaborators at St. Jude, and we observed 80% similarity of dendrite position on average between our results and the manual results. In most instances, the differences were due to missed branches or false branch detections in one of the algorithms. Using the segmented soma and dendrite skeleton, we developed an algorithm to compute the graph structure of the dendrites in terms of nodes and edges. From this structure, we were able to compute several features of the cells, including dendrite positions, angles, lengths, and branching order, that may be discriminatory with respect to genotype. We are currently working to develop this feature set and quantitatively characterize all the neurons in our dataset with respect to these features. In addition, we have developed neuron migration analysis tools that can track the motion of multiple neurons in culture in a completely automated fashion. Tracking is performed on the soma, the leading and trailing processes, and the centrosomes within the cell. Time lapse movies of moving cerebellar neurons in culture were captured on a fluorescent microscope by our collaborators at St. Jude. The focus of the research in FY 2010 has been on the continued development of tools to perform automated morphological analysis of fields of retinal neurons, extending the 2009 work on individual neuron analysis. The morphology of a neuron consists of the cell body, or soma, and the dendrites that extend from the soma that allow the cells to transfer signals between one another. Algorithms have been written and tested to automatically identify all of the somas within a field of retinal neurons and then trace the individual neurites of these cells. Once this is done, the morphological features are extracted from the dendritic trees such as number of dendrites, length of dendrites, branching patterns, angle of branches, etc. These features can then be used to compare one neuron to a database of neurons so that a researcher can locate similar morphological features within a historical database. Three new publications were written in 2010 as part of this project. Finally, a grant proposal was submitted to the NIH focused on the development of computational tools to quantify neuronal migration in cell cultures and histological slices. This grant was submitted in February 2010. It was reviewed and was not funded. We are in the process of preparing a resubmission of this grant for March 2011. Information Shared Kerekes, R. A., S. S. Gleason, R. A. P. Martins, and M. Dyer. 2010. “Fully automated segmentation and characterization of the dendritic trees of retinal horizontal neurons.” BSEC 2010: Annual ORNL Biomedical Science and Engineering Conference. Kerekes, R. A., S. S. Gleason, N. Trivedi, and D. J. Solecki. 2010. “Automated method for tracing leading and trailing processes of migrating neurons in confocal image sequences.” Medical Imaging 2010: Image Processing, Edited by Benoit M. Dawant and David R. Haynor (Eds.), Proceedings of the SPIE 7623, 76233T–76233T-10. 230
Seed Money Fund— Measurement Science and Systems Engineering Division 00515 Remote Microfluidic Platform Using Smart Materials and Structures: A Diagnostic and Interventional Tool for Critical Structural Anomalies during Fetal Development Boyd M. Evans III, Timothy E. McKnight, M. Nance Ericson, John B. Wilgen, Justin S. Baba, Anthony Johnson, Ken J. Moise, Jr., Allen J. Tower, and Douglas J. Villnave Project Description This multidisciplinary project involves the development of highly miniaturized, remotely activated, microfluidic valving systems. The project involves investigating thermally responsive polymer materials based on poly(N-isopropylacrylamide) or p(NIPAAm) and the development of radio frequency (RF) methodologies for remote activation of these materials. P(NIPAAm)-based polymers exhibit a dramatic reduction in size as temperature increases through a lower critical solution temperature (LCST), which can be influenced by copolymer formulations of the material. This property will be used to create a “normally closed” valve that can be thermally opened via wireless RF excitation. The scalability of this responsive-polymer approach will enable the production of wireless valving systems suitable for a wide range of flows. Such valves will provide value for both industrial and research applications and will be particularly useful as wireless, implantable biomedical devices. Towards this end, we focus development on the fabrication and testing of a remotely actuated valve designed for therapeutic intervention of congenital diaphragmatic hernia. Mission Relevance The DOE mission statement includes the overarching theme to promote scientific discovery and innovation to strengthen U.S. economic competitiveness and to improve quality of life through innovations in science and technology. Scalable wireless valving systems can dramatically impact all sectors of industry and technology by providing means of controlling fluidic transport using wireless signaling, with specific advantages in distributed control and actuation networks, harsh environment systems, and control elements where interconnectivity limitations impact system design. Our chosen proof-of-principle target, fluidic intervention in congenital diaphragmatic hernia, will demonstrate the technological advances of the project in a sector that will realize the most immediate benefit— implantable valving systems for therapeutic applications. Results and Accomplishments This effort is a collaboration between a medical team (Baylor College of Medicine), a commercial biomedical device manufacturer (NuMed Inc.), and ORNL. Baylor and NuMed have both made significant in-kind contributions to the effort. NuMed has designed and fabricated a number of custom balloon valves, compatible with our valve design. Our surgical collaborators at Baylor have procured animals and conducted preliminary animal tests of the tracheal occlusion approach using the NuMed balloon implant modified with our polymer valve system. The polymeric valving system has been fabricated and optimized for operation at physiological temperatures using remote and direct thermal powering. The valve system comprises a thermally reactive copolymer annulus surrounding an internal heating element and an external solid valve body. The current embodiment of this configuration has been designed to insert into the 0.060 in. inner diameter valve lumen of a dual-lumen balloon implant, supplied by our commercial collaborator, NuMed Inc. A flow stand has been assembled enabling the simultaneous evaluation of multiple independent valves. In flow tests simulating the operating pressure of the fetal trachea (80 mm water column pressure), the current embodiment of this normally closed valve has demonstrated stopped flow in the closed condition (room temperature) and up to 6 mL/min in the fully 231
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FY2010 - Oak Ridge National Laboratory

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