<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="font-family: arial; font-size: 14px; line-height: 19px; "><h1 style="line-height: 104%; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; font-weight: normal; margin-top: 0px; margin-right: 0px; margin-bottom: 0.5em; margin-left: 0px; font-size: 210%; background-color: transparent; color: rgb(170, 0, 0); ">Opportunities in the Megason Lab @ Harvard Medical School</h1><p style="margin-top: 1em; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; background-color: transparent; ">The Megason Lab is comprised of people with diverse backgrounds including genetics, developmental biology, imaging, optics, physics, and computer science (bioinformatics and image analysis) united by a common passion for science.</p><h3 style="line-height: 104%; font-weight: normal; font-size: 135%; display: block; padding-top: 0.1em; padding-right: 5px; padding-bottom: 0.1em; padding-left: 5px; margin-top: 1em; margin-right: -5px; margin-bottom: 0.35em; margin-left: -5px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 1px; border-left-width: 0px; border-top-style: solid; border-right-style: solid; border-bottom-style: solid; border-left-style: solid; height: auto; background-color: transparent; color: rgb(170, 0, 0); border-top-color: rgb(233, 228, 210); border-right-color: rgb(233, 228, 210); border-bottom-color: rgb(233, 228, 210); border-left-color: rgb(233, 228, 210); "><span class="Apple-style-span" style="font-size: 29px; line-height: 30px; ">Intern Projects</span><a name="Summer_Interns"></a></h3><span class="Apple-style-span" style="color: rgb(170, 0, 0); font-size: 29px; line-height: 30px; "></span></span><div><span class="Apple-style-span" style="font-family: arial; font-size: 14px; line-height: 19px; ">The Megason lab is always open to exceptional undergrads interested in pursuing research in a multidisciplinary lab. We particularly encourage students to begin research in the summer with the possibility of continuing during the school year. If you are interested please submit an application to <a href="mailto:megason@hms.harvard.edu" style="text-decoration: underline; color: rgb(0, 102, 204); background-color: transparent; ">megason@hms.harvard.edu</a> by April 15, 2009. The application should include a cover letter, CV, statement of research interests, and contact information for 2 references. Fellowships are available through the <a href="https://webapps.sciences.fas.harvard.edu/apply/csb-intern/" target="_top" style="text-decoration: underline; color: rgb(0, 102, 204); background-color: transparent; ">FAS Center for Systems Biology</a>. Work will be undertaken with supervision from senior Image Processing Researcher and PostDocs, as well as Biologist. See (<span class="Apple-style-span" style="font-family: Helvetica; font-size: 12px; line-height: normal; "><a href="http://www.na-mic.org/Wiki/index.php/MegasonLab">http://www.na-mic.org/Wiki/index.php/MegasonLab</a><span class="Apple-style-span" style="font-family: arial; font-size: 14px; line-height: 19px; ">) for information of the lab's involvement in NA-MIC.</span></span></span></div><div><span class="Apple-style-span" style="font-family: arial; font-size: 14px; line-height: 19px; "><h2 style="line-height: 104%; font-weight: normal; font-size: 160%; display: block; padding-top: 0.1em; padding-right: 5px; padding-bottom: 0.1em; padding-left: 5px; margin-top: 1em; margin-right: -5px; margin-bottom: 0.35em; margin-left: -5px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 1px; border-left-width: 0px; border-top-style: solid; border-right-style: solid; border-bottom-style: solid; border-left-style: solid; height: auto; color: rgb(170, 0, 0); background-color: rgb(253, 250, 241); border-top-color: rgb(226, 220, 200); border-right-color: rgb(226, 220, 200); border-bottom-color: rgb(226, 220, 200); border-left-color: rgb(226, 220, 200); "><a name="Applied_Math_Computational"></a>Applied Math / Computational</h2><h3 style="line-height: 104%; font-weight: normal; font-size: 135%; display: block; padding-top: 0.1em; padding-right: 5px; padding-bottom: 0.1em; padding-left: 5px; margin-top: 1em; margin-right: -5px; margin-bottom: 0.35em; margin-left: -5px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 1px; border-left-width: 0px; border-top-style: solid; border-right-style: solid; border-bottom-style: solid; border-left-style: solid; height: auto; background-color: transparent; color: rgb(170, 0, 0); border-top-color: rgb(233, 228, 210); border-right-color: rgb(233, 228, 210); border-bottom-color: rgb(233, 228, 210); border-left-color: rgb(233, 228, 210); "><a name="Project_1_Computational_Geometry"></a>Project 1 - Computational Geometry: Building a statistical dynamic model of cell shape and division using image analysis</h3>In this project, the student will work on building a statistical model of the shape of the cell membrane and nucleus of cells 1) as a function of cell type, and 2) as a function of phase in the cell cycle. A dynamic model of cell division is required for solving more complex problems such as automatic cell type identification, cell tracking, and construction of cell lineage trees. The student will have multiple sets of 5D images (3D+time+multispectral) of zebrafish embryogenesis acquired using a multiphoton microscope to validate the model. The images capture the movement and division of cells during embryogenesis in zebrafish with the nucleus and membranes labeled in different colors. The cell cycle consists of 4 distinct phases, of which mitosis (M-phase) is critical for division. The M-phase by virtue of its small duration in the cell cycle is sparsely sampled in time. Moreover, a significant challenge lies in understanding the geometrical restructuring of the cell membrane and nucleus during the division process. Appropriate mathematical models need to be proposed or designed for representing these structures and then fit the data to select appropriate parameters. The student will receive adequate computational support, microscopy datasets and guidance in completing this project with a team of image analysis developers. The model will be used in other projects to solve segmentation and tracking problems.<h3 style="line-height: 104%; font-weight: normal; font-size: 135%; display: block; padding-top: 0.1em; padding-right: 5px; padding-bottom: 0.1em; padding-left: 5px; margin-top: 1em; margin-right: -5px; margin-bottom: 0.35em; margin-left: -5px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 1px; border-left-width: 0px; border-top-style: solid; border-right-style: solid; border-bottom-style: solid; border-left-style: solid; height: auto; background-color: transparent; color: rgb(170, 0, 0); border-top-color: rgb(233, 228, 210); border-right-color: rgb(233, 228, 210); border-bottom-color: rgb(233, 228, 210); border-left-color: rgb(233, 228, 210); "><a name="Project_2_Graph_Theory_Atlas_bas"></a>Project 2 - Graph Theory: Atlas-based registration and matching of lineage trees</h3>In this project, we are interested in matching 4D (spatio-temporal) lineage trees generated by tracking cells during zebrafish embryogenesis. Lineage trees are essentially linear, attributed graph structures (binary trees) with many thousands of nodes corresponding to cell divisions. In the embryological context, these nodes have specific coordinates in space and time as well as attributes such as cell type and cell shape. The lineage trees are correlated in structure across different embryos in a complex and poorly understood way. There are likely correlations in the location of divisions, frequency of divisions, pattern of cell lineage, speed of cell migration to name a few. We are interested in using these correlations to help compare and “register” lineage trees extracted from different embryos. Therefore, we are interested in developing routines that match a pair of lineages and also build an atlas of their structure. There is a significant amount work in the graph theory literature on graph matching that the student can make use of. The student will receive adequate computational support, microscopy datasets and guidance in completing this project with a team of image analysis developers. This work will critically help us in understanding significant biological problems in embryogenesis.<h3 style="line-height: 104%; font-weight: normal; font-size: 135%; display: block; padding-top: 0.1em; padding-right: 5px; padding-bottom: 0.1em; padding-left: 5px; margin-top: 1em; margin-right: -5px; margin-bottom: 0.35em; margin-left: -5px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 1px; border-left-width: 0px; border-top-style: solid; border-right-style: solid; border-bottom-style: solid; border-left-style: solid; height: auto; background-color: transparent; color: rgb(170, 0, 0); border-top-color: rgb(233, 228, 210); border-right-color: rgb(233, 228, 210); border-bottom-color: rgb(233, 228, 210); border-left-color: rgb(233, 228, 210); "><a name="Project_3_Information_Visualizat"></a>Project 3 - Information Visualization: Visualizing 5+ dimensional, cellular resolution data of zebrafish embryogenesis.</h3>In this project, we are interested in enabling a biologist to discover and explore relations in high-dimensional data of zebrafish embryogenesis. We use timelapse confocal/2-photon imaging of developing zebrafish embryos to capture subcellular resolution, 4d (xyzt) movies. These movies contain cell membranes in one color, nulclei in another color, and may additionally contain information on protein expression and localization in additional color(s). We segment these movies to generate information on cell shape, velocity, and lineage for thousands of cells. Visualizing this large wealth of data requires new approaches due to both its large size as well as its novel and interconnected data types. The student will receive adequate computational support, microscopy datasets and guidance in completing this project with a team of image analysis developers. This work will critically help us in understanding significant biological problems in embryogenesis.</span></div></body></html>