[vtkusers] ITK/VTK-related summer internships at Harvard Medical School

[alex gouaillard]

Opportunities in the Megason Lab @ Harvard Medical School
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.
Intern Projects
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 megason at hms.harvard.edu 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 FAS Center for  
Systems Biology. Work will be undertaken with supervision from senior  
Image Processing Researcher and PostDocs, as well as Biologist. See (http://www.na-mic.org/Wiki/index.php/MegasonLab 
) for information of the lab's involvement in NA-MIC.
Applied Math / Computational
Project 1 - Computational Geometry: Building a statistical dynamic  
model of cell shape and division using image analysis
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.
Project 2 - Graph Theory: Atlas-based registration and matching of  
lineage trees
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.
Project 3 - Information Visualization: Visualizing 5+ dimensional,  
cellular resolution data of zebrafish embryogenesis.
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.
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