[Insight-users] ITK/VTK-related summer internships at Harvard Medical School
alex gouaillard
alexandre_gouaillard at hms.harvard.edu
Wed Jan 14 22:35:23 EST 2009
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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