Semester project Life Sciences/EPFL

3D image analysis of large data structures

Laboratory: Lab of neuronal microcircuitry (LNMC)
Head of Lab: Professor Henry Markram
Project supervisor: Dr. Jesper Ryge and Jean-Pierre Ghobril
Required skill: C++, python, image processing (basics)


Starting data: Fall 2013


Breakthroughs in microscopy have resulted in the routine generation of Tb sized
three-dimensional datasets. Currently visualization and processing lag behind. In
LNMC we are generating large 3D dataset of the intact mouse brain, for which
we need to develop appropriate tools for analysis and visualization.

We are currently looking for an informatics/engineering student with programming
skills to help create new solutions to access and analyze 3D volumes. This
involves creating a wrapper program for ITK (imaging toolkit) that enables access
to the complete ITK toolkit in an out-of-core data structure for real time data
manipulation.

The student will work in an interdisciplinary environment consisting of engineers
and biologist, in close collaboration with the team generating the data.

The proposed project will provide working knowledge of ITK and manipulation of
large data structures, in particular with the aim to create solutions to access sub-
volumes of the intact 3D object and their real-time manipulation, analysis and
visualization.

Further information about the lab can be found at http://markram-lab.epfl.ch/