Quantitaion of asymmetric mitosis by tracking the spindle poles using fluorescence images

Daniel Schmitter

Semester Master Project

Life Science, EPFL

June 2011

Abstract

The goal of this project was to develop a model to quantify the asymmetry of spindle pole bodies in yeast cells (S. Pombe) and to implement it as an ImageJ plugin. Plugins for dynamic (time lapse sequences) as well as for static (single) images were developed. The images can be either 2D or 3D. The processing steps leading to quantitaion are the follwing:

1. spot detection
2. cell segmentation
3. spot tracking (only on dynamic images)

Up to 4 proteins (2 proteins of interest and 2 reference proteins) can be tracked per cell and the number of cells to segment is unlimited. The results are dis- played in a table and 2 dierent kymographs can be generated. The results can be saved in an tab-delimited text le for further analysis with other software (excel, matlab, etc.). After denoising and LoG-ltering of the raw data, the proteins are detected. The tracking is done through a dynamic programing algorithm which allows to nd the trajectory even through very noisy sequences. For the cell segmenta- tion an active contour model was developed which adapts to the rod shaped cell structure. A plugin just to segment rod shaped cells was individually developed.