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Bioinformatics Advance Access first published online on July 4, 2009
This version published online on July 6, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp405
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

DYNAMIK: A Software Environment for Cell DYNAmics, Motility, and Information TracKing, with an Application to Ras Pathways

Stefan Jaeger *, Qingfeng Song * and Su-Shing Chen *

Partner Institute of Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Max-Planck Society, Shanghai 200031, China

*To whom correspondence should be addressed. Dr. Stefan Jaeger, E-mail: jaeger{at}picb.ac.cn, songqingfeng{at}picb.ac.cn, suchen{at}picb.ac.cn


  Abstract

The emergence of new microscopy techniques in combination with the increasing resource of bioimaging data has given fresh impetus to utilizing image processing methods for studying biological processes. Cell tracking studies in particular, which are important for a wide range of biological processes such as embryonic development or the immune system, have recently become the focus of attention. These studies typically produce large volumes of data that are hard to investigate manually and therefore call for an automated approach. Due to the large variety of biological cells and the inhomogeneity of applications, however, there exists no widely accepted method or system for cell tracking until today. In this paper, we present our publicly available DYNAMIK software environment that allows users to compute a suit of cell features and plot the trajectory of multiple cells over a sequence of frames. Using chemotaxis and Ras pathways as an example, we show how users can employ our software to compute statistics about cell motility and other cell information, and how to evaluate their test series based on the data computed. We see that DYNAMIK's segmentation and tracking compares favorably with the output produced by other software packages.

Associate Editor: Prof. John Quackenbush

Received on January 16, 2009; revised on June 22, 2009; accepted on June 28, 2009

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