Paper Abstract

CellTracer: Software for automated image segmentation and lineage mapping for single-cell studies

Quanli Wang, Lingchong You & Mike West

Duke University

June 2008

Imaging of single-cell dynamics is playing an increasingly central role in systems biology studies. Frame-by-frame cell segmentation and lineage analysis from image sequences is central to the goal of data extraction for systems studies, and poses challenges for automating analyses that will apply to multiple studies with differing cell types. From this motivating perspective, we have developed a novel and comprehensive method for automating cell segmentation/lineage reconstruction; this is encoded in CellTracer, a software package to access these methods through an integrated graphical user interface written in Matlab. The software provides manual or semi-automated tools to correct problems from auto-mated algorithms. Studies in dynamic imaging and lineage recon-struction with bacteria, yeast and human cells, as well as multiple other examples of segmentation of different object types, demon-strate the analysis and effective improvements over existing tools as a multi-purpose and easy-to-use analysis approach.


This note describes the implementation of the open source CellTracer software that is available to interested research groups. Further details are in the imaging technical report.

Here are several supplementary notes and movies as well as many more examples of image segmentation, in a variety of applied areas.


Research partially supported by the National Science Foundation (DMS-0342172, BES- 0625213) and National Institutes of Health (NCI U54-CA-112952). Any opinions, findings and conclusions or recommendations expressed in this work are those of the authors and do not necessarily reflect the views of the NSF or NIH.