The rapid assessment of how cells respond to pathologic, biological, environmental, and endogenous agents is critical for understanding how such responses may increase genomic instability, disease development and, ultimately, affect quality of life. Recently, we have applied the technique of DNA fiber analysis to increase our understanding of how DNA damaging agents influence DNA replication . The major drawback to this technique, however, is the length of time needed to manually assess the replication dynamics, i.e., 40 hours per experimental condition. We introduce in this paper an automatic and effective image analysis framework for accurate quantification of various replication tracks for high throughput DNA analysis, called Computer Assisted Selection and Analysis (CASA). This algorithm is implemented in two major steps: random-walk-based DNA fiber tracking and pattern-recognition-based measurement of the replication tracks. Experimental results show that the proposed method can yield results which are highly consistent with manual analysis and needs only 160-fold less processing time, without manual involvement.