TY - GEN
T1 - Automated DNA fiber tracking and measurement
AU - Wang, Yaping
AU - Chastain, Paul
AU - Yap, Pew Thian
AU - Cheng, Jie Zhi
AU - Kaufman, David
AU - Guo, Lei
AU - Shen, Dinggang
PY - 2011
Y1 - 2011
N2 - 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 [1]. 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.
AB - 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 [1]. 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.
KW - DNA fiber tracking
KW - DNA pattern recognition
KW - DNA replication tracks
KW - random walk
UR - http://www.scopus.com/inward/record.url?scp=80055029446&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=80055029446&partnerID=8YFLogxK
U2 - 10.1109/ISBI.2011.5872650
DO - 10.1109/ISBI.2011.5872650
M3 - Conference contribution
AN - SCOPUS:80055029446
SN - 9781424441280
T3 - Proceedings - International Symposium on Biomedical Imaging
SP - 1349
EP - 1352
BT - 2011 8th IEEE International Symposium on Biomedical Imaging
T2 - 2011 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI'11
Y2 - 30 March 2011 through 2 April 2011
ER -