Automated DNA fiber tracking and measurement

Yaping Wang, Paul Chastain, Pew Thian Yap, Jie Zhi Cheng, David Kaufman, Lei Guo, Dinggang Shen

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Citations (Scopus)

Abstract

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.

Original languageEnglish
Title of host publication2011 8th IEEE International Symposium on Biomedical Imaging
Subtitle of host publicationFrom Nano to Macro, ISBI'11
Pages1349-1352
Number of pages4
DOIs
Publication statusPublished - 2011
Event2011 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI'11 - Chicago, IL, United States
Duration: 2011 Mar 302011 Apr 2

Publication series

NameProceedings - International Symposium on Biomedical Imaging
ISSN (Print)1945-7928
ISSN (Electronic)1945-8452

Other

Other2011 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI'11
CountryUnited States
CityChicago, IL
Period11/3/3011/4/2

Keywords

  • DNA fiber tracking
  • DNA pattern recognition
  • DNA replication tracks
  • random walk

ASJC Scopus subject areas

  • Biomedical Engineering
  • Radiology Nuclear Medicine and imaging

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  • Cite this

    Wang, Y., Chastain, P., Yap, P. T., Cheng, J. Z., Kaufman, D., Guo, L., & Shen, D. (2011). Automated DNA fiber tracking and measurement. In 2011 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI'11 (pp. 1349-1352). [5872650] (Proceedings - International Symposium on Biomedical Imaging). https://doi.org/10.1109/ISBI.2011.5872650