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Proceedings Paper

An automated approach for single-cell tracking in epifluorescence microscopy applied to E. coli growth analysis on microfluidics biochips
Author(s): Catalin Fetita; Boris Kirov; Alfonso Jaramillo; Christophe Lefevre
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Paper Abstract

With the accumulation of knowledge for the intimate molecular mechanisms governing the processes inside the living cells in the later years, the ability to characterize the performance of elementary genetic circuits and parts at the single-cell level is becoming of crucial importance. Biological science is arriving to the point where it can develop hypothesis for the action of each molecule participating in the biochemical reactions and need proper techniques to test those hypothesis. Microfluidics is emerging as the technology that combined with high-magnification microscopy will allow for the long-term single-cell level observation of bacterial physiology. In this study we design, build and characterize the gene dynamics of genetic circuits as one of the basic parts governing programmed cell behavior. We use E. coli as model organism and grow it in microfluidics chips, which we observe with epifluorescence microscopy. One of the most invaluable segments of this technology is the consequent image processing, since it allows for the automated analysis of vast amount of single-cell observation and the fast and easy derivation of conclusions based on that data. Specifically, we are interested in promoter activity as function of time. We expect it to be oscillatory and for that we use GFP (green fluorescent protein) as a reporter in our genetic circuits. In this paper, an automated framework for single-cell tracking in phase-contrast microscopy is developed, combining 2D segmentation of cell time frames and graph-based reconstruction of their spatiotemporal evolution with fast tracking of the associated fluorescence signal. The results obtained on the investigated biological database are presented and discussed.

Paper Details

Date Published: 14 April 2012
PDF: 11 pages
Proc. SPIE 8317, Medical Imaging 2012: Biomedical Applications in Molecular, Structural, and Functional Imaging, 83170Z (14 April 2012); doi: 10.1117/12.911371
Show Author Affiliations
Catalin Fetita, ARTEMIS, CNRS, TELECOM SudParis (France)
Boris Kirov, SYNTH-BIO Group, Institute of Systems & Synthetic Biology, CNRS (France)
Alfonso Jaramillo, SYNTH-BIO Group, Institute of Systems & Synthetic Biology, CNRS (France)
Christophe Lefevre, ARTEMIS, CNRS, TELECOM SudParis (France)


Published in SPIE Proceedings Vol. 8317:
Medical Imaging 2012: Biomedical Applications in Molecular, Structural, and Functional Imaging
Robert C. Molthen; John B. Weaver, Editor(s)

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