TY  - JOUR
AU  - Jean-Pascal Jacob
AU  - Mariella Dimiccoli
AU  - Lionel Moisan
PY  - 2016//
TI  - Active skeleton for bacteria modeling
T2  - CMBBE
JO  - Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualization
SP  - 274
EP  - 286
VL  - 5
IS  - 4
KW  - Bacteria modelling
KW  - medial axis
KW  - active contours
KW  - active skeleton
KW  - shape contraints
N2  - The investigation of spatio-temporal dynamics of bacterial cells and their molecular components requires automated image analysis tools to track cell shape properties and molecular component locations inside the cells. In the study of bacteria aging, the molecular components of interest are protein aggregates accumulated near bacteria boundaries. This particular location makes very ambiguous the correspondence between aggregates and cells, since computing accurately bacteria boundaries in phase-contrast time-lapse imaging is a challenging task. This paper proposes an active skeleton formulation for bacteria modeling which provides several advantages: an easy computation of shape properties (perimeter, length, thickness, orientation), an improved boundary accuracy in noisy images, and a natural bacteria-centered coordinate system that permits the intrinsic location of molecular components inside the cell. Starting from an initial skeleton estimate, the medial axis of the bacterium is obtained by minimizing an energy function which incorporates bacteria shape constraints. Experimental results on biological images and comparative evaluation of the performances validate the proposed approach for modeling cigar-shaped bacteria like Escherichia coli. The Image-J plugin of the proposed method can be found online at this http URL
L1  - http://refbase.cvc.uab.es/files/JDM2015.pdf
UR  - http://dx.doi.org/10.1080/21681163.2015.1100099
N1  - MILAB
ID  - Jean-Pascal Jacob2016
ER  -