Active skeleton for bacteria modeling

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 http://fluobactracker.inrialpes.fr.Comment: Published in Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualizationto appear i

Fast and robust curve skeletonization for real-world elongated objects

We consider the problem of extracting curve skeletons of three-dimensional, elongated objects given a noisy surface, which has applications in agricultural contexts such as extracting the branching structure of plants. We describe an efficient and robust method based on breadth-first search that can determine curve skeletons in these contexts. Our approach is capable of automatically detecting junction points as well as spurious segments and loops. All of that is accomplished with only one user-adjustable parameter. The run time of our method ranges from hundreds of milliseconds to less than four seconds on large, challenging datasets, which makes it appropriate for situations where real-time decision making is needed. Experiments on synthetic models as well as on data from real world objects, some of which were collected in challenging field conditions, show that our approach compares favorably to classical thinning algorithms as well as to recent contributions to the field.Comment: 47 pages; IEEE WACV 2018, main paper and supplementary materia

Experiences on a motivational learning approach for robotics in undergraduate courses

This paper presents an educational experience carried out in robotics undergraduate courses from two different degrees: Computer Science and Industrial Engineering, having students with diverse capabilities and motivations. The experience compares two learning strategies for the practical lessons of such courses: one relies on code snippets in Matlab to cope with typical robotic problems like robot motion, localization, and mapping, while the second strategy opts for using the ROS framework for the development of algorithms facing a competitive challenge, e.g. exploration algorithms. The obtained students’ opinions were instructive, reporting, for example, that although they consider harder to master ROS when compared to Matlab, it might be more useful in their (robotic related) professional careers, which enhanced their disposition to study it. They also considered that the challenge-exercises, in addition to motivate them, helped to develop their skills as engineers to a greater extent than the skeleton-code based ones. These and other conclusions will be useful in posterior courses to boost the interest and motivation of the students.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech