Biological Imaging and machine vision for 3D shape reconstruction

Summary

The aim of this project will be to construct and use a 3D imaging system to record the motion of worms crawling and swimming in fluid environment. Using machine vision, 3D shape reconstruction will be performed, and the shapes obtained will be modeled using statistical methods. A first prototype system already exists, including the hardware and image detection and tracking software.

The worms under investigation are known as C. elegans (Caernohabditis elegans). In their natural habitat, these microscopic (1mm in the adult) worms must navigate complex and heterogeneous environments in 3D. And yet to date, their behaviour has only been characterised in 2D (See e.g. Berri et al, HFSP J. 3, 186-19 2009, Stephens et al, PLoS Comput Biol 4, e1000028 2008, and Padmanabhan et al. arXiv:1202.2832 2012). The ability to record, track and characterise their behaviour in 3D will be a first step towards the modeling of the neural control of the observed behaviors.

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