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Post-doctoral Position: Modelling axon growth from in vivo 2 photon 3D image sequences and Static confocal 3D images 

Collaborators: Xavier Descombes (INRIA), Florence Besse (iBV) and Caroline Medioni (iBV)

Institute : INRIA CRI-SAM

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Summary: The trajectories followed by axons during their growth define the morphologies of mature axons and therefore underlie neuron network connectivity. Defective axon growth has been linked to various motor and mental disorders (Nugent et al., 2012). F. Besse team at iBV has identified genes controlling axon growth and has defined a protocol to obtain in vivo image sequences of axons during the growing process in Drosophila brains.  We have recently developed a method to automatically extract the axon trajectories from the two-photon microscopy data and to extract mature axons from confocal microscopic images.

The goal of this post-doc project is to propose a growth model based on Markov Chains, to simulate this model and to estimate its parameters from in vivo data of axons of different populations.  We will consider different biological features in the model such as the axon elasticity, an attractive vector field toward a predefined target and the branching process. The model parameters estimated from the image data will characterize the different individuals. The different datasets will be registered to compare individuals. The mean axon elasticity and a space map representing the attractive vector field will then characterize a population. We will first consider a 2D model based on the maximum intensity projection (MIP) images and extend it to 3D in a second step.

Different populations of Drosophila axons, including mutant ones will be compared. The output of the study will consist in assessing if a given mutation affects the attractive vector field, the axon elasticity and/or the ability of an axon to produce branches.


Koene R.A. et al. (2009). NETMORPH: a framework for the stochastic generation of large scale neuronal networks with realistic neuron morphologies. Neuroinformatiks, 7:195-210.

Vitriol E. and Zheng J. (2012). Growth cone travel in space and time: the cellular ensemble of cytoskeleton, adhesion, and membrane. Neuron, 73(6):1068-81.

Young P. and Feng G. (2004). Labeling neurons in vivo for morphological and functional studies. Curr. Opin. Neurobiol, 14: 642-646.

Nugent A et al., (2012). Human disorders of axon guidance. Curr. Opin. Neurobiol, 22:1-7




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