Extraction of protein profiles from primary neurons using active contour models and wavelets

Abstract

The function of complex networks in the nervous system relies on the proper formation of neuronal contacts and their remodeling. To decipher the molecular mechanisms underlying these processes, it is essential to establish unbiased automated tools allowing the correlation of neurite morphology and the subcellular distribution of molecules by quantitative means. We developed NeuronAnalyzer2D, a plugin for ImageJ, which allows the extraction of neuronal cell morphologies from two dimensional high resolution images, and in particular their correlation with protein profiles determined by indirect immunostaining of primary neurons. The prominent feature of our approach is the ability to extract subcellular distributions of distinct biomolecules along neurites. To extract the complete areas of neurons, required for this analysis, we employ active contours with a new distance based energy. For locating the structural parts of neurons and various morphological parameters we adopt a wavelet based approach. The presented approach is able to extract distinctive profiles of several proteins and reports detailed morphology measurements on neurites. We compare the detected neurons from NeuronAnalyzer2D with those obtained by NeuriteTracer and Vaa3D-Neuron, two popular tools for automatic neurite tracing. The distinctive profiles extracted for several proteins, for example, of the mRNA binding protein ZBP1, and a comparative evaluation of the neuron segmentation results proves the high quality of the quantitative data and proves its practical utility for biomedical analyses.