DOI: https://doi.org/10.15588/1607-3274-2019-1-10

VORONOI-BASED SKELETONIZATION ALGORITHM FOR SEGMENTING THE NETWORK OF BIOLOGICAL NEURONS

D. V. Kotsur, V. M. Tereshchenko

Abstract


Context. The problem of automated processing and analysis of microscopy image data is of high relevance due to its extreme impact on the research and recent developments in the field of biology and medicine. Efficient image processing algorithms facilitate the development of new medical diagnostic tools and therapy processes. They help us to broaden our knowledge of underlying
mechanisms and processes inside living organisms. The primal focus of this paper is the processing of the microscopy images of the biological neural network. This aims to facilitate further studies of biological neural network that would lead to the development of better methods for diagnosis, prevention and cure of the related deceases.
Objective. The goal of the work is to development of an efficient image processing algorithm for segmenting the network of biological neurons based on the fluorescent microscopy image data.
Method. The introduced algorithm for segmenting the network of biological neurons comprises several steps. Firstly, we apply image processing routines, which aim to enhance the quality of the image data and extract the contours of the biological neural network. Then we construct the skeleton of the network applying the Voronoi diagram for line segments extracted from the object’s contours. We employ Voronoi skeleton to identify the cellular somas and differentiate them from axons and dendrites.
Results. The developed Voronoi-based algorithm allows us to segment individual neurons, localize their somas, axons and dendrites and extract graph representation of the neural network. The underlying Voronoi diagram data structure allows us to compute such graph efficiently in O(N log N) operations (where N is a number of contour points). The proposed segmentation method was
implemented in the C++/Python programming language and evaluated on the fluorescent images from CellImageLibrary (CIL).
Conclusions. The proposed segmentation method aims to facilitate studies of biological neural networks. It computes segmentation of the network of biological neurons in O(N log N) operations using the Voronoi diagram data structure. This data structure, in turn, gives us an attributed graph representation of the segmented network. Therefore, classical graph processing algorithms can be
applied to analyze the neural and compute such network’s characteristics as the number of connections between individual neurons, the shortest signal transduction path between two neurons, etc.


Keywords


microscopy; image processing; Voronoi diagram; Voronoi polygon; neurons; segmentation; graph.

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