Evaluating deep learning techniques for optimal neurons counting and characterization in complex neuronal cultures

Abstract

The counting and characterization of neurons in primary cultures have long been areas of significant scientific interest due to their multifaceted applications, ranging from neuronal viability assessment to the study of neuronal development. Traditional methods, often relying on fluorescence or colorimetric staining and manual segmentation, are time consuming, labor intensive, and prone to error, raising the need for the development of automated and reliable methods. This paper delves into the evaluation of three pivotal deep learning techniques: semantic segmentation, which allows for pixel-level classification and is solely suited for characterization; object detection, which focuses on counting and locating neurons; and instance segmentation, which amalgamates the features of the other two but employing more intricate structures. The goal of this research is to discern what technique or combination of those techniques yields the optimal results for automatic counting and characterization of neurons in images of neuronal cultures. Following rigorous experimentation, we conclude that instance segmentation stands out, providing superior outcomes for both challenges. Graphical abstract Identifying the optimal pathway for characterizing neurons in complex cultures through structured experimentation