NeuroQuantify – An image analysis software for detection and quantification of neuron cells and neurite lengths using deep learning

The segmentation of cells and neurites in microscopy images of neuronal networks provides valuable quantitative information about neuron growth and neuronal differentiation, including the number of cells, neurites, neurite length and neurite orientation. This information is essential for assessing the development of neuronal networks in response to extracellular stimuli, which is useful for studying neuronal structures, for example, the study of neurodegenerative diseases and pharmaceuticals. We have developed NeuroQuantify, an open-source software that uses deep learning to efficiently and quickly segment cells and neurites in phase contrast microscopy images. NeuroQuantify offers several key features: (i) automatic detection of cells and neurites; (ii) post-processing of the images for the quantitative neurite length measurement based on segmentation of phase contrast microscopy images, and (iii) identification of neurite orientations. NeuroQuantify overcomes some of the limitations of existing methods in the automatic and accurate analysis of neuronal structures. It has been developed for phase contrast images rather than fluorescence images. In addition to typical functionality of cell counting, NeuroQuantify also detects and counts neurites, measures the neurite lengths, and produces the neurite orientation distribution. We offer a valuable tool to assess network development rapidly and effectively. The user-friendly NeuroQuantify software can be installed and freely downloaded from GitHub at https://github.com/StanleyZ0528/neural-image-segmentation. •Automatic detection of cells and neurites using deep learning.•Quantification of cells and neurites in 2D phase-contrast microscopy images.•Accurately measure neurite length and determine neurite orientations.•Analyze complex neuronal networks within seconds.