CABaNe, an automated, high content ImageJ macro for cell and neurite analysis

Measuring neurite length is crucial in neurobiology because it provides valuable insights into the growth, development, and function of neurons. In particular, neurite length is fundamental to study neuronal development and differentiation, neurons responses to drugs, neurodegenerative diseases and neuronal plasticity. Surprisingly, there is currently a lack of tools for high content neurite analysis. In this article, we present CABaNe, as an open source, high content, rule based Image J macro for cell analysis, including their neurite length. We explain the main steps, as well as guide users toward the use of this tool. This macro possess a graphical interface, metadata production, as well as verification means before and after analysis. Rule based and machine learning based programing have been tested for cell identification: After testing, we had better precision and adaptability using rule based cell identification. We challenged CABaNe with currently used techniques, which are manual or assisted. When tested on a small sample, CABaNe demonstrated a massive speed increase in capacity to treat dataset while maintaining or increasing precision when compared to manual measurement. When tested on a large data set, comparing different conditions, we successfully highlighted differences between conditions, in a fully automated and versatile manner. Therefore, CABaNe is viable as a high content option for cell analysis, for neurite length and other parameters, as well as a base of code for other analysis or to train deep learning models, using the output as annotation. In the future, we expect this tool to be widely used in both basic and applied neurobiology research.