CABaNe, an automated, high throughput 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 throughput neurite analysis. In this article, we present CABaNe, as an open source, high throughput, rule based Image J macro for cell analysis, including their neurite length. This macro possesses a graphical interface, metadata production, as well as verification means before and after analysis. Rule based and machine learning based programming have been tested for cell identification. Cell tested were N2A, a mouse neuroblastoma cell line. 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 analyzed the dataset of interest much faster than manual measurements, while maintaining or increasing precision. When tested on a large data set, comparing different conditions, we successfully highlighted differences between conditions, in a fully automated manner. Therefore, CABaNe is viable as a high throughput option for cell analysis, for neurite length and other parameters. It is a base of code that can be used for other analysis or to train deep learning models. In the future, we expect this tool to be widely used in both basic and applied neurobiology research. Significance statement When studying neuronal cell differentiation, an important morphological parameter is neurite length. This parameter requires measuring the protrusions length of analysed cells. However, this analysis done manually can be long, as each individual cell must be measured independently. Currently, efficient single cell tools exist to assist the measurement, such as NeuronJ. However, there is currently no available automated tool for this analysis, and manual techniques suffer operator bias. In this paper, we present a macro to fully automatize neurite length and other parameters measurement, for each cell, in each image, in each condition.