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

Thibieroz, N.; Cordelieres, F.; Lopes Cardoso Filho, J.-C.; Machillot, P.; Marchadier, L.; Singh, A.; Picart, C.; Migliorini, E.

doi:10.1101/2025.03.07.641590

bioRxiv · 10.1101/2025.03.07.641590

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

Thibieroz, N.·Cordelieres, F.·Lopes Cardoso Filho, J.-C.·Machillot, P.·Marchadier, L.·Singh, A.·Picart, C.·Migliorini, E.

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Abstract

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. 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. 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 manner. Therefore, CABaNe is viable as a high content 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 statementWhen 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.

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Thibieroz, N., Cordelieres, F., Lopes Cardoso Filho, J.-C., Machillot, P., Marchadier, L., Singh, A., Picart, C., Migliorini, E.. 2025-03-10. CABaNe, an automated, high content ImageJ macro for cell and neurite analysis. https://doi.org/10.1101/2025.03.07.641590

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