Cell Analyser in Batch for Neurite (CABaNe), an Automated, High-Throughput ImageJ Macro for Cell and Neurite Analysis

Area of Science:

• Neurobiology
• Cell Biology
• Image Analysis

Background:

• Neurite length is a critical parameter for understanding neuronal growth, differentiation, and function.
• Existing methods for neurite length measurement are often manual, time-consuming, and prone to operator bias.
• There is a significant need for automated, high-throughput tools for accurate neurite analysis.

Purpose of the Study:

• To introduce CABaNe, an open-source, rule-based Image J macro for automated high-throughput cell analysis, with a focus on neurite length measurement.
• To evaluate the performance of CABaNe against manual and assisted measurement techniques.
• To provide a versatile platform for various neurobiological analyses and potential deep learning model training.

Main Methods:

• Development of CABaNe, a rule-based Image J macro with a graphical interface and verification features.
• Testing of both rule-based and machine learning-based cell identification methods on N2A mouse neuroblastoma cells.
• Comparative analysis of CABaNe's performance against manual and assisted measurement techniques on small and large datasets.

Main Results:

• Rule-based cell identification demonstrated superior precision and adaptability compared to machine learning-based methods.
• CABaNe significantly reduced analysis time for small datasets while maintaining or improving precision.
• Automated analysis of large datasets successfully identified differences between experimental conditions.

Conclusions:

• CABaNe is a viable and efficient solution for high-throughput neurite length and other cell parameter analysis in neurobiology.
• The open-source nature of CABaNe allows for its adaptation to diverse research needs and future development, including training deep learning models.
• CABaNe offers a robust, automated alternative to manual measurements, reducing bias and increasing throughput in neurobiological research.