CalTrig: A GUI-based Machine Learning Approach for Decoding Neuronal Calcium Transients in Freely Moving Rodents

Abstract

Advances in in vivo Ca2+ imaging using miniature microscopes have enabled researchers to study single-neuron activity in freely-moving animals. Tools such as MiniAN and CalmAn have been developed to convert Ca2+ visual signals to numerical data, collectively referred to as CalV2N. However, substantial challenges remain in analyzing the large datasets generated by CalV2N, particularly in integrating data streams, evaluating CalV2N output quality, and reliably and efficiently identifying Ca2+ transients. In this study, we introduce CalTrig, an open-source graphical user interface (GUI) tool designed to address these challenges at the post-CalV2N stage of data processing. CalTrig integrates multiple data streams, including Ca2+ imaging, neuronal footprints, Ca2+ traces, and behavioral tracking, and offers capabilities for evaluating the quality of CalV2N outputs. It enables synchronized visualization and efficient Ca2+ transient identification. We evaluated four machine learning models (i.e., GRU, LSTM, Transformer, and Local Transformer) for Ca2+ transient detection. Our results indicate that the GRU model offers the highest predictability and computational efficiency, achieving stable performance across training sessions, different animals and even among different brain regions. The integration of manual, parameter-based, and machine learning-based detection methods in CalTrig provides flexibility and accuracy for various research applications. The user-friendly interface and low computing demands of CalTrig make it accessible to neuroscientists without programming expertise. We further conclude that CalTrig enables deeper exploration of brain function, supports hypothesis generation about neuronal mechanisms, and opens new avenues for understanding neurological disorders and developing treatments.