Automated Pipeline for Infants Continuous EEG (APICE): A flexible pipeline for developmental cognitive studies

Infant electroencephalography (EEG) presents several challenges compared with adult data: recordings are typically short and heavily contaminated by motion artifacts, and the signal changes throughout development. Traditional data preprocessing pipelines, developed mainly for event-related potential analyses, require manual steps. However, larger datasets make this strategy infeasible. Moreover, new analytical approaches may have different preprocessing requirements. We propose an Automated Pipeline for Infants Continuous EEG (APICE). APICE is fully automated, flexible, and modular. The use of multiple algorithms and adaptive thresholds for artifact detection makes it suitable across age groups and testing procedures. Furthermore, the preprocessing is performed on continuous data, enabling better data recovery and flexibility (i.e., the same preprocessing is usable for different analyzes). Here we describe APICE and validate its performance in terms of data quality and data recovery using two very different infant datasets. Specifically, (1) we show how APICE performs when varying its artifacts rejection sensitivity; (2) we test the effect of different data cleaning methods such as the correction of transient artifacts, Independent Component Analysis, and Denoising Source Separation; and (3) we compare APICE with other available pipelines. APICE uses EEGLAB and compatible custom functions. It is freely available at https://github.com/neurokidslab/eeg_preprocessing, together with example scripts.