Table 1.

Overview of functions provided with the BEMOVI package. Functions are ordered according to the analysis flow

Step	Function name	Short description
Setup	check_video_file_names	Checks whether video files are either of *.avi or *.cxd format
	check_threshold_values	Assists finding manually an appropriate threshold for image segmentation
Locate, measure, and reconstruct trajectories	locate_and_measure_particles	Segments and thresholds video by difference image segmentation, then runs particle analysis to locate and measure the morphological properties of each particle on all frames
	link_particles	Reconstructs the movement trajectory of a given particle by linking its coordinates through time and calculates movement metrics such as turning angles and step lengths
Merge data	merge_data	Creates a database merging morphology and trajectory information with a description of the experimental design
Process data	summarize_trajectories	Summarizes the mean morphology and movement and its variability on the trajectory level
	filter_data	Filters the data, excluding very short, almost non-moving and low detection trajectories
Validation	create_overlays	Creates an overlay of the original video and the trajectories identified in the segmentation and tracking steps; two different visualization options are possible; if the species was predicted, trajectories can be colored according to the species they were predicted to belong to