Behavioural phenotypic analysis using small aquatic model organisms is becoming an important toolbox in aquatic ecotoxicology and neuroactive drug discovery. Digital film recording with subsequent analysis of video files using specialized animal tracking software has become a standard in obtaining behavioral biometric data. At present animal tracking algorithms are largely capable of detecting and tracking small number of animals and extracting quantitative endpoints associated with specific behavioral traits based on reconstruction of movement trajectories and occupancy heatmaps. However, there is a lack of standardization and consistency in acquiring high quality videos with a high quantity of subjects that are able to be easily tracked by existing algorithms. In this work we discuss evaluated parameters of video file characteristics, video optimization techniques and establish a guide for researchers to easily acquire videos that allow for evaluation of behavioural endpoints.