Tracking Multiple Zebrafish Larvae Using YOLOv5 and DeepSORT

Guoning Si, Fuhuan Zhou, Zhuo Zhang, Xuping Zhang

Research output: Contribution to book/anthology/report/proceedingArticle in proceedingsResearchpeer-review

Abstract

Accurate tracking of zebrafish larva movements is essential to examine their dynamic behaviors in biomedical and pharmaceutical applications. However, the characteristic 'burst' and sleep-like stationary movements of zebrafish will cause inconsistency in the detection and tracking, which hinders the observation of their identities and trajectories. To address these problems, this paper develops an accurate and reliable tracking system for multiple zebrafish larvae based on the current state-of-the-art detection technology YOLOv5 and multi-target tracking technology DeepSORT. The detection-based tracking system divided into two parts: detection and tracking. In the detection stage, the zebrafish larvae's head position detected by using the trained YOLOv5 model. In the DeepSORT tracking phase, a Cascade matching algorithm utilized to match the identification of zebrafish larvae, which utilizes information on movement and appearance of larvae. On the one hand, the Mahalanobis distance used to evaluate the predicted value by the Kalman filter and the detected value by the YOLOv5 model. On the other hand, the appearance features model of the fish head trained and utilizes Cosine distance to evaluate between the stored values of the appearance features and the current frame appearance information. The proposed tracking system has been evaluated by using CLEAR MOT Metrics on five groups of zebrafish larvae videos under various complex imaging conditions. The results showed that the system had good performance in reducing the ID switch problem in complex environments, and the tracking accuracy could be up to 88.8%.

Original languageEnglish
Title of host publication2022 8th International Conference on Automation, Robotics and Applications, ICARA 2022
Number of pages5
PublisherInstitute of Electrical and Electronics Engineers Inc.
Publication dateMar 2022
Pages228-232
ISBN (Electronic)9781665483834
DOIs
Publication statusPublished - Mar 2022
Event8th International Conference on Automation, Robotics and Applications, ICARA 2022 - Virtual, Online, Czech Republic
Duration: 18 Feb 202220 Feb 2022

Conference

Conference8th International Conference on Automation, Robotics and Applications, ICARA 2022
Country/TerritoryCzech Republic
CityVirtual, Online
Period18/02/202220/02/2022
SeriesProceedings - 2022 8th International Conference on Automation, Robotics and Applications, ICARA 2022

Keywords

  • DeepSORT
  • ID switch
  • tracking
  • YOLOv5
  • zebrafish larvae

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