Fish are a critical component of marine biology; therefore, the accurate identification and counting of fish are essential for the objective monitoring and assessment of marine biological resources. High‐frequency adaptive resolution imaging sonar (ARIS) is widely used for underwater object detection and imaging, and it quickly obtains close‐up video of free‐swimming fish in high‐turbidity water environments. Nonetheless, processing the massive data output using imaging sonars remains a major challenge. Here, the authors developed an automatic image‐processing programme that fuses K‐nearest neighbour background subtraction with DeepSort target tracking to automatically track and count fish. The automatic programme was evaluated using four test data sets with different target sizes and observation ranges and differently deployed sonars. According to the results, the approach successfully counted free‐swimming fish targets with an accuracy index of 73% and a completeness index of 70%. Under appropriate conditions, this approach could replace time‐consuming semi‐automatic approaches and improve the efficiency of imaging sonar data processing, while providing technical support for future real‐time data processing.
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