Cameron Scott Bodine , Daniel David Buscombe , Rebecca J Best, Jennylyn A Redner, Adam J Kaeser

The characterization of benthic habitats is essential for aquatic ecosystem science and management, but is frequently limited by waterbody visibility and depth. Recreation-grade side scan sonar systems are increasingly used to aid scientific inquiries in shallow water due to their relative low-cost, ease of operation, low-weight, and ease of mounting on a variety of vessels. However, existing procedures and software for post-processing these data are either limited, closed source, or fail on data from new sonar models; limiting development of reproducible workflows. Here we present PING-Mapper, an open source and freely available side scan sonar post-processing toolset for processing and mapping sonar recordings from popular Humminbird instruments. The modular software automatically: 1) decodes sonar recordings from any Humminbird system; 2) exports ping attributes from every sonar channel; 3) uses sonar sensor depth for water column removal; and 4) exports sonogram tiles and georectified mosaics. Sonar channels are processed in parallel for quick decoding and metadata extraction. Workflows for major processing workflows including georectification and image export scale with computing resources. The software has been extensively tested using data from several river distributaries of varying character and distribution of depths, but could also be used in estuarine and lacustrine environments. Usage of PING-Mapper is illustrated in three case studies focused on mapping large woody debris, bathymetric mapping, and visual interpretation and mapping of substrates for select reaches of the Pearl and Pascagoula river systems in Mississippi.