Abstract In-situ visual observations of marine organisms is crucial to developing behavioural understandings and their relations to their surrounding ecosystem. Typically, these observations are collected via divers, tags, and remotely-operated or human-piloted vehicles. Recently, however, autonomous underwater vehicles equipped with cameras and embedded computers with GPU capabilities are being developed for a variety of applications, and in particular, can be used to supplement these existing data collection mechanisms where human operation or tags are more difficult. Existing approaches have focused on using fully-supervised tracking methods, but labelled data for many underwater species are severely lacking. Semi-supervised trackers may offer alternative tracking solutions because they require less data than fully-supervised counterparts. However, because there are not existing realistic underwater tracking datasets, the performance of semi-supervised tracking algorithms in the marine domain is not well understood. To better evaluate their performance and utility, in this paper we provide (1) a novel dataset specific to marine animals located at http://warp.whoi.edu/vmat/ , (2) an evaluation of state-of-the-art semi-supervised algorithms in the context of underwater animal tracking, and (3) an evaluation of real-world performance through demonstrations using a semi-supervised algorithm on-board an autonomous underwater vehicle to track marine animals in the wild.

This paper describes a recent study in which an autonomous underwater vehicle (AUV) with a high resolution stereo-imaging system was used to document nocturnal camouflage behaviour in cuttlefish at a well known spawning site in Whyalla, South Australia. The AUV's ability to fly at low altitude during day and night while closely following a desired survey pattern provided improved data collection compared to divers and previous work with a small ROV. Over the course of the week long expedition, the AUV Sirius was deployed on 38 dives at three sites in the survey area and collected tens of thousands of stereo images. Of these, nearly a thousand were seen to contain cuttlefish during post cruise analysis, with a large proportion showing evidence of camouflage. The distribution of images containing cuttlefish suggest that the animal concentrations were substantially higher closer in to shore in shallow waters, where the flat rocky substrate occurs; females lay their eggs on the underside of these rocks. Results demonstrate the strengths of using an AUV for surveying near-shore benthic habitats of ecological interest, with a particular emphasis on the ability to operate during both day and night time operations.