Towards automated scyphistoma census in underwater imagery: a useful research and monitoring tool

Manual annotation and counting of entities in underwater photographs is common in many branches of marine biology. With a marked increase of jellyfish populations worldwide, understanding the dynamics of the polyp (scyphistoma) stage of their life-cycle is becoming increasingly important. In-situ studies of polyp population dynamics are scarce due to small size of the polyps and tedious manual work required to annotate and count large numbers of items in underwater photographs. We devised an experiment which shows a large variance between human annotators, as well as in annotations made by the same annotator. We have tackled this problem, which is present in many areas of marine biology, by developing a method for automated detection and counting. Our polyp counter (PoCo) uses a two-stage approach with a fast detector (Aggregated Channel Features) and a precise classifier consisting of a pre-trained Convolutional Neural Network and a Support Vector Machine. PoCo was tested on a year-long image dataset and performed with accuracy comparable to human annotators but with 70-fold reduction in time. The algorithm can be used in many marine biology applications, vastly reducing the amount of manual labor and enabling processing of much larger datasets. The source code is freely available on GitHub.