Large-area image acquisition techniques are essential in underwater investigations: high-resolution 3D image-based reconstructions have improved coral reef monitoring by enabling novel seascape ecological analysis. Artificial intelligence (AI) offers methods for significantly accelerating image data interpretation, such as automatically recognizing, enumerating, and measuring organisms. However, the rapid proliferation of these technological achievements has led to a relative lack of standardization of methods. Remarkably, there are notable differences in procedures for generating human and AI annotations, and there is also a scarcity of publicly available datasets and shared machine-learning models. The lack of standard procedures makes it challenging to compare and reproduce scientific findings. One way to overcome this problem is to make the most used platforms by coral reef scientists interoperable so that the analyses can all be exported into a common format. This paper introduces functionality to promote interoperability between three popular open-source software tools dedicated to the digital study of coral reefs: TagLab, CoralNet, and Viscore. As users of each platform may have different analysis pipelines, we discuss several workflows for managing and processing point and area annotations, improving collaboration among these tools. Our work sets the foundation for a more seamless ecosystem that maintains the established investigation procedures of various laboratories but allows for easier result sharing.