Development of a multi-excitation fluorescence (MEF) imaging method to improve the information content of benthic coral reef surveys

Benthic surveys are a key component of monitoring and conservation efforts
for coral reefs worldwide. While traditional image-based surveys rely on
manual annotation of photographs to characterise benthic composition,
automatic image annotation based on computer vision is becoming
increasingly common. However, accurate classification of some benthic
groups from reflectance images presents a challenge to local ecologists
and computers alike. Most coral reef organisms produce one or a
combination of fluorescent pigments, such as Green Fluorescent Protein
(GFP)-like proteins found in corals, chlorophyll-a found in all
photosynthetic organisms, and phycobiliproteins found in red macroalgae,
crustose coralline algae (CCA) and cyanobacteria. Building on the
potential of these pigments as a target for automatic image annotation, we
developed a novel imaging method based on off-the-shelf components to
improve classification of coral and other biotic substrates using a
multi-excitation fluorescence (MEF) imaging system. We used RGB cameras to
image the fluorescence emission of coral and algal pigments stimulated by
narrow-waveband blue and green light, and then combined the information
into 3-channel pseudocolour images. Using a set of a priori rules defined
by the relative pixel intensity produced in different channels, the method
achieved successful classification of organisms into three categories
based on the dominant fluorescent pigment expressed, facilitating
discrimination of traditionally problematic groups. This work provides a
conceptual foundation for future technological developments that will
improve the cost, accuracy and speed of coral reef surveys.