person with equipment underwater on reef

Hyperspectral sensors

Investigating spectral signatures to help observe reef communities

AIMS is investigating exciting potential applications of mapping the electromagnetic spectrum reflected by reefs, sea creatures and research specimens.

This can provide detailed information about coral reef composition and health and is already being used to improve the accuracy and efficiency of marine research.  

It could also be used to assist with reef reseeding for restoration after destructive events, to identify reefs at risk of coral bleaching to allow time for preventative measures to be implemented, to identify where destructive crown-of-thorns starfish outbreaks are occurring and to monitor and manage water quality, fish and other seafood populations.

What is hyperspectral imaging? 

Everything on earth reflects electromagnetic radiation from a light source (e.g. the sun or a lamp). The human eye processes some of this electromagnetic radiation as colour. Radiation outside this band of colour is invisible to the naked eye. 

Every object or organism has a unique ‘spectral signature’ – which has been likened to a human fingerprint because of the amount of information that can be read from it.   

A material's electromagnetic reflectance property can change depending on its physiological state.  

Hyperspectral imaging (HSI) measures these reflectance properties to observe distinct features or to measure changes. It can help researchers locate objects, identify materials or detect processes. It can tell scientists the composition of a reef and how the organisms are dispersed. 

It is a unique imaging technique that provides information-rich output without destroying the organism being studied, which is a common outcome using most traditional research methods. 

Peer-reviewed research has measured HSI prediction accuracy at about 98 percent.

AIMS hyperspectral imaging systems

We have several platforms capable of gathering hyperspectral data including:  


A trolley-based system is used to scan live animals, such as corals, in a holding tank using HSI technology.  

Corals in our National Sea Simulator, SeaSim, are currently bred for destructive sampling in research programs, such as those used to better understand coral health and resilience. This means most individual coral can only be studied at a single point in time in the research program as it is usually destroyed for analysis. 

HSI technology allows for a coral to be continually sampled throughout a growth stage, or after the application of different variables, such as increased water temperature or lower pH level. 

In addition to getting more information from corals, using the technology means fewer samples are required and the impact of changed conditions is more directly measurable.

A timelapse of hyperspectral imaging in the National Sea Simulator

Aerial drone 

Launched from land or sea vessels, an aerial drone with HSI capability can map data at high resolution over large areas of interest.  

Imaging from a drone was used to categorise the composition of John Brewer Reef in 2018 and 2019.


Hand-operated by a diver or attached to an automated underwater vessel (AUV) or remotely operated vehicle (ROV), HSI underwater housing can go as deep as 200m, however artificial lighting is required below 6m.  

Using HSI to map reef conditions and composition in the wild provides scientists and managers with close-up information for better decision making. 

It also allows AIMS to test and validate research processes and methods developed in SeaSim in the real world in an unobtrusive and non-destructive way.

Potential applications

Our researchers are working to identify early physiological indicators of coral bleaching. Using HSI, it is possible coral reefs at risk of bleaching could be identified weeks before discolouration begins, allowing preventative measures to be deployed by reef managers. 

As HSI provides detailed information about the composition of a reef community, it could also be used to identify the best areas to undertake reef reseeding to help restore a degraded reef. 

Other applications being explored include: assessing seagrass health, water quality (e.g. detecting high chlorophyll content as an indicator of algal blooms), detecting outbreaks of the coral-eating crown-of-thorns starfish and as a non-destructive method to monitor scallop populations and to inform fishery management.