*2.3. Limitations of Non-Invasive Monitoring*

As outlined previously, a variety of data can be collected using these different methods of assessment to indicate coral 'health'. Each technique generally gives multiple metrics that can be used, as summarised in Figures 3 and 4.

**Figure 3.** Diver image based techniques and examples of the types of data produced from the main techniques.

**Figure 4.** The types of data from each type of spectral system at the different levels from satellites to underwater systems. Images from the Jet Propulsion Lab (JPL) (2020) and Eric J. Hochberg, Bermuda Institute of Ocean Sciences. UUV: Unmanned underwater vehicle.

The use of spectral techniques to look at other parameters such as distinguishing between coral species and identifying diseases and bleaching suffers from limiting factors that include phenotypic plasticity in the host, differing symbiont pigment compositions [99], and changing physical parameters of the water column [100] such as turbity.

In order to derive meaning from colour and its relation to bleaching, bar a simple presence vs. absence, the exact symbiont density and chlorophyll-a content needs to be quantified to link to their corresponding wavelengths. Unfortunately, this procedure is destructive. Typically, whole corals or tissue samples are removed for laboratory analysis. Coral health is assessed based on the composition of extracted Symbiodiniaceae and chlorophyll content [101]. Laboratory bleaching experiments allow links to be made between the effects of bleaching and pigment intensity. These experiments link the levels of symbiont density to spectral peaks and approximate the stage of bleaching that can be determined using in situ hyperspectral imagery [33]. Effective coral monitoring in this way can thus become a victim of itself; effective identification in a plethora of sites featuring the signatures of coral bleaching creates an insurmountable requirement for downstream laboratory based truthing.

Nevertheless, as outlined in Tables 2 and 3, the techniques described have many features that contribute to their overall suitability for coral monitoring including cost, spatial scale, spectral resolution, and any additional data taken alongside sample acquisition. The choice of instrumentation is normally governed by research requirements [102,103]. The cost of the instrumentation is often the most prohibitive factor in the adoption of improved sensing strategies. For instance, to determine the global extent of coral bleaching, airborne and satellite imagers are best suited despite their cost and problems assessing deep reefs. However, as stated, ground truthing data would be required to validate and correct for atmospheric and aqueous attenuation correction algorithms. For in situ surveys that require high spectral resolution, an underwater hyperspectral system is best suited. This provides the desired spectral resolution at a non-prohibitive cost whilst simultaneously gathering related supporting measurements (see Table 4).

Therefore, the choice of the underwater spectroscopy tool is also crucial. Each imaging technique has a number of defining qualities and trade-offs regarding spectral range, resolution, scale of operation, depth rating, and cost. These determine their suitability and effectiveness in any given situation.

Looking towards the future, new spectral tools will likely emerge to address these issues. A range of underwater imagers identified by Liu (2020) [69] (Table 1) were compared as well as the new "Bi-Frost" digital single-lens reflex (DSLR) hyperspectral camera system presented in Section 2.1. Whilst spectral performance and cost are key factors, other considerations should be considered. Of particular importance are how the device is interfaced and how portable it is.


**Table 1.** A comparison of the selection of underwater spectral imaging systems as outlined by Liu et al., 2020 [69] including the HyRi/HyFi ordered by cost.

LUMIS: Low-light-level underwater multispectral imaging system; UMSI: Underwater spectral imaging system; HyRi/HyFi: Hyperspectral reflectance/fluorescence imager; TuLUMIS: Tunable LED-based underwater multispectral imaging system; UHI OV: Ocean Vision (costs derived from manufacturers quotes with exchange rate applied on 8 October 2020.

**Technique Cost Spatial Scale Spatial Resolution Additional Data Gathered Notes** RGB imaging (Based on GoPro) Very Low Moderate Very High Photogrammetry Limited spectral data obtained Spectrometers (Waltz Diving PAM) Moderate Very Low Very High N/A N/A Bi-Frost DSLR Low Moderate Very High Photogrammetry, Fluorescence (HyFi) Night-time imaging required for Fluorescence Current UHI systems (See Table 4) Moderate to High Moderate Very High to Moderate N/A Often large and cumbersome or designed specifically for UUVs Drone multi/hyperspectral imaging [81] Moderate to High Moderate Moderate N/A Requires Ground truthing Aeroplane multi/hyperspectral imaging [61,107] High High Moderate to Low N/A Requires Ground truthing Satellite multi/hyperspectral imaging [108] \* Very High Very High Low to Very Low SST, RGB images (Dependant on additional sensors equipped) Requires Ground truthing

**Table 2.** Optical techniques rated by cost, spatial scale, spatial resolution, and additional data gathered.

HyFi: hyperspectral fluorescence imaging, UUV's: unmanned underwater vehicles, SST: Sea surface temperatures. \* Based on total cost of building and launching into orbit.

**Table 3.** Guide to rankings for each classification outlined in Table 2.


**Table 4.** An outline of the ability of the different optical techniques to assess important criteria used in coral surveyance as outlined by Leujak and Ormond, 2007 [103].


\* Repeatability was defined as the possibility of returning to exactly the same sampling unit in future monitoring.
