# Nearshore Benthic Mapping in the Great Lakes:
## 2 Materials and Methods
### Airborne Data Pre-Processing  
Airborne hyperspectral imagery (HSI) and topobathymetric lidar data were collected by the JALBTCX over the study area using the CZMIL system. This system is an integrated sensor suite that includes a circular scanning lidar system, an Itrees Compact Airborne Spectrographic Imager (CASI)-1500 hyperspectral sensor, and a true-color digital frame Phase One 150 MP camera with a sensor fusion concept for improved coastal mapping (benthic classification, water column characterization, etc.) in challenging shallow water environments that are often turbid or have breaking waves [34,35]. Eight shore-parallel flights were flown at 400 m altitude on 17 July 2018 on a fixed-wing aircraft. The CASI-1500 was programmed to collect 48 spectral bands (375-1050 nanometers; 14 nanometer bandwidth) at 1 m spatial resolution, offering advantages with high spectral resolution (narrow bands) that have shown utility for seafloor mapping in shallow, turbid waters [8,9,12,19,23]. Topobathymetric lidar data were collected using the Teledyne Optech CZMIL Nova system including 10 kHz bathymetric full waveform lidar (green laser in the 532 nanometer wavelength) with the effective rate increased to 70 kHz on land and in optically shallow water using a segmented detector [34]. The CZMIL collected lidar data with topographic and shallow channel bathymetric point densities of 2 points per square meter (nominal point spacing of 0.7 m) and deep channel bathymetric point densities of 0.25 points per square meter (nominal point spacing of 2 m); in this region, the CZMIL switched from shallow to deep channel coverage at approximately the 9 m depth mark. Unlike passive sensors, active sensor technology like lidar measures time of flight from light pulses emitted from  
Figure 1: Study area at southwest Lake Michigan, USA. the sensor to estimate depth using the 532 nanometer (green) wavelength for seafloor applications [8,9]. Maximum possible depth for this survey occurred at 14 m (\(\pm\)0.5 m). Both the HSI and topobathymetric lidar data were pre-processed using Teledyne's HydroFusion software and the standard National Research Council's Committee on Data Management and Computation (CODMAC) levels for HSI and lidar data pre- and post-processing as well as product generation to prepare data for analysis. For the HSI, HydroFusion standard pre-processing procedures included (1) radiometric calibration (conversion of digital numbers to at-sensor radiance), (2) geometric correction for distortion removal using topobathymetric lidar data, (3) water glint and ripple correction, (4) atmospheric correction to surface reflectance adapted from the Simple Model of the Atmospheric Radiative Transfer of Sunshine (SMARTS) model [36] developed by the National Renewable Energy Laboratory [37] resulting in a 1 m spatial resolution mosaicked image (personal communication [PERSON], USACE). HydroFusion software was also used to conduct standard lidar pre-processing in which lidar point clouds were classified and used to generate seamless topobathymetric first return and bare earth digital elevation model grids at 1 m spatial resolution. Additional products generated from the standard products in HydroFusion software included the following: (1) bathymetry grid, (2) water-leaving hyperspectral reflectance image (atmospherically corrected reflectance; water surface and water column were not removed) with 29 spectral bands between 375 and 780 nanometers (spectral subset from the 48 bands), and a (3) fusion image (atmospherically corrected with sun glint and water ripples, water surface rugosity, removed and scaled and resampled to match the lidar depth grid) with 48 spectral bands between 380 and 1050 nanometers (Figure 2, panels a-c). The water-leaving reflectance (WLR) and fusion (FU) images were further transformed to reduce data dimensionality and noise using the Minimum Noise Fraction (MNF) transform tool in ENVI v5.5 (L3 Harris Geospatial, Boulder, Colorado) software.