## 2 Materials and Methods
### Airborne Hyperspectral Imagery (HSI)  
The airborne HSI was acquired over a period of 5 years from 2011-2016. Two HSI sensors that record complementary regions of the electromagnetic spectrum were used: a Compact Airborne Spectrographic Imager 1500 (CASI-1500, hereafter referred to as CASI) and a Shortwave Airborne Spectrographic Imager (SASI-644, hereafter referred to as SASI) (ITRES Ltd., Calgary, AB, Canada). The programmable CASI samples a maximum of 288 spectral channels between 375 nm and 1054 nm, with 1493-1498 across track pixels, and a field of view of 39.9\({}^{\circ}\). The SASI samples 160 spectral channels from 883 nm to 2523 nm, with 640 across track pixels, and a field of view of 39.7\({}^{\circ}\)[31; 38]. In this study, we used 18 flight-lines from the SASI (2011-2016) for the estimation of the water table position (Table 1). NEE estimation was derived from 4 individual flight lines and 4 full bog mosaics from the CASI (for 2016) (Table 2). The mosaics are comprised of 12 flight lines with a 20% overlap. The higher temporal frequency of HSI acquisition in 2015 and 2016 is due to Mer Bleue being designated a validation site for Sentinel-2 and Landsat 8 OLI satellite data products [39]. Figure 1: **(A)** Shortwave airborne spectrographic imager (SASI) shortwave infrared (SWIR) hyperspectral imagery (HSI) mosaic of 12 flight lines acquired 24 May 2016 (R: 1052 nm G: 1624 nm B: 2122 nm) illustrating the entire bog study area. Location of the eddy covariance tower is indicated. Inset shows the location of Mer Bleue (star) in the Province of Ontario (green); **(B)** nadir UAV photograph from 35 m AGL over the eddy covariance tower; **(C)** UAV photograph looking west towards the eddy covariance tower illustrating the small-scale hummock-hollow microtopography and sparse trees; **(D)** UAV photograph looking south from the eddy covariance tower illustrating one of the beaver ponds with open water, _Typha angustifolia_, and floating _Sphagnum_ moss. Mixed forest on one of the fluvial sand/gravel sections can be seen beyond the beaver pond; **(E)** UAV photograph looking east towards the center of the bog from above the eddy covariance tower. Photographs in b and d were taken 23 June 2016, while c and e were taken 2 July 2017. A 360\({}^{\circ}\) aerial panorama of the site is available at: [[https://bit.ly/mbpano2017](https://bit.ly/mbpano2017)]([https://bit.ly/mbpano2017](https://bit.ly/mbpano2017)). As described in [31], the individual HSI flight lines were spectroradiometrically calibrated to units of spectral radiance (uW cm\({}^{-2}\) sr\({}^{-1}\) nm\({}^{-1}\)). The preprocessing steps to calibrate the imagery from raw digital number to radiance were performed using software modules developed by the sensors' manufacturer [40]. The subsequent geocorrection process was performed using results from a bundling calibration designed to relate the inertial measurement unit (C-MIGITS II) (IMU--a combined GPS and inertial navigation system) to the sensor geometry. The preprocessing modules include an image-based \begin{table}
\begin{tabular}{c c c c} \hline \hline
**Date** & **SZA** & **SAA** & **RAA** \\ \hline \multicolumn{4}{c}{**Spring**} \\ \hline
29 April 2015 & 33.4 & 211.8 & 38.8 \\
6 May 2015 & 29.7 & 163.5 & 180.1 \\
15 April 2016 & 35.3 & 182.1 & 197.6 \\
20 April 2016 & 35.5 & 157.0 & 172.1 \\
27 April 2016 & 44.4 & 122.7 & 145.9 \\
11 May 2016 & 30.1 & 150.5 & 169.0 \\
24 May 2016 & 26.4 & 154.1 & 174.9 \\ \hline \multicolumn{4}{c}{**Summer**} \\ \hline
20 July 2011 & 25.0 & 189.3 & 201.3 \\
10 July 2014 & 32.9 & 125.3 & 128.7 \\
4 June 2015 & 21.1 & 188.4 & 25.2 \\
17 June 2015 & 33.6 & 120.3 & 144.5 \\
28 August 2015 & 36.8 & 196.8 & 27.2 \\
10 June 2016 & 24.7 & 149.5 & 171.8 \\
23 June 2016 & 29.0 & 131.3 & 151.8 \\
24 June 2016 & 35.5 & 116.7 & 137.8 \\ \hline \multicolumn{4}{c}{**Fall**} \\ \hline
18 September 2013 & 44.3 & 168.9 & 173.8 \\
16 September 2015 & 43.7 & 194.3 & 22.5 \\
4 November 2015 & 61.1 & 172.6 & 3.6 \\ \hline \hline \end{tabular}
\end{table}