# Sensitivity of Common Vegetation Indices to the Canopy Structure of Field Crops
## Materials and Methods  
### Study Area and Field Measurements  
This study was carried out at the Viikki agricultural test field located in Helsinki (Finland) (60.224\({}^{\circ}\)N, 25.021\({}^{\circ}\)E). The size of the research area was approximately 4 km \(\times\) 4 km. The annual average temperature in Helsinki is 6 \({}^{\circ}\)C; in July, the average temperature is 18 \({}^{\circ}\)C. Six crop species were included in this study growing on 162 plots: faba bean (_Vicia faba_ L. \"Kontu\"), narrow-leafed lupin (_Lupinus angustifolius_ L. \"Haags Blaue\"), turnip rape (_Brassica rapa_ L. ssp. _oleifera_ (DC.) Metzg. \"Apollo\"), wheat (_Triticum aestivum_ L. emend Thell. \"Amaretto\"), barley (_Hordeum vulgare_ L. \"Streif\", \"Chill\" and \"Fairytale\") and oat (_Avena sativa_ L. \"Ivory\" and \"Mirella\"). The largest plots were 600 m\({}^{2}\) (50 m \(\times\) 12 m) and the smallest ones 20 m\({}^{2}\) (10 m \(\times\) 2 m). The soil types in the area were fertile luvic stagnationol, haplicleysol and sulfc cryaquet. The plots differed in seeding density (55-700 m\({}^{-2}\)) and fertilizer treatment (0-150 kg N m\({}^{-2}\)) leading to LAI range of 1.1-5.0 and a chlorophyll content range of 26-94 \(\upmu\)g cm\({}^{-2}\) (see the Table 1 in the reference [20]). Canopy leaf-angle distribution was determined using the photographic approach [17], validated and extended to field crops [20] on 6 July 2012 in the same growth stage as during the spectroscopy measurement. Canopy photographs were taken using a Nikon D1X digital camera mounted on a tripod and leveled with bubble level outside of the plots approximately 1 m away from the edge of the field. The camera height was between 30 and 50 cm depending on crop height. Five to six photographs were taken for each species from one or several plots. Finally, the inclination angles of 75-100 leaves or leaf fragments oriented perpendicularly to the viewing direction were measured using ImageJ 1.47 software, which is an open source image processing program [34], and used for the calculation of the leaf mean tilt angle (MTA). We assumed LAD to be species-specific, as it has been shown to vary more among species than within species [8; 13; 35]. A more detailed description of the test site and the photographic method was given by [PERSON] et al. [20]. Airborne spectroscopy imagery covering the study area was acquired using an AISA Eagle II imaging spectrometer (Specim Ltd., Oulu, Finland) on 25 July 2011. The data were collected between 09:36 and 10:00 local time at approximately 600 m above ground. The flight direction was parallel with the sunrays. The solar zenith angle varied between 50.4\({}^{\circ}\) and 48.1\({}^{\circ}\) and the measurement zenith angle between 0 and 18.9\({}^{\circ}\) was determined by the swath width of the sensor and aircraft orientation changes. Reflected radiation was measured in 64 channels in the visible and NIR spectrum (400-1000 nm) with a spectral resolution of 9-10 nm and a spatial resolution of 0.4 m. The spectroscopic imagery was radiometrically calibrated using the CaliGeo 4.9.9 software package (Specim Ltd., Oulu, Finland) and georectified using Parge (ReSe Applications Schlapfer, Wil, Switzerland). Finally, the radiometric data were converted to top-of-canopy hemispherical-directional reflectance factors using ATCOR-4 (ReSe Applications Schlapfer, Wil, Switzerland). The spectroscopic data were extracted from the imagery and averaged as average plot spectra. A SunScan ceptometer (Delta-T Devices, Cambridge, UK) was used to measure LAI in the field. The data used in this study were collected within five days of the airborne campaign. The SunScan ceptometer bar was entered from the edge of the plot at approximately 45\({}^{\circ}\) to the row direction to minimize the row effects on LAI measurement as suggested in the instrument manual. LAI was calculated from the measured transmittance following the model implemented in the SunScan hardware.