Computational protocol: The Effect of Leaf Stacking on Leaf Reflectance and Vegetation Indices Measured by Contact Probe during the Season

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Protocol publication

[…] After reflectance measurements, fresh leaves were scanned and the leaf area determined by ImageJ freeware. Then the leaves were dried and weighed for assessment of LMA (leaf mass per area unit). The leaf water content was determined as the percentage of water in the fresh leaves (the fraction of weight decrease after drying at 80 °C for 48 h until constant weight) and EWT (equivalent water thickness) was calculated according to []. The total chlorophyll content was determined in dimethylformamide extract using a spectrophotometric assessment based on the equations reported in []. [...] According to Cavender-Bares [] we divided full leaf spectra to four spectral ranges: VIS (400–700 nm), NIR (740–1140 nm), SWIR1 (1500–1800 nm) and SWIR2 (2000–2400 nm). In purpose of quantification the effect of the MS in those spectral ranges, the difference between the reflectances measured on a leaf stack of 5 leaves and a single leaf (i.e., 1 leaf), (R5L subtraction R1L = ∆R5L–1L), was calculated for each wavelength. Thus, the value of ∆R5L–1L expresses the additional variability in leaf spectra introduced by increasing LAI, LMA and the internal leaf surface area as a potential scattering interface. Stacking of the leaves in a laboratory can be regarded as approximation of the contact measuring setup to the measurement at the canopy level.Vegetation indices were computed in the statistic program R-3.2.3 (the open source version of Statistica) from the reflectance measured in both measurement setups (a single leaf, a leaf stack). In total, 74 pigment-related indices and 7 water-related indices were determined. For all tested indices and their references see . For demonstration of temporal dynamics of the selected indices, their values were transformed into standardized z-scores to enable their comparability and independence of their physical dimensions. Z-scores generally express how far from the mean the particular value is in terms of the standard deviations. […]

Pipeline specifications

Software tools ImageJ, Statistica
Applications Miscellaneous, Microscopic phenotype analysis
Chemicals Chlorophyll