A spectrophotometer was used to scan the canopy vegetation at four sites along Imnavait Creek in the Kuparuk Watershed near Toolik Lake LTER, Alaska. The resulting reflectance spectra were used to calculate average vegetation indices for each site and collection day.
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The Imnavait watershed is equipped with four instrument towers associated with the AON project . The Fen Tower , the Mid-Ridge Tower and the Ridge Tower all have instrument arrays for Eddy Covariance analysis of CO2 fluxes. The Radiation Tower is equipped with instruments for monitoring weather. Canopy vegetation within the footprint of each of these towers was scanned with a handheld spectrophotometer several times throughout the 2008-2010 growing seasons and average vegetation indices were calculated for each site and collection day. More information about these sites is available through the AON project website (http://aon.iab.uaf.edu/AON_IC_Site_Location.html).
A spectrophotometer measures incoming irradiance and radiance reflected by the canopy vegetation. The ratio of these signals (irradiance to reflected radiance) is used to generate a reflectance spectrum. In 2008, a single channel spectrophotometer was used (Unispec SC, see INSTRUMENTATION) to perform these measurements. In 2009 and 2010 either a single or a dual channel (Unispec DC, see INSTRUMENTATION) was used.
On each collection day, replicate scans were performed at each site in the footprint of the instrument towers. An aluminum "T" frame was used to position the spectrophotometer’s foreoptic cable at a consistent height and orientation relative to the vegetation. When using this frame, the foreoptic cable is 1.09m above the vegetation and has a field of view with a radius of approximately 40 cm.
Data was processed and interpolated to the nanometer using the program Multispec V.5 (available at http://specnet.info/specnet_toolkit.htm).
Single channel spectrophotometer:
A single channel spectrophotometer (Unispec SC, PP Systems, Amesbury, Massachusetts, USA) uses one foreoptic cable to measure first incoming irradiance and then radiance reflected by the vegetation canopy. The foreoptic cable (UNI-684) extends from the machine and is equipped with a ferrule over which a 100mm hypotube (UNI-688) is placed. This produces a field of view that extends at an angle of 20 degrees from the end of the hypotube. The hypotube is held vertically over the target vegetation during a data scan. The foreoptic cable is connected to a miniature photodiode array detector in the instrument that produce signals ranging from zero to 65,000 A/D counts for 256 wavebands. These wavebands represent 3.3 nm wide portions of the visible and near infrared spectrum from 310 to 1100 nm. A scan is performed over a period of milliseconds with the exact integration time determined by the user based on current light conditions.
At the time of data collection, a reference scan is performed by positioning the foreoptic cable over a white standard (UNI-420). This reference scan represents the incoming irradiance due to the highly reflective nature of the white standard. A dark scan is also performed by covering the foreoptic with a dark cloth. The raw signal from the dark scan is used by the machine to correct for background noise. Canopy reflectance is calculated for each waveband as follows :
Reflectance= (Icanopy / Ireference)
Icanopy= signal from foreoptic during data scan (radiance reflected from target vegetation)
Ireference= signal from the foreoptic during reflectance scan (incoming irradiance)
Dual channel spectrophotometer:
A dual channel spectrophotometer (Unispec DC, PP Systems, Amesbury, Massachusetts, USA) utilizes two foreoptic cables to simultaneously measure incoming irradiance and radiance reflected by the canopy vegetation. One foreoptic cable (UNI-684) is oriented downwards and is equipped with a ferrule over which a 100mm hypotube (UNI-688) is placed. This produces a field of view that extends at an angle of 20 degrees from the end of the hypotube. The other foreoptic cable (UNI-686) is oriented upwards and is fitted with a cosine receptor (UNI-435). The two foreoptic cables are connected to two miniature photodiode array detectors that produce signals ranging from zero to 65,000 A/D counts over 256 wavebands. These wavebands represent 3.3 nm wide portions of the visible and near infrared spectrum from 310 to 1100 nm. A scan is performed over a period of milliseconds with the exact integration time determined by the user based on current light conditions.
At the time of data collection, a dark scan is performed by covering the foreoptics with a dark cloth. The raw signals from the dark scan are used by the machine to correct for background noise. A reference scan is also performed by positioning the downward foreoptic cable over a white standard (UNI-420). Canopy reflectance is calculated for each waveband as follows:
Reflectance= (Idata down / Idata up) x (Ireference up/ Ireference down)
Idata down = signal from downward foreoptic during data scan (radiance reflected from target vegetation)
Idata up = signal from the upward foreoptic during data scan (incoming irradiance)
Ireference up= signal from the upward foreoptic during reflectance scan (incoming irradiance)
Ireference down= signal from the downward foreoptic during reflectance scan (radiance reflected from white standard)
VEGETATION INDEX CALCULATIONS:
For MODIS indices, Spectral bands are defined as follows:
Normalized Difference Vegetation Index
NDVI (MODIS) = (NIR-Red)/(NIR+Red)
Enhanced Vegetation Index
EVI (MODIS) =2.5*(NIR-Red)/(NIR+6*Red-7.5*Blue+1)
Enhanced Vegetation Index 2
EVI2 (MODIS) =2.5*((NIR-Red)/(NIR+2.4*Red+1))
Photochemical Reflective Index
PRI (550 Reference) =(550nm-531nm)/(550nm+531nm)
Photochemical Reflective Index
PRI (570 Ref) = (570nm -531nm)/(570nm+531nm)
Water Band Index
Reflectance values equal to or greater than one were replaced with "NaN" before indices were calculcated. Reflectance values equal to or less than zero were also replaced with "NaN" before vegetation indices were calculated.
Vegetation Indices were calculated for all replicate scans and were then averaged to produce the values and standard deviations presented here.
OTHER DATA FILES TO REFERENCE:
FOR MORE INFORMATION CONTACT: Gus Shaver, The Ecosystems Center, Woods Hole, MA, 02543, USA
FORMAT OF DATA FILE: ASCII
Updated Metadata sheet
Version 2: Checked keywords against the LTER network preferred list and replaced non-preferred terms. Jim L 15Jan14
June 2019-Version 4: Changed site names/descriptions to be consistent with flux data sets. Added XML for ADC harvesting. BK
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