Vegetation indices calculated for ITEX harvest plots in 2004-2009 at Toolik, Alaska; Abisko, Sweden; Svalbard, Norway; Zackenberg, Northeast Greenland; and Barrow, Alaska

Abstract: 

A spectrophotometer was used to scan the canopy vegetation of ITEX harvest plots. The resulting reflectance spectra were used to calculate several vegetation indices of interest (NDVI, EVI, EVI2, PRI, WBI, Chlorophyll Index). Average values of these vegetation indices for each ITEX harvest plot are presented here. These plots also had biomass harvests performed and were analyzed for leaf area and nitrogen content (see 2003-2009gsharvest.csv, 2003-2009gsharvestLAI-N.csv).

Project Keywords: 

Data set ID: 

10154

EML revision ID: 

5
Published on EDI/LTER Data Portal

Citation Suggestion: 

Shaver, G. 2012. Vegetation indices calculated for ITEX harvest plots in 2004-2009 at Toolik, Alaska; Abisko, Sweden; Svalbard, Norway; Zackenberg, Northeast Greenland; and Barrow, Alaska Environmental Data Initiative. http://dx.doi.org/10.6073/pasta/273dc3a7f43fb71e90d786fcd69c6c96
People
Dates

Date Range: 

Thursday, July 15, 2004 to Friday, August 14, 2009

Publication Date: 

Wednesday, December 12, 2012

Methods: 

METHODS:
For each ITEX harvest plot, a spectrophotometer (Unispec SC, PP Systems, Amesbury, Massachusetts, USA) was used to scan the canopy vegetation and produce reflectance spectra. The end of the fibre optic was centered above the harvest frame and held at a height above the ground surface that resulted in a view of the vegetation approximately the size of the frame. For most plots, only one replicate scan was performed.

The Unispec SC instrument generates reflectance spectra by measuring incoming irradiance and radiance reflected by the canopy vegetation. A foreoptic cable (UNI-684) extending from the machine 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 using the program Multispec (available at http://specnet.info/specnet_toolkit.htm).:
 
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)
 
In most cases, data was processed and immediately interpolated from 3.3nm wavebands to single nanometer intervals in the Multispec program. For some of the data presented here, the reflectance spectra was originally produced for only for 3.3nm wavebands. This data was later linearly interpolated to produce spectra with 1 nm intervals to allow for compilation into this database.

Reflectance spectra were used to calculate the following vegetation indices for each replicate scan performed. Indices from replicate scans were then averaged to produce the values and standard deviations presented here.

Reflectance values equal to or less than zero were replaced with "NaN" before vegetation indices were calculated.
Reflectance values equal to or greater than one were also replaced with "NaN" before vegetation indices were calculated.

VEGETATION INDEX CALCULATIONS:

For MODIS indices, Spectral bands are defined as follows:
NIR=avg(841nm-876nm)
RED=avg(620nm-670nm)
Blue=avg(459nm-479nm)

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
WBI= 900nm/970nm
Chlorophyll Index
CHL=(750nm-705nm)/(750nm+705nm)

RESEARCH LOCATIONS:

Toolik, AK, USA 2004
18 - 20x20 cm quadrat harvests were collected around Toolik Lake (16 harvests) and the Imnavait Creek watershed (2 harvests). All Toolik Lake harvests were from fertilized plots at the Toolik Lake Long Term Ecological Research Sites.

Abisko, Sweden 2005
12 - 26cm diameter harvests were taken from within ITEX flux plots.

Zackenberg, Greenland 2006
30 - 26cm diameter harvests

Barrow, AK, USA 2009
23- 20 cm diameter harvests

Toolik, AK, USA 2009
54- 20 cm diameter harvests

FOR MORE INFORMATION CONTACT: Gus Shaver, The Ecosystems Center, Woods Hole, MA, 02543, USA

OTHER DATA FILES TO REFERENCE:
2004-2009gsITEXfluxindices.csv (average vegetation indices calculated for all collection days)
2004-2009gsITEXfluxspectra.csv(full reflectance spectra for all ITEX flux plots)
2004-2009gsITEXharvestspectra.csv(full reflectance spectra for all ITEX harvest plots)
2003-2009gsharvest.csv(Data from biomass harvest of ITEX flux plots)
2003-2009gsharvestLAI-N.csv (LAI and N content of biomass harvest of ITEX harvest plots)

FORMAT OF DATA FILE: ASCII

See Methods

Sites sampled.

Download a comma delimited (csv) or Excel file (includes metadata and data sheets).

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