Arctic LTER Database

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Shaver, G. 1989. Above ground biomass in acidic tussock tundra experimental site, 1989, Arctic LTER, Toolik, Alaska. Arctic LTER, Marine Biological Lab, Woods Hole, Ma 02543. 1989gsttbm http://ecosystems.mbl.edu/arc/terrest/biomass/index.shtml 

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Data sets were provided by the Arctic LTER. This material is based upon work supported by the National Science Foundation under Grants #DEB-981022, 9211775, 8702328; #OPP-9911278, 9911681, 9732281, 9615411, 9615563, 9615942, 9615949, 9400722, 9415411, 9318529; #BSR 9019055, 8806635, 8507493.

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Dataset URLs:METADATA: HTML, Rich Text, XML(EML compliant)
DATA: Comma Delimited, Excel file with Metadata and data, Dataset via LTER Data Poral
Dataset ID:2008-2010gsImnavaitindices.02
Dataset Title:Vegetation indices calculated from canopy reflectance spectra at four sites along Imnavait Creek, AK during the 2008-2010 growing seasons.
Investigator 1: 
First Name:Gus
Last Name:Shaver
Organization:The Ecosystems Center, MBL
Address line 2:7 MBL St.
Address line 3:
City:Woods Hole
State:MA
Zip Code:02543
Country:USA
Associate Investigators:
Keywords:canopies, reflectance, spectra, vegetation indices, radiation, irradiance, normalized difference vegetation index, MODIS, Enhanced Vegetation Index, Enhanced Vegetation Index 2, Photochemical Reflectance Index, Water Band Index, chlorophyll, Imnaviat, disturbance
Abstract: 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.
For questions about the Metadata and data contact the Investigators.
For information about this web site contact:
Arctic LTER Information Manager
The Ecosystems Center
Marine Biological Lab
7 MBL St
Woods Hole, MA 02543
Phone (508) 289 7496
Email: arc_im@mbl.edu
Online URL: http://ecosystems.mbl.edu/ARC/
DATA FILE INFORMATION:
Data File URL http://metacat.lternet.edu/das/dataAccessServlet?docid=knb-lter-arc.10155&urlTail=AON/reflectance/data/2008-2010gsImnavaitindices.csv
Data File Name 2008-2010gsImnavaitindices
Beginning Date 6/13/2008
End Date 7/31/2010
Number of Data Records 79
Other Files to Reference 2008-2010gsImnavaitspectra.csv
Availability Status Type 1
Quality Control Information Reflectance values greater than one or less than zero were replaced with "NaN" before vegetation indices were calculated
Maintenance Description
Log of Changes: Updated Metadata sheet
Version 2: Checked keywords against the LTER network preferred list and replaced non-preferred terms. Jim L 15Jan14
 
RESEARCH LOCATION:          
Location Name Fen Tower Site Mid-ridge Tower Site Radiation Tower Site Ridge Tower Site  
Geographic Description Fen Tower Site Mid-ridge Tower Site Radiation Tower Site Ridge Tower Site  
Location Bounding Box          
West Bounding Coordinate          
East Bounding Coordinate          
North Bounding Coordinate          
South Bounding Coordinate          
OR if single point location          
Latitude 68.606 68.606 68.613 68.607  
Longitude -149.311 -149.304 -149.313 -149.296  
Elevation 920m 930m 920m 940m  
Link to Google Map View on Google Map View on Google Map View on Google Map View on Google Map  
           
 
TAXONOMIC COVERAGE:
Organisms studied
 
Methods:METHODS
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).


INSTRUMENTATION
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:

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)

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:
2008-2010gsImnavaitspectra.dat

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

FORMAT OF DATA FILE: ASCII

Data Table

Variable Name Variable Description Data Type Units DateTime Format Code Information Missing Value Code
Site Area where reflectance scans were performed, all named for their corresponding instrument tower text        
Date Day of data collection datetime   DD-MMM-YYYY    
Count of Rep Number of replicate scans performed on the plot. Index values were calculated for each scan and then averaged. number dimensionless     NaN=Missing or Not Measured
Average of NDVI (MODIS) Average value of calculated NDVI (see METHODS, CALCULATIONS) number dimensionless     NaN=Missing or Not Measured
StdDev of NDVI (MODIS) Standard Deviation of averaged NDVI (see METHODS, CALCULATIONS) number dimensionless     NaN=Missing or Not Measured
Average of EVI (MODIS) Average value of calculated EVI (see METHODS, CALCULATIONS) number dimensionless     NaN=Missing or Not Measured
StdDev of EVI (MODIS) Standard Deviation of averaged EVI (see METHODS, CALCULATIONS) number dimensionless     NaN=Missing or Not Measured
Average of EVI2 (MODIS) Average value of calculated EVI2 (see METHODS, CALCULATIONS) number dimensionless     NaN=Missing or Not Measured
StdDev of EVI2 (MODIS) Standard Deviation of averaged EVI2 (see METHODS, CALCULATIONS) number dimensionless     NaN=Missing or Not Measured
Average of PRI (550 Reference) Average value of calculated PRI, 550 reference (see METHODS, CALCULATIONS) number dimensionless     NaN=Missing or Not Measured
StdDev of PRI (550 Reference) Standard Deviation of averaged PRI, 550 reference (see METHODS, CALCULATIONS) number dimensionless     NaN=Missing or Not Measured
Average of PRI (570 Ref) Average value of calculated PRI, 570 reference (see METHODS, CALCULATIONS) number dimensionless     NaN=Missing or Not Measured
StdDev of PRI (570 Ref) Standard Deviation of averaged PRI, 570 reference (see METHODS, CALCULATIONS) number dimensionless     NaN=Missing or Not Measured
Average of WBI Average value of calculated WBI (see METHODS, CALCULATIONS) number dimensionless     NaN=Missing or Not Measured
StdDev of WBI Standard Deviation of average WBI (see METHODS, CALCULATIONS) number dimensionless     NaN=Missing or Not Measured
Average of Chl Index Average value of calculated Chl index (see METHODS, CALCULATIONS) number dimensionless     NaN=Missing or Not Measured
StdDev of Chl Index Standard Deviation of averaged Chl index (see METHODS, CALCULATIONS) number dimensionless     NaN=Missing or Not Measured