Summary of three methods used to estimate the Leaf Area Index (LAI) of 19 1m x 1m plots sampled with a point frame near the LTER Shrub plots at the Toolik Field Station in AK the summer of 2012. The methods used were: (1) exponential relationship between LAI and NDVI as measured above the canopy with a Unispec spetroradiometer; (2) Delta-T SunScan canopy analyzer held at 5 cm above the ground under both direct and diffuse light conditions; (3) pin-drop point frame tequnique. Where values have been averaged (such as for the NDVI and SunScan measurements), the standard deviation is given. Raw data are available upon request for the Unispec data; the raw SunScan data is available under the file "PF_SunScan_LAI".
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MAXIMUM CANOPY HEIGHT
We measured the maximum canopy height of each chamber flux and point frame plot by measuring the five highest branches in the shrub canopy. Each height is measured from the soil, defined as the end of the green plant tissue, to the heighest point on each branch. The maximum height was always measured from different individual plants, thus only one branch from any particular plant was sampled even if there might be multiple "highest" branches from a single plant. See the file "MaxCanopyHeight" for more detailed information.
POINT FRAME PIN-DROP METHOD:
We preferentially selected tall shrub canopies dominated either by Betula nana or Salix pulchra, that is canopies that were greater than 75 cm height. Care was taken to select fairly uniform canopies, that is avoiding the edge of a shrub stand or areas where the canopy had a large gaps, suggesting the area may have been disturbed.
We used point frames constructed from a 1.1 m x 1.1 m aluminum square with holes in each corner to accomodate steel rod posts used as the legs of the point frame. In this way, the frame could rest upon the four leg posts that had been hammered into the ground and remain adjustable in each corner. The frame had a level on each side, and great care was taken to ensure that the frame was (a) unable to be pushed deeper into the ground and, (b) level on all four sides prior to taking measurements. These factors were important to the measurement to have accurate data regarding the distance from the frame and the overall height of each point sampled in the canopy.
The aluminum frame had numbered, regularly spaced holes on two opposite sides in order to accomodate a metal bar that could be placed across the frame and locked into place. [These holes on the frame are the row numbers.] The bar that was placed across the frame similarly had numbered, evenly spaced holes in order to accomodate a pin--a long (100-200cm) metal rod with a diameter of ~3.175 mm. [The holes on this bar are the pin hole numbers.] Measurements were only ever taken from odd row numbers, and alternated even/odd pin hole numbers with each row; in this way, for every plot 25 evenly spaced locations were sampled covering an area of one square meter.
The length of the pin was marked every half-centimeter so that the distance could be read easily. Measurements were made by lowering the pin through a pin hole and, once encountering a leaf or stem, recording the following: row#, pin hole#, hit#, and the species hit. If the object hit was not a leaf, the plant tissue was noted; the diameter of each stem hit was estimated in millimeters, and the length of every graminoid blade hit was recorded from the point at which it was hit to the tip. As the primary species of interest for this project were for a select number of species (B. nana, S. pulchra, S. glauca, S. reticulata, V. uliginosum, V. vitis, L. palustre), species that were not the target of interest were classified as functional groups--e.g. graminoid spp., forb, moss. The last pin-hit recorded for each pin hole was always at the "soil" which was considered to be the transition between the green and brown plant material, often in a mossy layer.
In order to calculate the overall LAI as well as the LAI contrubution from each species, the total number of hits for each species was multiplied by 0.04 m2 (the data was calculated both with and without stem-hits).
NDVI and LAI FROM UNISPEC MEASUREMENT:
We measured NDVI on each point frame using a single channel Unipec spectral analysis system (PP Systems Inc, Amesbury, MA, USA). The unispec spectral analyser measures reflected light intensity in 256 portions of the visible spectrum from ~300nm to ~1100nm. A foreoptic cable transmits light reflected from the target to the instrument, a measurement scan lasts for ~15-80ms. Nine scans were measured in a regular grid for each of the point frame plots. The end of the fibre optic was kept approximately 30cm vertically above the top of the canopy. The NDVI values were calculated using the equation below and then the NDVI values averaged together for each of the nine scans. Each scan was corrected for both incident radiation as well as sensor error. The incident radiation was accounted for with a "reference scan" taken by holding the foreoptic cable vertically above a white, reference standard under the same light conditions as subsequent measurements. The scans were also corrected for with a "dark scan" taken with the sensor exposed to complete darkness (covering the sensor input with a black cloth) to account for the intrinsic error in the sensor itself. The program Multispec5.1.5.exe was used to compile and integrate the Unispec reflectance spectra from the raw target spectra.
NDVI quantifies “greenness” and is strongly related to leaf area (Van Wijk and Williams 2005). We measured the NDVI using a single-channel Unispec spectral analyzer (PP systems) and used the equation derived by Street et al (2007) to calculate LAI as dexcribed below.
DELTA-T SUNSCAN LAI METHOD
The data included in this document are only from measurements taken at ground level (~5cm), thus those measurements representing the LAI of the entire canopy. These methods, however, describe all LAI measurements taken with the DeltaT SunScan wand; the complete dataset is available under the title "2012_GS_ITEX_SunScan_LAI".
We measured the LAI using a DeltaT SunScan wand in conjuction with the BF3 sensor (Delta-T Devices Ltd, Burwell Cambridge, UK). The SunScan wand compares indident light readings measured on the BF3 sensor with the 64-PAR readings on the light wand to calculate LAI along the length of the 1m-long wand. LAI was measured by inserting the SunScan wand as near to the ground as possible--typically ~5cm from the ground as the wand rested on top of moss--and then measured vertically every 15 cm with the last measurement being above the canopy. Measurements were taken from the side of the chamber or point frame opposite the sun at three locations under both direct (ambient) and diffuse light conditions . In many cases the replicates at each height were differentiated by row (1-3, or occasionaly 3-8 which correspond to the point frame pins). Typically diffuse light conditions were achieved by shading both the BF3 sensor and the shrub canopy with photographic diffuser panels. On occasion, measurements were taken during cloudy light conditions where the diffuse light fraction was greater than 0.7 and no diffuser panel was needed; on these occasions the direct and diffuse light estimates may have been taken in slightly different locations as they were taken at different times and the precise position of the SunScan wand could not be replicated exactly.
The SunScan wand measures PAR along 64 points along a 1-m horizontal profile. When sampling PAR within the shrub canopy, the data are from the raw output from each PAR sensor. When sampling LAI, there is an internal calculation performed though the Delta-T software that compares the reading above the canopy to the reading within the canopy, and takes into account the percent of absorbed PAR (assumed to be 0.85), and the ellipsoidal leaf angle distribution parameter (ELADP*) (assumed to be 1.0).
In addition to the LAI values, the Delta-T SunScan instrument gives an output of other variables including: transmitted light, spread among sensors, beam fraction, and zenith angle. These values are further described here:
Transmitted Light: the fraction of incident light that passes through a given canopy. It can refer to Direct, Diffuse, or Total incident light.
Spread: the standard deviation of the 64-PAR sensors on the SunScan wand.
Beam Fraction: the fraction of the Total incident PAR in the Direct beam.
Zenith Angle: the angle between the centre of the sun and the point directly overhead.
Zenith angles are calculated from latitude, longitude, and local time using standard astronomical equations as given in Practical Astronomy. The location used to determine the local zenith angle was: 68° 37' 39" N, Longitude 149° 35' 51" W.
*"ELADP is a way of characterizing the horizontal or vertical tendency of leaves in a canopy." p 37 of SS1 User Manual v2.0 (SunScan Canopy Analysis System, type SS1. Delta-T Devices Ltd. May 19, 2008)
NDVI = (RII-RI)
(RI + RII)
where RI = average reflectance from 570nm to 680nm
RII = average reflectance from 725nm to 1000nm.
LAI = 0.0026 * e^(8.0783 * NDVI) - From (Street et al. 2007)
LAI = (Total number of pin-hits) * [(average number of hits per location) / (number of locations sampled)]
LAI = (Total # hits) * (1/25)
Street L. E. Shaver G. R. Williams M. and van Wijk M. T. 2007. What is the relationship between changes in canopy leaf area and changes in photosynthetic CO2 flux in arctic ecosystems? Journal of Ecology 95: 139-150.
van Wijk M. T. Williams M. and. Shaver G. R. 2005. Tight coupling between leaf area index and foliage N content in arctic plant communities. Oecologia 142: 421–427.
This was a season-long project, though it followed similar methods to ITEX projects performed starting in 2003 that are likely to be replicated in the future for reasearch at the Toolik Field Station, AK.
Version 2: Missing values changed to #N/A. CH 28Jan2013
Version 3: Metadata updated to newer form (with sites sheet). CH April 2013.
Version 4: Corrected eml excel file name wrong extension. JimL 16May13
Version 5: Corrected Distrubution URL. It had xlsfiles in the path. Jim L 19Jun14
Version 6: Changed Distrubution URL since the LTER network DAS system is being discontinued. JimL 9Apr2015
Full Metadata and data files (either comma delimited (csv) or Excel) - Environmental Data Initiative repository.
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