Scanopy, an advanced canopy analysis system for scientific research
Canopy Analysis
With Fish-Eye Imaging

WinSCANOPY 2006a

New Measurements & Features

Gap Size Distribution Analysis (Pro)

Gap size distribution (GSD), i.e. the number of gaps in function of their size, can be used in combination with gap fractions to quantify the degree of clumpiness at the tree level and to use this information to increase the accuracy of LAI measurements. For a canopy of a given gap fraction with randomly distributed foliage elements, it is possible to make a theoretical probability of gaps occurring in function of their size. By comparing the measured GSD to this theoretical distribution, foliage clumpiness can be measured.

At the base of GSD analysis, is the classification of gaps in two categories; those which are normally expected for a given randomly distributed leaf area and those which are not. The latter are larger gaps that are present because of foliage clumping at the crown level and can be seen between tree crowns. These are called between-crown gaps while random gaps are called within-crown gaps. WinSCANOPY has two methods of classifying gaps into these two groups; Chen and Cihlar 95's method based on transect length (a one dimensional data), which is also used in a sunfleck based commercial instrument, and a new simpler, but efficient, method of our own based on gap area (a two dimensional data).
GSD analyses can be done on hemispherical or cover images. Between-crown gaps are drawn in blue,
within-crown gaps are drawn in yellow.
Other features of GSD
> On-screen visualisation of between-crown and within-crown gaps. Can also be saved to standard tiff image files.
> The automatic gap classification can be modified with simple mouse clicks. It can also be done completely manually.
> Clumping index is measured in function of view zenith angle and globally for the hemisphere or for any view angles range that you choose. Clumping index in function of zenith can be displayed in the graphic above the image during the analysis.
Canopy Cover Images Analysis (Pro)

Canopy cover images have a narrow view angle (5 to 25 degrees) directed toward the zenith or close to it (see figure below). This kind of analysis is an alternative method to hemispherical images analysis to compute LAI and other canopy structural parameters (crown porosity, crown cover, foliage cover, clumping index).

Full-Frame Fish-Eye Images Analysis (Pro)

Full-frame fish-eye images are acquired with a fish-eye lens but do not have a circular projection. The 180 degrees (or less) typical field-of-view spans over the diagonal of the image sensor rather than the vertical image dimension. For a given image sensor size, a full frame fish-eye image is obtained by using a fish-eye lens with a longer focal length than a regular fish-eye circular projection lens or simply by zooming in. One of their advantage is to increase the effective image resolution as all pixels are used for canopy and sky information (no black pixels). The analysis that can be done on these images are identical to those of regular fish-eye images.
Standard fish-eye image
Full-frame fish-eye image
Cover image
Two methods to measure LAI or leaf density of isolated tree

One method (Pro) was first described by Lindsey and Bassuk 1992 and later modified and tested by Peper and McPherson 1998. The other (Reg) is a modification to the LAI2000 LAI method which consists in substituting the default normalized path lengths for those of the tree canopy (length traveled by light in the canopy at the five rings view angle).

Individual leaf area measurement from non fish-eye images (Pro)

Turns WinSCANOPY into a basic individual leaf area meter, disease quantifier (see WinFOLIA for more sophisticated measurements) and soil foliage cover quantifier.

An additional LAI method (Reg): Spherical leaf angle distribution (with and without the logarithm average correction for clumping)

Leaf projection coefficient in function of view zenith angle (Reg)
Highest obstruction per azimuth analysis (Basic)

It gives the zenith angle of the highest obstacle (canopy, building or any object other than sky) in function of azimuth. Useful for shading analysis (solar panels, architecture) and communication equipment site comparisons.
Improvements to existing features
  • Automatic pixels classification is more accurate over a larger range of situations (from low to dense canopy cover).
  • You can choose among two light attenuation profiles when using the Solar and Zenith Thresholds. One is linear (as before), the other is like the SOC (Standard Overcast Sky) diffuse sky light distribution. You can also choose the amplitude of the attenuation.
  • There are more flexible pixels classification interactive adjustments. Modifications can now be done on pre-defined circular shapes (in addition to the previously available free-style regions made with the lasso tool) that can be centered on the zenith (per sky ring) or the sky brightest position.
  • The graphic above the image has three new data types; gap size distribution, clumping index and leaf projection coefficient in function of zenith.
  • It is now possible to analyse hemispheres that extend beyond the image boundary. Useful when the hemisphere radius is large (close to the image vertical size).
  • The Masks/New/Parametric command is faster.
  • During hemisphere creation, it is possible to display only its four edges simultaneously to ease the hemisphere centering in the region to analyse (for those who do not use our calibration).
  • The north direction indicator can be rotated faster (during an hemisphere creation).
  • Radiation received takes into account slope and aspect.
  • You can choose the zenith view angle at which the Bonhomme and Chartier LAI method is calculated. 57.5 degrees is the default.
  • The sky grid and suntracks can be displayed while the panoramic display mode is active. When you click it, the relevant information (zenith, orientation...) are displayed in the command area.
  • The clumping factors have been replaced by their reciprocal called clumping indexes (clumping index = 1.0/clumping factor). This allow to compare them to the new ones calculated by the gap size distribution analyses.
  • An option to save analysed images during batch analysis (all or a sub-sample of them for a random verification).
  • There are more image magnifications (zoom factors) and a fit-to-screen option (adjusts the magnification so that the image fits entirely in the main window using the maximum area available).
  • The command area is larger so it can display more information.
  • Elevation angles have been replaced by zenith angle. Previous versions used both "elevation" and "zenith" in various commands or data, now it is standardized on zenith.
  • Data/Data File Format has been renamed Data/Information & Global Data and has been simplified (information and data saving can be enabled/disabled by groups of items).
  • Data and information in global data lines have been reordered so that those related are grouped together.
  • In log average LAI methods, (Lang and Xiang 86) you have more choices regarding the processing of regions with a zero gap fraction (no sky pixels). You can choose between a default gap fraction value or a default number of pixels to be classified as gap (typically "1" but it can also be a fraction of a pixel).
  • Choose the number of rings used in the LAI 2000 LAI method.

Bug fixes
> Color channel change is now compatible with batch analysis.
> LAI will be calculated in more situations when masks are used (especially when complete rings are masked).

References

  • Chen J.M. and Cihlar J., 1995, Plant canopy gap-size analysis theory for improving optical measurements of leaf-area index, Applied Optics Vol. 34. no. 27, pp. 6211-6222
  • Lindsey P.A. and Bassuk N. L., 1992. A nondestructive image analysis technique for estimating whole-tree leaf area. HortTechnology, 2 (1) pp. 66-72
  • Peper P. J. and McPherson E. G., 1998. Comparison of five methods for estimating leaf area index of open grown deciduous trees. Journal of Arboriculture, 24 (2), pp. 98-111


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Last Revision: January 23, 2008