TITLE: An email about hemispherical photography
DATE: 2018-09-02
AUTHOR: John L. Godlee
====================================================================


This is a transcript of an email conversation with a colleague that
I had about hemispherical photography and the various merits of
different methods. I thought the content was useful and wanted to
record it so I’ve put it up here. I’ve cleaned up the email a tiny
bit, just to make things clearer.

Colleague’s email

 Dear John,

 My supervisor suggested that I get in contact regarding your
 knowledge of a new hemispherical camera that she thinks you’re
 using in your research. I’m not sure if it’s the tool for the job,
 but I’m trying to map the canopy cover of a very small area of
 woodland in the Scottish Borders.

 One part of my PhD research is looking at the influence of this
 strip of mixed woodland on downslope soil moisture and groundwater
 dynamics, so I’m mainly gathering sub-surface data on a transect
 across the woodland. However, I also need to estimate canopy cover
 in summer/winter as well as the extent of shading on the land
 either side of the woodland.

 I’m a geologist, not and ecologist, and I’m sure there are
 standard methods for doing this, so if you have any thoughts
 either using the hemispherical camera or other methods, I’d be
 interested in any quick thoughts that you have.

 Best wishes,

My reply

 Hi,

 Yep I got some money from the School last semester to buy some
 hemispherical photography gear for the equipment store, which is
 free to use. The available equipment consists of:

 -   1x Nikon D750 Digital SLR Camera (24.3 MP) 3.2 inch
     Tilt-Screen LCD with Wi-Fi
 -   1x SIGMA 8mm f/3.5 EX DG Circular Fisheye Lens (Nikon fit)
 -   1x Nikon 24-120mm f4 G AF-S ED VR Lens
 -   1x KamKorda Professional Camera Bag
 -   1x Neewer Hot Shoe Three Axis Bubble Spirit Level
 -   1x SanDisk UHS-II 3.0, SD Card Reader (In the post)
 -   2x Sandisk Ultra microSDHC 16GB - 80MB/s Class 10 UHS-I
 -   1x PeliCase 1520 Case With Foam - Orange

 I’ve used this camera to estimate canopy cover of savannas in
 southern Africa and I can only imagine that it would work fine for
 your patch of woodland as well.

 When you say “map” do you mean get a spatially explicit estimate
 of the canopy cover throughout the site? I’ve only ever used
 hemispherical photography to get a single plot level estimate of
 the canopy cover. Basically the mean and variance of the
 percentage canopy cover as estimated from many photographs taken
 at points on a regular grid laid out in the woodland area. Each
 photo is essentially a point estimate of the canopy cover. You
 could probably do a map, but you would have to increase the
 density of the grid quite a bit to truly capture the variation
 over space. To give you a rough idea, on a 100x100 m (1 Ha) plot,
 I normally take 100 photos to get a plot level estimate. Taking
 the photos doesn’t take very long at all, but setting up the grid
 can be a faff if the woodland is thick.

 Processing the hemispherical images can be a pain but is fairly
 automated once you have a workflow set up. In the past I’ve used
 imageJ ([https://imagej.net/Welcome]), and if you only want to
 estimate percentage canopy cover then I see no problem with using
 it. I have some imageJ macros to batch analyse images if you want.
 If you want to estimate more advanced things like Leaf Area Index
 (the unit leaf area per unit ground area) or available
 Photosynthetically Active Radiation below the canopy, you will
 need to use something more advanced. I’ve recently discovered a
 set of R scripts collectively known as HemiPhot
 ([https://github.com/naturalis/Hemiphot]) which can estimate these
 parameters.

 The main thing to remember when taking hemispherical photos of the
 canopy is that you have to do them early in the morning or late in
 the evening, before the sun is overhead and too bright but with
 some ambient light, otherwise you will find that you get a sun
 flare on the lens, which makes the image basically unusable for
 analysis.

 I’ve attached a few papers which you can read if you want to on
 the subject of how hemispherical photography (and other methods)
 is used in forest/woodland/plantation contexts to estimate tree
 canopy structure. By no means should you read them all, but they
 might be useful further down the line.

 There are other methods for estimating canopy cover, but having
 experimented with most of them, I think hemispherical photography
 gives the most accurate result. Other options are to use a convex
 mirror densiometer
 ([http://www.forestry-suppliers.com/Images/Original/1397_43887_p1.jpg])
 or to use a periscope densitometer
 ([http://www.grsgis.com/densitometer.html]). The periscope
 densitometer might be an option for making a high point density
 map of your site, as the measurements are quite quick so you can
 do more of them. The periscope densitometer method just requires
 you to talk along the grid and at each point take a yes/no reading
 of whether there is canopy touching the crosshairs of the
 periscope mirror. You wouldn’t be able to make a map of percentage
 canopy cover with the periscope densitometer, only a plot level
 estimate as it uses the binomial nature of the measurement (yes or
 no) to statistically estimate percentage cover, the value of each
 point on its own isn’t useful. I wouldn’t EVER recommend the
 convex mirror densiometer as they suffer from pretty serious
 researcher bias.

 Measuring the shade on the land either side of the woodland would
 require a different method I think, though I’ve never done it
 myself. I get the impression that in a closed canopy woodland at
 this high a latitude, you could assume that when the path from the
 Sun to the open ground adjacent to the woodland is blocked by the
 woodland, all the direct sunlight is blocked. Considering this,
 you could just measure the maximum tree height at increments along
 the edge of the woodland using a clinometer or a laser range
 finder, measure the orientation of the woodland edge, then use
 that to model how long the shadow is at different times of the
 year and how many hours during the day a given distance from the
 woodland is shaded as the angle of the Sun changes. This has some
 assumptions/caveats though, 1) the woodland is thick enough to
 block all direct sunlight, and 2) the boundary of the woodland
 edge is a straight line. If the woodland edge isn’t a straight
 line it gets marginally more difficult as you would have to
 include more measurements of the distance of the woodland edge
 into your calculations of shade at different points.

These are the papers I attached:

-   Jonckheere et al. (2004). Review of methods for in situ leaf
   area index determination Part I. Theories, sensors and
   hemispherical photography
-   Breda (2003). Ground-based measurements of leaf area index: a
   review of methods, instruments and current controversies
-   Welles & Cohen (1996). Canopy structure measurement by gap
   fraction analysis using commercial instrumentation
-   Korhonen et al. (2006). Estimation of Forest Canopy Cover: a
   Comparison of Field Measurement Techniques
-   Pekin & Macfarlane (2009). Measurement of Crown Cover and Leaf
   Area Index Using Digital Cover Photography and Its Application
   to Remote Sensing
-   Gardingen et al. (1999). Leaf area index estimates obtained for
   clumped canopies using hemispherical photography
-   Cook et al. (1995). Spherical Densiometers Produce Biased
   Estimates of Forest Canopy Cover
-   Fournier & Hall (eds.) (2017). Hemispherical Photography in
   Forest Science: Theory, Methods, Applications

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