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.jp
g]) 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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