In an effort to make life easiest, I spent some time building out the pipeline entirely in R, including a sourceable function for converting spherical panos to hemispherical images (all available on this repo).

The easiest way to convert all of your spherical panos to hemispherical projections is to source the function from my github:

source("https://raw.githubusercontent.com/andisa01/Spherical-Pano-UPDATE/main/Spheres_to_Hemis.R")

When you source the script, it will install and load all necessary packages. It also downloads the masking file that we will use to black out the periphery of the images.

The script contains the function convert_spheres_to_hemis, which does exactly what is says. You’ll need to put all of your raw spherical panos into a subdirectory within your working directory. We can then pass the path to the directory as an argument to the function.

convert_spheres_to_hemis(focal_path = "./raw_panos/")

This function will loop through all of your raw panos, convert them to masked, north-oriented upward-facing hemispherical images and put them all in a folder called “masked_hemispheres” in your working directory. It will also output a csv file called “canopy_output.csv” that contains information about the image.

Below, I will walk through the steps of the workflow that happened in the convert_spheres_to_hemis function. If you just want to use the function, you can skip to the analysis. I’ve also written a script to do all of the conversion AND analysis in batch in the repo titled “SphericalCanopyPanoProcessing.R”.

library(tidyverse) # For data manipulation
library(exifr) # For extracting metadata

R is not really the best tool for working with image data. So, we’ll use the magick package to call the ImageMagick program from within R.

library(magick) # For image manipulation
# Check to ensure that ImageMagick was installed.
magick_config()$version

You should see a numeric version code like ‘6.9.12.3’ if ImageMagick was properly installed.

# ImageR also requires ImageMagick
library(imager) # For image display

For binarizing and calculating some canopy metrics, we will use Chiannuci’s hemispheR package, which we need to install from the development version.

library(devtools)
devtools::install_git("https://gitlab.com/fchianucci/hemispheR")
library(hemispheR) # For binarization and estimating canopy measures

To get started, you’ll need to have all of your raw equirectangular panoramas in a folder. I like to keep my raw images in a subdirectory called ‘raw_panos’ within my working directory. Regardless of where you store your files, set the directory path as the focal_path variable. For this tutorial we’ll process a single image, but I’ve included scripts for batch processing in the repo. Set the name of the image to process as the focal_image variable.

focal_path <- "./raw_panos/"
focal_image <- "PXL_20230519_164804198.PHOTOSPHERE_small.jpg"

focal_image_path <- paste0(focal_path, focal_image)
focal_image_name <- sub("\\.[^.]+$", "", basename(focal_image_path))

Let’s take a look at the equirectangular image.

pano <- image_read(focal_image_path)
pano # Visualize the pano

Note: One advantage of spherical panos is that they are large, and therefore, high resolution. The images from my Google Pixel 4a are 38 mega pixels. For this tutorial, I downsized the example pano to 10% resolution to make processing and visualizing easier. For your analysis, I’d recommend using full resolution images.

Spherical panoramas contain far more metadata than an average image. We can take a look at all of this additional information with the read_exif function.

read_exif(focal_image_path) %>%
  glimpse()

We’ll extract some of this information about the image, the date it was created, the georeference, and altitude, etc. to output alongside our canopy metrics. You can decide which elements are most important or useful for you.

xmp_data <- read_exif(focal_image_path) %>%
  select(
    SourceFile,
    Make,
    Model,
    FullPanoWidthPixels,
    FullPanoHeightPixels,
    SourcePhotosCount,
    Megapixels,
    LastPhotoDate,
    GPSLatitude,
    GPSLongitude,
    GPSAltitude,
    PoseHeadingDegrees
  )

The first image processing step is to convert the equirectangular panorama into a hemispherical image. We’ll need to store the image width dimension and the heading for processing. The pose heading is a particularly important feature that is a unique advantage of spherical panoramas. Since the camera automatically stores the compass heading of the first image of the panorama, we can use that information to automatically orient all of our hemispherical images such that true north is the top of the image. This is critical for analyses of understory light which requires plotting the sunpath onto the hemisphere.

# Store the pano width to use in scaling and cropping the image
pano_width <- image_info(pano)$width
image_heading <- read_exif(focal_image_path)$PoseHeadingDegrees

The steps to reproject the spherical panorama into an upward-looking hemispherical image go like this:

Crop the upper hemisphere (this is easy with smartphone spheres because the phone’s gyro ensures that the horizon line is always the midpoint of the y-axis).

Rescale the cropped image into a square to retain the correct scaling when reprojected into polar coordinate space.

Project into polar coordinate space and flip the perspective so that it is upward-looking.

Rotate the image so that the top of the image points true north and crop the image so that the diameter of the circle fills the frame.

We can accomplish all of those steps with the code below.

pano_hemisphere <- pano %>%
  # Crop to retain the upper hemisphere
  image_crop(geometry_size_percent(100, 50)) %>%
  # Rescale into a square to keep correct scale when projecting in to polar coordinate space
  image_resize(geometry_size_percent(100, 400)) %>%
  # Remap the pixels into polar projection
  image_distort("Polar",
                c(0),
                bestfit = TRUE) %>%
  image_flip() %>%
  # Rotate the image to orient true north to the top of the image
  image_rotate(image_heading) %>%
  # Rotating expands the canvas, so we crop back to the dimensions of the hemisphere's diameter
  image_crop(paste0(pano_width, "x", pano_width, "-", pano_width/2, "-", pano_width/2))

The resulting image looks funny because the outer pixels are extended by interpolation and we’ve rotated the image which leaves white space at the corners. Most analyses define a bounding perimeter to exclude any pixels outside of the circular hemisphere; so, the weird border shouldn’t matter. But, we can add a black mask to make the images look better.

I’ve included a vector file for a black mask to lay over the image in the repo.

# Get the image mask vector file
image_mask <- image_read("./HemiPhotoMask.svg") %>%
  image_transparent("white") %>%
  image_resize(geometry_size_pixels(width = pano_width, height = pano_width)) %>%
  image_convert("png")

masked_hemisphere <- image_mosaic(c(pano_hemisphere, image_mask))

masked_hemisphere

We’ll store the masked hemispheres in their own subdirectory. This script makes that directory, if it doesn’t already exists and writes our file into it.

if(dir.exists("./masked_hemispheres/") == FALSE){
  dir.create("./masked_hemispheres/")
} # If the subdirectory doesn't exist, we create it.

masked_hemisphere_path <- paste0("./masked_hemispheres/", focal_image_name, "hemi_masked.jpg") # Set the filepath for the new image

image_write(masked_hemisphere, masked_hemisphere_path) # Save the masked hemispherical image

At this point, you can use the hemispherical image in any program you’d like either in R or other software. For this example, I’m going to use Chiannuci’s hemispheR package in order to keep this entire pipeline in R.

The next step is to import the image. hemispheR allows for lots of fine-tuning. Check out the docs to learn what all of the options are. These settings most closely replicate the processing I used in my 2021 paper.

fisheye <- import_fisheye(masked_hemisphere_path,
                          channel = '2BG',
                          circ.mask = list(xc = pano_width/2, yc = pano_width/2, rc = pano_width/2),
                          gamma = 2.2,
                          stretch = FALSE,
                          display = TRUE,
                          message = TRUE)

Now, we need to binarize the images, converting all sky pixels to white and everything else to black (at least as close as possible). Again, there are lots of options available in hemispheR. You can decides which settings are right for you. However, I would suggest keeping the zonal argument set to FALSE. The documentation describes this argument as:

zonal: if set to TRUE, it divides the image in four sectors
(NE,SE,SW,NW directions) and applies an automated classification
separatedly to each region; useful in case of uneven light conditions in
the image

Because spherical panoramas are exposing each of the 36 images separately, there is no need to use this correction.

I also suggest keeping the export argument set to TRUE so that the binarized images will be automatically saved into a subdirectory named ‘results’.

binimage <- binarize_fisheye(fisheye,
                 method = 'Otsu',
                 # We do NOT want to use zonal threshold estimation since this is done by the camera
                 zonal = FALSE,
                 manual = NULL,
                 display = TRUE,
                 export = TRUE)

Unfortunately, hemispheR does not allow for estimation of understory light metrics like through-canopy radiation or Global Site Factors. If you need light estimates, you’ll have to take the binarized images and follow my instructions and code for implementing Gap Light Analyzer.

Assuming all you need is canopy metrics, we can continue with hemispheR and finalize the whole pipeline in R. We estimate canopy metrics with the gapfrac_fisheye() function.

gapfrac <- gapfrac_fisheye(
  binimage,
  maxVZA = 90,
  # Spherical panoramas are equidistant perforce
  lens = "equidistant",
  startVZA = 0,
  endVZA = 90,
  nrings = 5,
  nseg = 8,
  display = TRUE,
  message = TRUE
)

Finally, we can estimate the canopy metrics with the canopy_fisheye() function, join those to the metadata from our image, and output our report.

canopy_report <- canopy_fisheye(
  gapfrac
)

output_report <- xmp_data %>%
  bind_cols(
    canopy_report
  ) %>%
  rename(
    GF = x,
    HemiFile = id
  )

glimpse(output_report)

Rows: 1
Columns: 32
$ SourceFile            "./raw_panos/PXL_20230519_164804198.PHOTOSPHERE_small.jpg"
$ Make                  "Google"
$ Model                 "Pixel 4a"
$ FullPanoWidthPixels   8704
$ FullPanoHeightPixels  4352
$ SourcePhotosCount     36
$ Megapixels            0.37845
$ LastPhotoDate         "2023:05:19 16:49:57.671Z"
$ GPSLatitude           41.33512
$ GPSLongitude          -72.91103
$ GPSAltitude           -23.1
$ PoseHeadingDegrees    86
$ HemiFile              "PXL_20230519_164804198.PHOTOSPHERE_smallhemi_masked.jpg"
$ Le                    2.44
$ L                     3.37
$ LX                    0.72
$ LXG1                  0.67
$ LXG2                  0.55
$ DIFN                  9.981
$ MTA.ell               19
$ GF                    4.15
$ VZA                   "9_27_45_63_81"
$ rings                 5
$ azimuths              8
$ mask                  "435_435_434"
$ lens                  "equidistant"
$ channel               "2BG"
$ stretch               FALSE
$ gamma                 2.2
$ zonal                 FALSE
$ method                "Otsu"
$ thd                   116

Be sure to check out my prior posts on working with hemispherical images.

I am deep in the Alaskan Arctic,  300 miles from the nearest road system, attempting to conduct the kind of science that usually requires a specialized laboratory. We rowed 30 miles of meandering flatwater today, bringing our total to 200 river miles in 12 days since we landed at a lonely gravel bar on the headwaters of Ambler River in Gates of the Arctic National Park.

Mosquitoes spangle the tent canopy arching over me. Backlit by summer solstice sun, the silhouettes of the insects make an inverted night sky of shifting constellations. The sun never sets on the banks of the Kobuk River this time of year. It hangs high above the horizon even now at 11 p.m., transforming my tent into a solar oven as I, ironically, work to uncover the secrets of a frog that can turn into ice.

… Read the rest of the article here.

— I originally wrote this post for the Sitka Conservation Society‘s website in 2014. This trip was part of the Stika Community Wilderness Stewardship Project.

The day we headed out from Hoonah was like most days in Southeast Alaska. Grey clouds diffused the light and an almost imperceptible rain left everything damp. We were headed to the Inian Islands, a cluster of knobby isles on the western end of Icy Strait, just inside the entrance to Cross Sound where the Inside Passage meets the angry Pacific. Our trip held a dual mission: to conduct volunteer wilderness monitoring for the Forest Service and to gather traditional subsistence foods for the Hoonah locals on the trip: Owen James and Gordon Greenwald, our boat captains and wizened culture-bearers, two young men named Randy and Sam, and another adult volunteer, Kathy McCrobie.

The Inians along with two other large islands make up the Pleasant/Lemesurier/Inian Island Wilderness. The PLI Wilderness is one of 19 areas within the Tongass National Forest designated as Wilderness, the highest form of protection public lands can receive. The islands are also historic gathering and hunting grounds of the Huna Tlingit, the native tribe who call this section of northern Southeast Alaska home. Because the Inians are close to the open sea, they are rich with unique flora and fauna. A trip to these distant islands is an opportunity to collect delicacies not common in interior waters near the town of Hoonah. For instance, one of our subsistence targets was black seaweed, a species that thrives in the cold, wave-washed intertidal zone of the outer coast, but is rarely found more than a few miles into the Southeast archipelago.

The outside waters can be a harsh place in the summer and downright inhospitable in the winter. Although the Huna Tlingit are seasoned open ocean travelers and motorized skiffs make the 40-mile journey from the village of Hoonah to the islands much more manageable than a Tlingit canoe, it is still a sizable trip for locals. The same factors—difficult access and a short season—also make it difficult for the Forest Service Wilderness Rangers who are headquartered in Hoonah to access these areas that they are tasked with managing and protecting.

On the first day of our trip we arrived at the Inian Islands after a few hours of skiffing over unusually calm waters. Our first stop was at low tide on a rocky beach, the perfect habitat for Black Katy chitons, one of the traditional foods commonly called Gumboots which we hoped to return with.

The beach also looked like it could be a prime camping area, so while the rest of the crew flipped rocks and pried unsuspecting chitons from their hiding spots, I headed up the beach to look for recreational impacts. Monitoring impacts from visitors is one of the tasks the Forest Service has asked us to assist with. Wilderness areas are intended to preserve nature in its wildest state, but trash, campfire rings, and other signs of previous visitors detract from the wild character of these places. Also, once a site has been impacted, the trend is a downward slope to a trashed site. To prevent cumulative impact, we check known campsites and cleanup and naturalize any human traces we find. Fortunately, this site was in the same condition it’s probably been in since it was uncovered by the glacier, so I spent some time flipping rocks and adding to the gumboots collection.

As the tide neared its apex, Gordon pointed out a small rock island set apart from the larger Inian Islands. For generations, this rock had been the prize destination for Huna families. Set far from land and too small to support trees, the rock is the perfect nesting grounds for seabirds like gulls and cormorants. We had timed our trip perfectly to harvest the new eggs.

As we approached the rock in skiffs, Gordon and Owen explained the protocol: as the swell surges, he runs the skiff up to the rock, one person jumps off, and he pulls the bow away before the swell drops the boat onto the shore, then he resets and we try again for the next person to leap from the bow onto the island. Before they maneuvered the skiffs toward the rock, they carefully taught the boys the traditional method to appropriately harvest the eggs. If done in an ecologically responsible way, these practices will be able to continue forever. (Learn more about the regulations regarding egg collection by Alaskan Natives and locals for subsistence).

Sam was the first to make the jump. The birds immediately erupted in a cacophony of squawks and feathers. Randy and I traded apprehensive glances. I made an excuse that I needed to pack my camera gear in drybags before I could jump…really I just wanted one more chance to see how it was done. Randy landed an impressive leap, despite receiving a bootfull of water. I followed him up the rock.

Blankets of birds flapped above us. The few green tufts of grass made a stark contrast to the guano-bleached stone and the blue-grey sky and water. It took no time for Sam and Randy to collect plenty of eggs to share with family and elders back in Hoonah. With concentration, steady boat handling, and good timing, we all made it safely back aboard the skiffs.

As the day went on, I was impressed with the way Owen and Gordon pointed out new landmarks to the two young men. Every remark about a headland or bay included not only geographical references, but also historical, cultural, and subsistence context. That night, while we ate chowder made with local salmon, smoked octopus, and cockles, I reflected on the education Randy and Sam had inherited on this trip. I have no doubt that they were more interested in learning about hunting spots, edible shellfish, and traditional stories than they were about the Wilderness land designation of their home. But, I would like to think that by relating the cultural values and subsistence practices of the Inian Islands along with the Wilderness values that will continue to protect this place for those practices, they have a better chance of retaining a favorable perspective of public lands, too. In the end, the idea and values of Wilderness are stories, stories that must be repeated and retold to maintain their relevance. Gordon and Owen have endeavored to pass those stories to Hoonah youth. My esteem and thanks goes out to them for including the value of respect for public lands in the stories they tell.

Sunset over Icy StraitThe Inians along with two other large islands make up the Pleasant/Lemesurier/Inian Island Wilderness in Icy Strait, Alaska.

Collecting black seaweedThe Inian Islands are the perfect spot to collect black seaweed, a species that thrives in the cold, wave washed intertidal zone of the outercoast, but is rarely found more than a few miles into the Southeast archipelago.

The nesting islandFor generations, this small rock island within the Inian Islands has been a prize destination for Huna families seeking sea gull eggs.

Preparing for the leapAs we approached the rock in skis, Gordon and Owen explained the protocol: as the swell surges, we run the ski up to the rock, one person jumps

Leaping onto the islandAs we approached the rock in skis, Gordon and Owen explained the protocol: as the swell surges, we run the ski up to the rock, one person jumps

Searching for gull eggsI was impressed with the way Owen and Gordon pointed out new landmarks to the two young men. Every remark about a headland or bay included not only geographical references, but also historical, cultural, and subsistence context

Gull nest with eggThe traditional method to harvest gulls eggs, done in an ecologically responsible way, these practices will be able to continue forever

Some nests are difficult to reachFor generations, this rock had been the prize destination for Huna families. Set far from land and too small to support trees, the rock is the perfect nesting ground for seabirds like gulls

Harvesting gull eggsFor generations, this rock had been the prize destination for Huna families. Set far from land and too small to support trees, the rock is the perfect nesting ground for seabirds like gulls

Collecting gull eggsBlankets of birds flapped above us. The few green tufts of grass made a stark contrast to the guano-bleached stone and the blue-grey sky and water.

Bounty of the harvestIt took no time for Sam and Randy to collect plenty of eggs to share with family and elders back in Hoonah.

Harvesting gumbootsAfter the Gumboots have been collected, they are typically canned for preservation and storage.

Gumboot (Black Katy chiton)Black Katy chiton (Katharina tunicata) is a traditional food, commonly called Gumboots.

Black Katy chitonGumboots live in the intertidal zone, and are particularly susceptible to contamination from development and timber harvest. Wilderness designation ensures that these fragile ecosystems and the subsistence foods within will be protected in perpetuity.

Flipping rocks for gumbootsOwen instructs the students on the art of Gumboot hunting.

Take me to the photos!

Step 1: Come up with a hair-brained scheme.

My labmate Yara and I had been dreaming up the idea studying wood frog genomes from across the species’ range since she started her PhD. Wood frogs have the largest range of any North American amphibian. They also happen to be the only North American amphibian that can survive North of the Arctic circle.

Dr. Julie Lee-Yaw had done a similar study back in 2008. She embarked on a road trip from Quebec all the way up to Alaska to collect wood frog tissue. So, out first step was to ask Dr. Lee-Yaw if she would collaborate and share her samples.

Those samples gave us a solid backbone across the wood frog range, but we were missing population in expansive regions north and west of the road systems. We worked with the Peabody Museum to search for tissue samples that were already housed in natural history collections around the world. We filled a few gaps, but huge portions of the range were still missing.

We knew that there must be samples out there sitting in freezers and labrooms that were not catalogued in museum databases. So, our next step was to begin sleuthing. We looked up author lists from papers and cold-called leads. I even reached out to friends on Facebook (…which actually turned out to be a big success. The aunt of a friend from undergrad happens to do herpetology research in Galena, Alaska and was able to collect fresh samples for us this year!). This effort greatly expanded our sample coverage with new connections (and friends) from Inuvik and Norman Wells in the Northwest Territories, Churchill on the Hudson Bay, and the Stikine River Delta in Southeast Alaska.

But as the points accumulated on the map, we noticed some glaring holes in our coverage. Most importantly, we had no samples from Northwestern Alaska. Populations in this region are the most distant from the ancestral origin of all wood frogs in the southern Great Lakes. If we wanted a truly “range-wide” representation of wood frog samples, we needed tissue from that blank spot on the map!

Step 2: Convince your advisor and funders it’s a good idea.

This might be the hardest step. In our case, Yara and I were lucky that our advisor, Dave, was immediately supportive of the project. After we made the case for the importance of these samples, funders came around to the idea as well.

Step 3: Make a plan …then remake it …then make a new plan yet again.

Once we knew where we required samples from, we needed to figure out how to get there. Alaska in general is remote, but northwestern Alaska is REALLY remote. The road system doesn’t stretch farther than the middle of the state. All of the communities–mainly small villages–are only accessible by plane, and most of them only have runways for tiny prop planes. Travelling out from the villages into the bush is another layer of difficulty. Most people here either travel by boat on the river or by snowmachine during the winter. Traveling on land, over the soggy and brush-choked permafrost, is brutal and most locals only do it when necessary, if at all.

Prior to academia, I made a career of organizing expeditions to the most remote places in the rugged southeastern archipelago of Alaska. Despite my background, the logistic in the Arctic were even inscrutable to me. Fortunately, I had a couple of friends, Nick Jans and Seth Kantner, who know the area well. In fact, Seth grew up in a cabin out on the Kobuk. (Seth and Nick are both talented authors. I suggest checking out Ordinary Wolves by Seth and The Last Light Breaking by Nick). With their help, I was able to piece together the skeleton of a trip.

After many logistic iterations, Yara and I decided to follow in the footsteps of local hunters who, for generations, have used the rivers as conduits into the heart of the wilderness. Our plan was to travel down one of the major arterial rivers and hike inland to search for frog as we went.

Our original itinerary was to raft the 100 mile section of the Kobuk River from just north of Ambler village to the village of Kiana. But at the last minute (literally), our plans changed. As we were loading up the plane, the pilot told us that he couldn’t fly into our planned starting point. Instead, he suggested that we fly into a gravel bar 30 miles up river in Gate of the Arctic. Those “30 miles” turn out to be AIR MILES. Following the river, it ended up adding over 60 miles to our trip.

We packed two inflatable oar rafts, almost 150 pounds of food, and another 300 pounds of camping, rescue, and science gear, into the balloon-wheeled plane. For the next two weeks, we rowed down the swift Ambler River from the headwaters to the confluence of the Kobuk. Then, we rowed down the massively wide and meandering Kobuk River, eventually extending our trip by an additional 30 miles, by-passing Kiana, and continuing to Noorvik, the last village on the river.

Step 4: Recruit a crew.

Despite being the worlds first and only Saudi Arabian Arctic Ecologist with limited camping experience, I knew Yara would be a stellar field partner. But I never like traveling in brown bear country with fewer than four people. Plus, expedition research involves too many daily chores for the two of us to manage alone. So, we recruited a team.

Sam Jordan is a dry land ecologist, but he had been willing to help me with my dissertation fieldwork in wetlands before, so I knew he would be willing to defect for a good adventure. Sam is also an exceptional whitewater paddler and all-around outdoor guru. Plus, he’s just a great guy (when he leaves his banjo at home). He and I spend two weeks floating the Grand Canyon in the dead of winter and there are few people I would want along on a remote river trip.

Kaylyn Messer and I guided sea kayak expeditions in Southeast Alaska back in our youth. I am a bit particular about how I manage my camp system (read: “extremely picky and fastidious to a fault”) on big trips. Kaylyn is one of the few people as scrupulous as me, but she’s also a super amenable Midwesterner at heart. I knew she’d be a huge help out in the field.

We fell into an effective rhythm on the trip.  Each morning we woke, made breakfast, broke camp, packed the boats, and launched early in the day. While one person on each boat rowed, the other person checked the maps for frog surveying spots, fished, or photographed. We stopped along the way to bushwhack back into wetlands we’d identified from satellite images. We typically arrived at camp late. Yara and I would set up one tent to process the specimens from the day while Same and Kay made camp and cooked dinner. One of the hidden disadvantages of 24-hour Arctic sunlight is that it is easy to overwork. Most nights we only managed to get sampled finished, dinner cleaned up, and camp bearproofed with enough time to crawl into tents with just eight hours till beginning again the next day.

Step 5: Do the science.

Doing science in the field is difficult. Tedious dissections seem impossible while baking in the omnipresent sun and being alternately hounded by hundreds of mosquitoes or blasted by windblown sand. Trading lab coats for rain jackets and benchtops for sleeping pads covered in trashbags compounds the trouble. Not to mention, keeping tissues safe and cool. Organization and adaptability go a long way.

On remote, self-supported trips, it is inevitable that equipment fails or is lost. On one of the first days, we discovered that our formalin jar was leaking—and formalin is not something you want sloshing around! We cleaned the boats and found a creative solution to replace the offending container: a 750ml Jack Daniel’s bottle!

Planning ahead and engineering backup plans also helps. One of our main struggles was figuring out how to preserve specimens and get them home. It is illegal to ship alcohol by mail and you can’t fly with the high-proof alcohol needed for genetic samples. You can ship formalin, but it is difficult to fly with. To make matters worse, we were flying in and out of “dry” or “damp” villages where alcohol is strictly regulated or forbidden. Also, we happened to be flying out on a Sunday, making it impossible to mail samples home. The solution we arrived at was to ship RNAlater and formaldehyde to our hotel room ahead of time. Tissue would remain stable in RNAlater for a couple of weeks and we could make formalin to fix the specimens. After fixing, we cycled the specimens through water to leach out the formalin. This made it possible for me to fly with all of the tissue tubes and damp specimens in my carry on. Other than a few concerned looks from the TSA folks, all of the samples made it back without issue!

Step 6: Enjoy the adventure.

Despite the hard work, there was a lot to appreciate about the Arctic. We witnessed major changes in ecology as we travelled from the steep headwater streams in the mountains to the gigantic Kobuk. Every day was an entirely new scene.

Here’s an illustrated thread on our collecting trip to the Alaskan Arctic for the @Yale @yalepeabody this past summer. 1/22 pic.twitter.com/Jh3VCqVEgx

— A. Z. Andis Arietta (@azandisarietta) August 24, 2021

Step 7: Forget the hardships

Looking back, it is really easy to forget the sweltering heat, swarms of mosquitoes, inescapable sun, and freak lightning storms. And, it’s probably better to forget those anyway!

Arctic CircleSam illustrates that we are, in fact, above the Arctic Circle.

GearGear (minus food and rafts) ready for weigh-in before loading the plane.

Upper Ambler RiverOur drop-off point on the braided upper reach of the Ambler River in Gate of the Arctic National Park.

Gates of the ArcticGetting dropped off on a gravel bar in Gates of the Arctic National Park.

The first dayUnloading the plane on the first day of the trip.

Camp, night 1Campsite along the Kobuk River.

Rigging the raftsPacking up the two-person rafts on the first day.

Kaylyn Messer at the helm.In the upper rivers, near the headwaters, the current was pleasantly swift.

Upper riverSam and Yara rowing down the Kobuk River.

Early morning rowingRowing the swiftwater on the headwaters of the Ambler River in Gates of the Arctic National Park.

Searching for frogs

First frogs!Yara and I after finding the first frogs of the trip!

Science in the fieldYara preparing to do the sciencing with a garbage back as a makeshift lab bench.

Dinner. night 6Dinner and a view on the banks of the Kobuk River.

Midnight sunTrying to avoid getting a sunburn while sleeping in the Arctic.

Midnight sunThe sun baking our tent at 1130pm.

Rainy rowingSam and Yara floating downstream.

Arctic frogYara proudly presents her first wood frog collection.

Kobuk viewsSmoke and clouds mute the midnight sun.

Sam JordanSam Jordan in his happy place.

Chocolate con culicidae.With hundreds of bugs circling your head at all times, it is impossible not to end up with a few in every meal.

CutbanksMassive cutbanks made much of the shore inaccessible for sampling.

StormA freak lightning storm.

SunsetBeautiful light from the midnight sun.

Field dissection Taking tissue samples for sequencing.

TadpolesTadpoles from "Seth's Pond".

Prepping collectionsYara and I taking tissue samples and prepping specimens.

Arctic Wood FrogBeautiful arctic wood frog.

Fixing specimensHere, I am fixing specimens with formalin to preserve them for the Peabody Museum.

Bushwhacking The view while bushwhacking in to search for frogs.

BugsA random sample of friendly mosquitoes.

BearGrizzly bear prints on the beach.

FishingSam with his first of many greyling.

The Kobuk River valleyThe Kobuk Valley watershed is just an endless expanse of wetlands.

The end of the tripFlying back to Kotzebue in a packed plane at the end of the trip.

Heading homeCatching a ride out to the airstrip with our truckload of gear on the last day of the trip.

Now, five years, four blog posts, and uncountable hours later, I can say that measuring canopy structure with hemispherical photos is surprisingly difficult.

One of the biggest hurdles is understanding the equipment and deploying it properly in the field. For me, nothing is more tedious than standing waste deep in a mucky, mosquito-infested pond while I fiddle around with camera exposure settings and fine-tuning my leveling device. Add to that the constant fear of dropping a couple thousands of dollars of camera and specialized lens into the water, and you get a good sense of my summers.

So, it is with great pleasure that I offer an alternative method for capturing canopy photos that requires nothing but a cell phone, yet produces higher quality images than a traditional DSLR setup. This new method exploits the spherical panorama function available on most cameras (or in the free Google Street View app). Hemispherical photos can then be easily extracted a remapped from the spheres. You can check out the manuscript at Forestry here (a PDF is available on my Publications page) or continue reading while I walk through the paper below.

The old way

The most common way to measure canopy structure these days is with the use of hemispherical photographs. These images capture the entire canopy and sky from horizon to horizon. Assuming proper exposure, we can categorize individual pixels as either sky or canopy and run simple statistics to count the amount of sky pixels versus canopy or the number and size of the gaps between canopy pixels. We can also plot a sun path onto the image and estimate the amount of direct and indirect light that penetrated through the canopy. (You can follow my analysis pipeline in this post).

All of this analysis relies on good hemispherical images. But the problem is that there are many things that can go wrong when taking canopy photos, including poor lighting conditions, bad exposure settings, improperly oriented camera, etc. Another problem is that capturing images of high-enough quality requires a camera with a large sensor, typically a DSLR, a specialized lens, and a leveling device, which can cost a lot of money. Most labs only have one hemispherical photography setup (if any), which means that we sacrifice the number of photos we can take in favor of high-quality images.

The new way

In the past few years, researchers have tried to figure out ways to get around this equipment barrier. Folks have tried eschewing the leveling device, using clip-on hemispherical lenses for smartphones, or using non-hemispherical smartphone images. I even tested using a hemispherical lens attachment on a GoPro.

But, none of these methods really produce images that are comparable to the images from DSLRs, for three reasons:

1. Smartphone sensors are tiny compared to DSLR, so there is a huge reduction in quality.
2. Clip-on smartphone lenses are tiny compared to DSLR, so again, there is a huge reduction in optical quality.
3. Canopy estimates are sensitive to exposure settings and DLSRs allow for more control over exposure.

The method I developed gets around all of these issues by using multiple, individual cell phone images to stitch together a single hemispherical image. Thus, instead of relying on one tiny cell phone sensor, we are effectively using many tiny cell phone sensors to make up the difference.

Another advantage of creating a hemispherical image out of many images is that each individual image only has to be exposed for a portion of the sky. This avoids the problems of glare and variable sky conditions that plague traditional systems. An added benefit is that, smartphone cameras operate in a completely different way than DSLRs, so they are much less sensitive to exposure issues in general.

Smartphones are less sensitive to exposure issues because, unlike DSLRs that capture a single instance on the sensor when you hit the shutter button, smartphone cameras use computational photography techniques that blend the best parts of many images taken in short succession. You may not realize it, but your smartphone is constantly taking photos as soon as you turn it on (which makes sense since you can see the scene from the camera on your screen). The phone stores about 15 images at a time, constantly dumping the older versions out of temporary memory as updated images pour in. When you hit the button to take a picture, your phone then automatically blends the last few images with the next few images. The phone’s software selects the sharpest pixels with the most even contrast and color from each image and then composites those into the picture presented to you. With every new software update, the algorithms for processing images get better and better. That’s why modern cell phones are able to take photos that can compete with mid-range DSLRs despite the limitations of their tiny sensors.

So, if each phone photos is essentially a composite of 15 images, and then we take 18 of those composite images and stitch them into a hemispherical image, we are effectively comparing a sensor the size of 270 individual phone camera sensors to the DSLR sensor.

The best part is that there is already software that can do this for us via the spherical panorama feature included with most contemporary smartphone cameras. This feature was introduced in the Google Camera app back in 2012 and iOS users can access the feature via the Google StreetView app. It is incredibly simple to use.

Update: Check out my post on tips for taking spherical panoramas

Once you’ve taken a spherical panorama, it is stored in your phone as a 2D JPEG in equirectangular format. The best part about the photo sphere software is that it utilizes your phone’s gyroscope and spatial mapping abilities to automatically level the horizon. This is advantageous for two reasons. First, it means we can ditch the tedious leveling devices. Second, it means that the equirectangular image can be perfectly split between the upper and lower hemisphere. We simply have to crop the top half of the rectangular image and remap it to polar coordinates to get a circular hemispherical image.

How to extract hemispherical images from spherical panoramas

UPDATE: Please see my latest post to process spherical images with R.

Command line instructions

If you are proficient with the command line, the easiest way to extract hemispherical images from photo spheres is to use ImageMagick. After you download and install the program you can run the script below to convert all of your images with just a couple lines of code.

cd "YOUR_IMAGE_DIR"

magick mogrify -level 2%,98% -crop 8704x2176-0-0 -resize "8704x8704!" -virtual-pixel horizontal-tile -background black +distort Polar 0 -flop -flip *jpg

You may need to make a few modifications to the script for your own images. The -crop 8704x2176-0-0 flag crops the top half of the image (i.e. upper hemisphere). Be sure to adjust this to 1.00×0.25 the dimensions of your panorama dimensions. The -resize "8704x8704!" flag resizes the image into a square in order to apply a polar transformation. Be sure to adjust this to 1.00×1.00 the width of your panorama

Note that the code above will convert and overwrite all of the .jpg files in your folder to hemispherical images. I suggest that you practice on a folder of test images or a folder of duplicates to avoid any mishaps.

GUI instructions

If you are intimidated by the command line, extracting hemispherical images from photo spheres is also easy with GIMP (I used GIMP because it is free, but you can follow the same steps in Photoshop).

Update: You can also try out this cool web app developed by researchers in Helsinki which allows you to upload spherical panoramas from your computer or phone and automatically converts them to hemispherical images that you can download. However, I would not suggest using this tool for research purposes because the app fixes the output resolution at 1000p, so you lose all of the benefits of high-resolution spherical images.

First, crop the top half of the rectangular photo sphere.

Second, scale the image into a square. I do this by stretching the image so that the height is the same size as the width. I go into why I do this below.

Third, remap the image to a polar projection. Go to Filter > Distort > Polar Coordinates

Fourth, I found that increasing the contrast slightly helps the binarization algorithms find the correct threshold.

All of these steps can be automated in batch with BIMP plugin (a BIMP recipe is available in the supplemental files of the paper). This can also be automated from the command line with ImageMagick (see scripts above and in the supplemental materials of the paper).

The result is a large image with a diameter equal to the width of the equirectangular sphere. Because we are essentially taking columns of pixels from the rectangular image and mapping them into “wedges” of the circular image, we will always need to down sample pixels toward the center of the circular image. Remember that each step out from the center of the image is the same as each step down the rows of the rectangular image. So, the circumference of every ring of the circular image is generated from a row of pixels that is the width of the rectangular image.

With a bit of geometry, we can see that, the circumference matches the width of our rectangular image (i.e. 1:1 resolution) at zenith 57.3 degrees. Zenith rings below 57.3 will be downsampled and those above will be scaled up and new pixels will be interpolated into the gaps. Conveniently, 57.3 degrees is 1 radian. The area within 1 rad, from zenith 0° to 57°, is important for canopy estimates as gap fraction measurements in this portion of the hemisphere are insensitive to leaf inclination angle, allowing for estimated of leaf area index without accounting for leaf orientation.

Thus, we retain most of our original pixel information within this critical portion of the image, but it does mean that we are expanding the pixels (increasing the resolution) closer to the horizon. I tested the impact of resolution directly in my paper and found almost no difference in canopy estimates; so, it is probably okay to downscale images for ease of processing if high resolution is not needed.

The hemispherical image produced can be now be analyzed in any pipeline used to analyze DSLR hemispherical images. You can see the pipeline I uses in this post.

How do images from smartphone panoramas compare to DSLR

In my paper, I compared hemispherical photos taken with a DSLR against those extracted from a spherical panorama. I took consecutive photos at 72 sites. Overall, I found close concordance between measures of canopy structure (canopy openness) and light transmittance (global site factor) between the methods (R² > 0.9). However, the smartphone images were of much greater clarity and therefore retained more detailed canopy structure that was lost in the DSLR images.

Although the stitching process occasionally produces artifacts in the image, the benefits of this method far outweigh the minor problems. Care when taking the panorama images, as well as ever-improving software will help to minimize imperfect stitching.

Overall, this method is not only a good alternative, it is probably even more accurate than traditional methods because of the greater clarity and robustness to variable exposure. My hope is that this paper will help drive more studies in the use of smartphone spheres for forest research. For instance, 360 horizontal panoramas could be extracted for basal measurement or entire spheres could be used to spatially map tree stands. The lower hemisphere could also be extracted and used to assess understory plant communities or leaf litter composition. Researchers could even enter the sphere with a virtual reality headset in order to identify tree species at their field sites from the comfort of their home.

Mostly, I’m hopeful that the ease of this method will allow more citizen scientists and non-experts to collect data for large-scale projects. After all, this method requires no exposure settings, no additional lenses, and is automatically levelled. The geolocation and compass heading can even be extracted from the image metadata to automatically orient the hemispherical image and set the location parameters in analysis software. Really, anyone with a cell phone can capture research-grade spherical images!

Be sure to check out my other posts about canopy research that cover the theory, hardware, field sampling, and analysis pipelines for hemispherical photos, and my tips for taking spherical panoramas.

As an ecologist (with a special interest in freshwater ecology), I felt incredibly fortunate to experience the new face of this watercourse which had been radically changed by a “High Flow Experiment” just a moth earlier. Also, I was out-of-my-mind excited to see some of the first wild-fledged California condors in Arizona while on the river. So, in addition to lots of photos from the trip, the end of this post contains a fair bit of nerd-splaining about river ecology and the condor recovery program.

This trip was especially important to me because it brought my career as an environmentalist full circle.

At the beginning of May 2007, I was in a 13-passenger van towing a trailer full of gear headed from northern Wisconsin to Arizona. At the helm was an English professor named Alan Brew. He was carting us out to the desert to spend a month reading the works of Edward Abbey while visiting all of the places where “Cactus” Ed had put those words to paper.

The discussions we had around the fire, during breathless hikes, and among sandy van seats helped form the bedrock of my wilderness ethics. And in no small way, that trip helped impel my career as a conservationist. To this day, when someone asks what I do for a living, my first impulse is to respond with a quote from one of Abbey’s books:

“My job is to save the fucking wilderness. I don’t know anything else worth saving.”

The most influential of Abbey’s books, for me, was his novel The Monkey Wrench Gang. It tells the story of a small posse of unlikely activists who refine the art of environmental sabotage (“monkey wrenching”) in escapades across the American West. The book culminates in the posse’s attempt to blow up the pinnacle of their ire–the Glen Canyon Dam, the dam that plugged the Colorado River just upstream of the Grand Canyon.

As it did for many generations before me, The Monkey Wrench Gang served as a distillation of all my frustration with the environmental catastrophe of modern society (the books was an inspiration for the first-wave of environmental activist organizations like Earth First! and later, for eco-terrorist groups like Earth Liberation Front). Above all else, the lesson I took from TMWG was that the Glen Canyon Dam represents the domestication of the willy Colorado River. It is a metaphor for everything wrong with our approach to natural systems. And I wanted nothing more than to see the fucker demolished.

Now, over a decade later, I got the chance to float the neutered stretch of the river between Glen Canyon Dam and the bolus of water backed up by the Hoover Dam downstream.

We put in just under Glen Canyon Dam on December 14 under a waxing moon and pulled out at Lee’s Ferry on Lake Mead 17 days later feeling (and smelling) like whole new people.

The High-flow Experiment:

So, why are dams so bad for river ecosystems?

River ecosystems, and especially desert riverine systems, are tough places for organisms to exist. Only specialized species can cut it here. River banks are constantly flooded and then parched. Entire sections of banks are washed away in high-flows and redeposited elsewhere downstream. During storms, the river turns turbulent and chocolate brown with suspended sediment, yet during the summer, the water can be still as glass, warm, and oxygen-starved.

Despite the hardships, or rather because of them, organisms have evolved to synchronize with the seasonal fluctuations of the river. Trees rely on bankful rivers to deposit seeds. Insects rely on high-flows to blast the silt out of the stony crevices they call home. Even frogs rely on the high pools left by receding waters as nurseries for tadpoles.

Dams stifle the natural flows of rivers and dampen natural flood events. Instead of seasonal peaks of silt-rich waters, dams reduce the river to a steady, nutrient-saturated but silt-poor trickle. In general, the entire system is engineered for the annual catastrophism of raging floods. Without that annual reset, a few species can come to dominate at the expense of overall biodiversity.

In order to restore down-stream ecosystems, researchers have begun to experiment with creating artificial floods by releasing high-volume surges from the bottom of dams. Releasing from the bottom of the dam purges the sediment build up behind the wall and flushes it downstream.

At Glen Canyon, the first High-Flow Experiment (HFE) was conducted in 1996. Follow-up trials were conducted in 2004 and 2008, and then annually since 2012. During an HFE, flows peak at between 38,000 and 45,000 cfs–about double the average base-flow.

While HFEs help simulate minor floods, they do not replicate natural flow patterns. Take a look at the flow plot from 1920-2010. Before Glen Canyon Dam, annual floods peaked over 100,000 cfs every five years or so, at times exceeding 150,000 cfs, which is double or triple the peaks of HFEs.

The HFE program is certainly better for the river than continual flows, but probably will not restore long-term ecological processes. For instance, during our trip, those folks who had been on the river in years past were surprised to see how some of the camping beaches had changed. Ecologically, that’s a good thing, because it establishes a natural successional regime. However, the changes were nominal and limited to the immediate banks while the upper beaches were unaffected. One reason for this is that a history of consistent flows allowed woody vegetation to develop deep roots that anchor the upper beaches in place. Historically, annual floods would have prevented most plants from this type of entrenched colonization, and the irregular massive floods would have removed those plants that had begun to establish themselves. The result is that a post-succession regime currently dominates most beaches, choking out important ephemeral habitats, and every year they grow more recalcitrant to floods.

California condors:

Up close, condors are ugly birds. They kind of look like Mitch McConnell wearing an Ewok suit. But when you see them gliding along the elevated skyline of the Grand Canyon’s rim, they seem both majestic and imposing. With a wingspan of 9.5 feet, they are the largest bird in North America.

The story of the condors is one of the greatest successes of the environmental movement. Due mainly to lead poisoning, the California condor population crashed to just 22 individuals in the entire world in 1982. Condors are carrion specialists and especially like the large carcasses left by hunters. Unfortunately, the lead shot in bullets remains in the carrion and ends up in the birds. Over the years, the populations dwindled as more and more birds died of lead toxicity before reproducing. Without intervention, the species would have been extinct by the end of the century.

Over the next 5 years, the Fish and Wildlife Service managed to capture all of the remaining birds and placed them in a captive breeding program. By 1992, the captive population had tripled and the first new birds were released back into the wild. Over the next couple of decade, the captive population grew and new captive breeding programs were established. At the same time, new individuals were released and new reintroduction sites were established, including the second release site in Arizona.

We saw condors on the first day of our trip, just a couple of miles downstream of the dam. Judging from the broken white bands under the wings, these were probably juveniles. That’s super exciting because it means that these were wild-fledged birds from released parents. As of 2017, there were over 60 wild-fledged condors and that number keeps rising.

The future of the condors looks hopeful. In 2011, for the first time since the recovery effort began, the number of condors in the wild exceeded the number in captivity–290 to 170 as of 2017.

But there remains cause for concern. Lead poisoning continues to impact the wild populations. In fact, USFWS expects that every wild bird will need to be treated for lead toxicity at some point in its lifetime and lead toxicity can be blamed for the majority of deaths. Finkelstein et al. (2012) used isotopic analysis to trace the origin of the lead found in birds—no surprise—the predominant source of lead was from ammunition.

Despite the fact that we’ve known for decades that lead causes major harm, no legislation has been passed to ban lead in bullets. We can continue to supplement wild populations with captive breeding programs, but until we manage to fix the problem of lead in the environment, condors will never be self-sustaining.

Fortunately, a lead ammunition ban is supposed to go into effect in California this year. However, populations in Arizona, Utah, and Mexico will continue to suffer from poor hunting practices.

Resources and references:

U.S. Fish and Wildlife – California Condor Recovery Program
National Park Service – Condor Re-introduction & Recovery Program

Glen Canyon Dam Adaptive Management Wiki

Finkelstein, M. E., Doak, D. F., George, D., Burnett, J., Brandt, J., Church, M., et al. (2012). Lead poisoning and the deceptive recovery of the critically endangered California condor. Proc. Natl. Acad. Sci. U. S. A. 109, 11449–11454.

Poff, N. L., and Schmidt, J. C. (2016). How dams can go with the flow. Science 353, 1099–1100.

West, C. J., Wolfe, J. D., Wiegardt, A., and Williams-Claussen, T. (2017). Feasibility of California Condor recovery in northern California, USA: Contaminants in surrogate Turkey Vultures and Common Ravens. doi:10.1650/CONDOR-17-48.1.

Speciation starts small. The path of divergence starts with minute change in just a handful of basepairs among the billions of bases in a genome. Overtime, these small differences create feedbacks that propagate further divergence.

That’s the idea of sympatric speciation, the emergence of two species out of one. I’m most interested in the very first steps of this process, but catching this kind of small-scale divergence is hard, because the difference are small and easy to overlook. We call noticeable differences within a species polymorphisms. In most cases, we notice polymorphisms that we can see. For instance, it is hard to miss difference in color morphs of chimpmunks. Many of the classic examples of polymorphisms are visually detectable: industrial melanism in moths, beak size in Galapagos finches, stripe and color pattern in Timema stick insects, etc.

 

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It’s been way too long since I celebrated #TaxidermyTuesday All of these specimens are the same species of Eastern chipmunk (Tamias striatus), but two of them have genetic quirks that make their coats either all black (melanistic) or all white (leucistic). #biology #naturalhistorymuseum #naturalhistory #specimen #taxidermy #chipmunk #zoology

A post shared by Andis A. (@azandis) on Mar 6, 2018 at 3:54am PST

But many polymorphisms cannot be detected visually. For instance, polymorphism in dart frogs is often detected by the chemical composition of their skin toxins. Divergence in birds is often diagnosed by the sound of their calls. I’m in the middle of a collaboration to detect possible divergence in clover populations within and outside of cities via cyanogenesis.
The reliance on our human sight to detect polymorphisms is a problem because human sight, while impressive, is very narrowly limited. There is no reason for us to expect that the most relevant variation (from an ecological or evolutionary perspective) in a population would fall within the range of our senses. For instance, there is a whole vision of the world in the ultra-violet frequency that we cannot see. Flowers that all appear a uniform color to you and me can exhibit huge variation in ultra-violet light. Since birds and bees see ultraviolet, it stands to reason that the strongest selection for divergence would occur in this frequency, completely unknown to us.

All of this led me to think about how we, as eco-evo scientists, can start to shift our paradigm to think about the world through the senses of the organisms we study, which would give us a much better ecological picture of the selection pressures maintaining polymorphisms. The first step, is to take one small step outside of our anthropocentric sense and see the world through the eyes of animals. Thanks to the Yale Center for Teaching and Learning, I was able to design an interactive digital project that helps take those first few steps along a Proustian walk.

From my field notes, 17 August 2018:

“Last night I slept on the flat bench of duff-covered ground at the base of the ‘camp tree,’ a white and skeletal cedar with the characteristic axe marks from decades-past Tlingit or Haida woodsmen who had notched the bark from the underhanging side of the leaning tree trunk. As Wayne, our on-hand anthropologist, explained, the notched wood of the tree would have died and dried in the rainshadow of the trunk making for ready tinder to be harvested the next season when the camp was reoccupied. The overhanging tree would have also provided the Native campers with shelter for fire or lean-to bivouac. One of the same purposes for with I utilize it today. 

As I fell asleep under the history-laden tree, I dreamed of a boat at anchor in high winds. As the gales tugged at the boat, the anchor dug into the muddy bottom and the rode strained taught to the windlass bolted to the foredeck. But the wind was strong, and the windlass was pulling from the deck boards and the road was splitting. With each gust, the planks screamed “Eeeeerrrrck!”

A few more heavy gusts would rend the boat from anchor, setting it adrift in the turbulence. Another gust and a louder “Eeeerrrrck!”

In my dreamy torpor I was frozen, I could do nothing but watch.

“EEEEEERRRRCK!” and I watched the windlass pull loose, hanging by a single bolt.

Just before the final fastener snapped, I woke up to the sun shining sidelong under my tarp and straight into my eyes. I could still hear the creaking Eeeeerrrck sound out in the cove and realized it was the agitate call of a belted Kingfisher. The sound of the gusts in my dream had been the sound of light swell washing the beach.”

One of my favorite quotes about Wilderness is from former Senator Clinton Anderson who said, “Wilderness is an anchor to windward. Knowing it is there, we can also know that we are still a rich nation, tending our resources as we should—not a people in despair searching every last nook and cranny of our land for a board of lumber, a barrel of oil, a blade of grass, or a tank of water.” No doubt, I must have had that quote on my mind as I fell asleep on the third night of our three week expedition in South Prince of Wales Wilderness.

South POW is one of the many forgotten Wilderness areas of Southeast Alaska, overshadowed by the iconic ice-filled fjords like Tracy Arm or Glacier Bay, and tourist hotspots like Misty Fjords. Nevertheless, it can easily compete in scale and dynamic topography, and what it lacks in defining photo-geniality, it more than makes up for in its isolation and profound solitude.

At just under 90,000 acres, South POW is the 10^th largest and the southern-most (narrowly outcompeting the southern point of Misty Fjords) of the twenty-four Wilderness Areas in Southeast Alaska. As its name implies, the designation was carved from the southern portion of Prince of Wales island, including the watersheds draining into Klakas Inlet, all watersheds south that drain to Cordova Bay and Barrier Islands. Encompassed in the boundary is a labarynith of convoluted (some might say fractal-like) shoreline. This is dynamic and magic country. It is intricate and you need to see it intimately, by kayak, or even better, by foot. Inlets and passages otherwise hidden from sight appear as if by incantation, the trees parting to a kayak-width channel only when you paddle immediately beside.

From my field notes, 18 August 2018:

“From our southernmost camp, we paddled out to the most seaward rocks and islands. Out here on the outside waters, among the breakers, expansive kelp beds, and scattered, battered islands with rocky headlands. White breaking water sparkled in the sun with each swell, but the water was otherwise calm. All of the branches of the few trees on these islands point leeward, like frozen weathervanes recording past winter storms originating from the Dixon Entrance to the south.”

From my field notes, 19 August 2018:

“After exploring the Barrier Islands, we spent time tracing the coastline of the main island which is punctuated by deep, multi-chambered inlets, bays, and saltchucks. For instance, a side channel in Hunter Bay opens into Biscuit Lagoon. At the back of Biscuit Lagoon, the Saltchuck opens at high water above a tidal waterfall. The shoreline is like walking through a labyrinth with new passages appearing and opening into whole new habitats.

We paddled up to the base of the Saltchuck where salmon were preparing to run at high water. Wayne, whose eyes always seem to catch any inorganic shape on the landscape, noticed that beneath our tethered kayaks, below the waterline, rocks had been arranged in a line. He reasoned that at lower water the stones would cordon off a pool. The Native fishermen would have either trapped salmon in the pool or used it as a holding pen for their catch pulled from the falls.”

The Wilderness is a mélange of habitats from wave washed coastal shores, to glass-still secluded bays, upland muskegs, lowland salal thickets, and rich estuaries throbbing with activity. The varied habitats granted us countless wildlife sightings, include a few once-in-a-lifetime encounters.

From my field notes, 19 August 2018:

“As we ate lunch next to the falls and pondered the rock wall, Kim noticed two wolves trotting up the shoregrass upwind from us. When the wolves saw us, the first bolted. The curiosity of the second got the best of him. With the wind preventing any scent information, he boldly came up to us for a close look. Satisfied, he trotted back away only to decide he still needed a closer look. This process repeated, with us standing like stones, the click of my camera shutter the only sound, until he dematerialized in to the forest.”

The Alexander Archipelago wolf are a controversial subspecies (Canus lupus ligoni) of North American wolf that occur only in the islands and mainland of Southeast Alaska. They are absent from the ABC islands which are dominated by brown bear, but the range is largely congruent with black bears in Southeast. No fossil evidence of the wolves exists, suggesting that the species colonized after the last glacial maximum.

Goldman (1944) was the first to describe the species and granted the name Alexander Archipelago wolf. A more recent molecular study (Weckworth et al. 2005), corroborated the original distinction, finding that the Southeast Alaska population was genetically delineated from the continental population and was itself highly structured and diverse. That same study found evidence that the Prince of Wales population formed its own unique and isolate subgroup within Southeast Alaska. Having spent a fair amount of time with wolves in Glacier Bay and Gustavus, our crew had guessed this was the case. In fact, it took us a split second to even realize we were staring down a wolf when it appeared–it was so dissimilar from the canids we had encountered up north. These island wolves appeared smaller, more dog-like, and with an unusual coat pattern.

The biogeography of the Prince of Wales wolves puts them in a particularly perilous position. It is a general rule in ecology that the smaller and more isolated a population, the more sensitive it will be to environmental and demographic fluctuations (for example, the case of Isle Royale wolves). Although Prince of Wales is an exceptionally large island (the 4^th largest in the U.S., just after Puerto Rico), the landscape itself has been highly fragmented and reduced by massive clearcuts and the most extensive road system in Southeast Alaska (about 2,500 miles; more roads than the rest of Southeast combined, many times over).

Roads are a major problem for POW wolves (even more so than for most widlife). Studies across all U.S. populations of wolves have shown a negative correlation between road density and wolf abundance. Wolves were absent where road densities exceed 0.9 mi/mi² (Jensen et al. 1986,
Mech et al. 1988, Fuller 1989, as cited in Schoen and Person, n.d.).  Most of the roads on POW were created by logging companies (on tax-payer dollars), which makes a strong correlation with roads and clearcuts, both of which are avoided by wolves (Person 2001).

Black-tailed deer, the wolves’ primary prey, require old-growth forest for summer browse and winter habitat to shelter from heavy snow. Clearcutting areas leads to a “succession debt” for wolves as logging removes habitat which removes deer. And logging continues on the island, driving the succession debt further into the red. In fact, habitat loss from logging alone is expected to reduce the wolf population by a further 25% before 2045 (Person 2001).

But habitat loss is not the only threat to POW wolves. Despite Canis lupus being listed as an endangered species in the lower 48, wolves are considered both big-game and furbears in Alaska, subjecting them to both hunting and trapping. Between the 1980s and 2010, around 175 wolves were killed in Southeast Alaska; 75 of those were from POW (Schoen and Person, n.d.).

As logging and associate road infrastructure continue to proliferate, “wolf populations on Prince of Wales and adjacent islands will be caught between two significant pressures: declining prey abundance and increasing hunting and trapping mortality” (Schoen and Person, n.d.).

The South POW Wilderness, at least, is a partial refuge for the wolves. While Wilderness designation prevents future roads and logging, it does not exclude hunting nor trapping; so, there really is no safe haven for these unique canids. My hope is that the isolation and extreme difficulty of hunting here compared to the road system will keep it to a minimum.

In addition to the wolves, we came nose-to-nose with loads of wildlife, including sandhill cranes, black bears, whales (alive and bones), and so many kingfishers and river otters.

From my field notes:

“More kingfishers than I’ve ever seen! The shoreline seems like it is just dripping with kingfishers from every low-hanging branch. And below, the tidal rocks are writhing with families of river otter. It must be a productive place for small carnivores and pescavores!”

We spent a large chunk of our time in Klakas Inlet, the long fjord that dominates the norther reach of the Wilderness. Although not too steep, the shoreline harbors very few beaches along the flanks. One exception is a grassy cove sheltering a pink and sockeye waterfall. We spent an entire day watching black bears filter through, try their luck with the flying salmon, and continue their up-fjord journey.

The density of black bears in Klakas was astounding. We paddled to the head of the inlet, where the fjord splinters into three massive estuaries, each full of late-running salmon. At one point, I could see 7 bears around the shore. They circled the shoreline of the fjord almost like a slow and dispersed school of fish circling a pond.

From my field notes, 27 August 2018:

“In the morning I watched multicolored bat stars pass beneath my kayak. Their five to six bright arms were like a dappled rainbow fluorescing against the dark water. Watching black bears pass by on shore is like the inversion of the bat stars. The dark fur seems to absorb light and looking for bears is more about looking for the absence of a bear or a bear shaped black hole in the otherwise colorful shoreline.”

From my field notes, 21 August 2018:

“On every trip, we try to make a point of hiking uphill, above the treeline, in order to look back down on the landscape. Experiencing a Wilderness is a lot like experiencing a painting. It takes time. You have to shift your focus and view it from different angles to take it all in. Look close, then step back. Put your nose right up to the canvas, then from across the room. In wild places, you have to paddle close to shore, get out and crawl through the brush of the forest, then get up high to see the whole thing. The detail and the composition are the functional integral of artistic mastery; same goes for the majesty of nature.”

So, we set our sights on a bald knob at the mouth of Klakas inlet and landed below a steep, even-aged stand of spruce and hemlock. We had envisioned a strenuous, patience-trying hike over old growth deadfall and bashing through endless under-story brush. It turned out that the stand had been beach logged many decades ago. The regenerating forest was the perfect age to shade out the under-story brush, but too young to accumulate much deadfall. It turned out to be one of the easiest routes we’d ever hiked. Surprisingly, there was not even brush at the transition from the forest to the subalpine bald, so we walked out into the sun and onto the rocks. From the top, we were treated to views of the entire southern half of Cordova Bay, up into Klakas Inlet and the ridges of the surrounding watersheds. In short, we could see almost the entire Wilderness area and the saltwater well out into the Pacific.

The pools on the bald were ringed by bright red sundews, a carnivorous plant that produces a sticky, sweet digestive enzyme from the tips of hairs on its leaves. Bug are attracted to the scent, land on the leaf, then wrap themselves up in the leaf as they struggle and adhere to more leaf hairs.

I see the round leaf sundew (Drosera rotundiflora) often, but I was surprised to see the English sundew (Drosera anglica) was more common and growing right alongside the D. rotundiflora.

From my field notes, 22 August 2018:

“The Native Haida and Tlingit folks who frequented this region made ample use of the fractal coastline. In almost every landable spot, Wayne noticed some trace of human occupation Some hints were subtle, like notches in trees or new forest growth indicating an area that had been cleared. Occasionally, the signs were more obvious, like the square foundations of old plank houses subsumed into the ground, and even pilons supporting old floor joists, now fixed in place by the roots of saplings growing atop them. The debris of stoves and other iron objects were sunk into the moss of a few such sites.

Wayne pointed out an iron ax head—the same type of ax head used to make the tree notches we’d been seeing all over the coast.”

After 16 days, we left the Wilderness toward Hydaburg. After days of calm waters and avoiding the oppressive sun, we found ourselves preparing for some exposed sections and large crossings in big water. The water shut us down and sent us back to camp for an extra night. We made progress despite lots of waiting and watching as the conditions fluctuated. We made our longest crossing of Cordova Bay in building, following seas. About midway across, we spotted black fins slicing the water miles away. As we thrashed onward on our heading, we watched the pod of orca surface and dive, rapidly closing the distance between us. The bull crossed comfortably forward of our bows, but the four females intersected our course. They surfaced with explosive spouts close enough to startle us. We exchanged some wide-eyed glances of concern while the females cavorted amidst out kayaks until they melted back into the water and joined the male far off to starboard.

From my field notes, 30 August 2018:

“South POW is a palimpsest. The page has been written by glaciers, over-written by many chapters of ecological succession, punctuated by interludes of logging, and a final chapter back to succession, all with the footnotes and interjections of Haida and Tlingit history throughout.
Now, having departed the Wilderness Area, our time there seems even quieter in contrast. Clear cuts appear over every ridge and we hear the whining buzz of outboards every few tens of minutes as boats zip in and out of Hydaburg.”

We paddled into Hydaburg on a quiet mid-morning diffused with grey. The brightly painted poles and homes seemed like holes pricked into the grey blanket of the day.

We found the folks in Hydaburg incredibly welcoming. We were invited into smokehouses and carving sheds, folks told us stories and we even made canine friends after saving a dog from drowning at the dock.

Overall, our South Prince of Wales expedition will remain one of my favorites. The immense quiet and solitude, the shoreline full of intrigue, the enigmatic wildlife—will define my memory of this place.

Route and Logistics:

Out trip could not have happened without Katy. We rented all of our kayaks through her, and in order to maximize our time in the Wilderness, Katy transported us to Klakas by skiff. She also picked us up and even stored our gear for us.

If you decide to paddle in South POW (and you should) keep in mind that camping can be sparse, weather can pick up quickly, parts of the coastline are committing, and communications are almost non-existent. Talk to locals, know your own skill level, and pour over your charts. Of course, I’m always happy to provide beta. Just drop me a line.

Check out my posts from other expeditions.

Check out other posts about designated Wilderness. 

References:

Fuller (1989) Population dynamics of wolves in northcentral Minnesota. Wildlife Monographs 105.

Goldman (1944) Classification of wolves. In S. Young and E. Goldman, eds., The wolves of North America, Part 2. Dover Publications, New York

Jensen, Fuller, and Robinson (1986) Wolf (Canis lupus) distribution on the Ontario to Michigan border near Sault St. Marie. Canadian Field Naturalist 100: 363-366.

Mech, Fritts, Radde, and Paul (1988) Wolf distribution and road density in Minnesota. Wildlife Society Bulletin 16:85-87.

Person (2001) Alexander Archipelago wolves: ecology and population viability in a disturbed, insular landscape (Doctoral dissertation). University of Alaska, Fairbanks, AK.

Schoen and Pearson, Chapter 6.4 “Alexander Archipelago Wolf.” In A Conservation Assessment and Resource Synthesis for The Coastal Forests and Mountains Ecoregion in the Tongass National Forest and Southeast Alaska. The Nature Conservancy.

Weckworth, Talbot, Sage, Person, and Cook (2005) A signal for independent coastal and continental histories among North American wolves. Mol. Ecol. 14: 917-931.

I’m currently on my way up to Alaska for another supremely short season of guiding (just two trips this years). I was going through some old photos and came across this image of the Milky Way from a trip back in 2014. It evoked a memory of the last time I paddled with Ken Leghorn in Windfall Harbor.

Ken Leghorn was a hero of the Alaskan conservation movement and a friend and mentor of mine who passed away a little over a year ago. I wrote down this recollection on the airline napkin:

The night was dead still under the stars as we scraped the final bites from our dishes and made the slippery pilgrimage over the popweed to wash plates at the waterline. As we cast our rinse water out, the splash excited thousands of tiny green sparks in the wake. Bioluminescent algae had flooded into Windfall Harbor with the rising tide and now the bay was dense with the tiny flashing organisms. Ken and I decided it was definitely worth the effort of pulling a tandem down from the woods. We slid off into the black indefinite water. Every paddle stroke lit up like an aquatic Christmas tree. We stopped paddling not far from shore and floated. As the hull lost momentum it ceased to perturb the algae. Now the water was a black mirror of the star-full sky. Between the silence, Ken and I traded similes: Our kayak was like a space ship floating in space. Our wake was like a ripple in space-time. The Alexander Archipelago was like a solar system hurtling through the universe and we were a satellite in orbit around a tiny island planet.

We paddle back and pulled the kayak back up into the treeline. Knotting the bowline, we agreed it was the best bioluminescence we’d ever seen in Southeast.

Since I shuttered my photoblog a few months ago, I realized that my original post from that trip to Windfall Harbor had been lost to the ether. So, I resurrected the photos and lightly edited that post below.

From August 2014:

There are only a few Wilderness areas in Southeast Alaska that I have not been to. Surprisingly, Admiralty Island/Kootznoowoo Wilderness, one of the larger Wildernesses in the Tongass is one that I had never visited. Along with Baranof Island and Chichagof Island, Admiralty Island has one of the highest concentrations of brown bears in the world. The average is one bear per square mile. In total, that means that the bears outnumber the people on these large islands. In fact, Admiralty itself has more bears on it than all of the lower 48 states combined.

Pack Creek is a special place for bears. It is a wildlife sanctuary in addition to its Wilderness designation. That means that there is no hunting of bears at Pack and the viewing at the Creek is strictly regulated. This is a great set up for bear viewing, as bears get much closer than would be normally comfortable. We arrived late in the season, well after the tourists, so we basically had the place to ourselves.

Many thanks to friend Ken Leghorn and Pack Creek Bear Tours for loaning us a kayak, sharing salmon dinner, and providing super helpfully detailed info about Pack. If you ever want to make the trip yourself. Pack Creek Bear Tours are the folks to call.

The inspiration for this trip was a visit from one of my best friends from middle school, Jordan, who came up to visit Alaska for the first time. After years hearing about the incredible bear viewing at Pack Creek, this seemed like the best excuse to spend a few days there. We boarded the float plane in Juneau and made the short flight to Windfall Harbor where the Forest Service maintains a small seasonal camp for their rangers on an island just a stone’s throw from the Creek. This is also where Pack Creek Outfitters store their kayaks. It was the end of the season, so Ken offered to let us use a kayak for a few days if we would help him move his fleet to the winter storage area.

The operation at Pack Creek is nothing like any other bear viewing site. There is no platform, no fences, no barriers. The viewing area is a 5 by 10 meter area of mown grass with a driftlog to sit on. The Forest Service and Fish and Game rangers are on-site at all times that people are present. They are trained to let the bears move about freely up to the edge of the mown grass line.

The unique situation at Pack Creek is a stamp of its history. In the 1930s a major conservation campaign sprouted with the intent of designating all of Admiralty Island a bear refuge, but succeeded only in protecting the Pack Creek drainage from hunting. In 1935, the Forest Service designated it an official bear viewing. Despite the restrictions, poaching was regular in the remote watershed. In 1956, a local miner and logger, Stan Price, rowed his floating cabin on shore at the mouth of Pack Creek and established a homestead with his wife, Edna. Rather than fear, they treated the local bruins as neighbors. Their presence helped to curtail poaching and also attracted new visitors. For almost 4 decades, the Prices lived with the bears. Over that time, new generations of cubs were born and reared with the Prices as a normal fixture of life. By the time Price died in 1989, just about every local bear was habituated to constant human presence.

In 1984, the tiny sliver of bear sactuary was expanded to a no-hunting zone encompassing Pack Creek and the adjacent watersheds, as well as the islands in Windfall Harbor. As the 80s progressed visitation increased to the point that the agencies decided to actively manage the area. Viewing times were limited, rangers were installed on-site, and visitation was limited to just 24 people per day.

As a result, generations of bears have come to associate Pack Creek as a safe haven from hunting and to ignore the small groups of human onlookers.

Sitting on a log, surrounded by Alaskan brown bears playing, snoozing, bathing, and snapping at salmon is a mesmerizing experience. We spent most of our time sitting on the log at the Creek mouth or walking up the trail to the viewing platform. But we managed a couple paddles around the Harbor, including a visit to the most impressive Sitka Spruce tree I’ve ever met.

On our second night, we sat under the clear night sky and discovered bioluminescent algae in the water. It is rare to see stars in Souheast Alaska. And it is a pleasure to see them reflected in the still waters. It is utterly, chest-caving, breathtaking to paddle the myth-like firmament of water sandwiched between a sky of stars above and swirls of bioluminesces below. Ken and I paddled out in a tandem just to sit and float. I can’t describe it. It was one of those utterly unique experiences that will forever bound my conception of hyperbole.

On the final evening of our visit, Jordan and I sat on the log with my friend Daven who happened to be the Forest Service Ranger on staff for the day.

The three of us sat in silence for most of the evening, occasionally swatting mosquitos, surveying the moldering ruins of Stan Price’s cabin, and potting bears across the river. With the sun dropping behind the mountains, we were contemplating packing up for the evening when a medium-sized rich-chocolate colored bear sauntered out of the trees. Daven recognized her immediately as Chino (her mother, a creamy brown bear, was named Mocha… get it?). Chino ambled across the streamlets and with no attention to us, came to rest in the tall grass at the edge of the viewing area. We were stunned into silence. I frantically switched lenses since she was closer than the focusing distance of my long lens and filled cards with her portrait.

I’ve seen many, many bears at very close range. But the general protocol for bear encounters is to make your presence known with the goal making it clear to the bear that you want your space. At Pack Creek, the tone is completely different, the intent is to discharge any discomfort, to let Chino forget we were even there. I learned that nonchalance is a powerful emotion when seen in the eyes of a bear.

We flew out on a clear day with Ken. Upon take off, we circled over the Swan River estuary which was expansive at low tide. The afternoon sun fluoresced the rivulets like veins under an X-ray. Out on the flats, we passed over a sow and two cubs. It takes a big landscape to make a 900lbs animal look like a speck, and it takes an even larger Wilderness area to ensure that such a landscape remains truly wild.

1. Hemispherical Light Estimates

2. Hardware for Hemispherical Photos

Once the theory and equipment are taken care of, you are ready to go out into the field and collect data. This post will cover the when, where, and how of shooting hemispherical photos. The next and final post deals with analyzing the photos you’ve captured.

When:

Hemispherical photos are very sensitive to lighting conditions. Because you are measuring an entire half hemisphere of the sky at once with each photo, it is important that the background (i.e. the sky) is as standardized as possible so that the canopy can be accurately distinguished without bias.

To imagine the wildly different exposures gradient across a hemispherical lens, wait until a clear sunset and walk out into an open field. Stare directly at the setting sun for a few seconds, then turn 180 degrees and try to make out the horizon. Even though our eyes are extremely well-equipped to quickly adjust for different lighting, you’ll probably have a hard time making out the dark horizon after looking at the bright sunset. Unlike your eye, which continuously adjusts to light conditions even at these extremes, cameras are stuck in one setting. Even the best camera sensors are limited in their tolerances, so we need to take photos at times when lighting in the entire hemisphere fits within a narrow range.

The best time to shoot is on uniformly overcast days. Overcast cloud cover yields a nice homogeneous white background that makes strong contrast to the edges of leaves and branches.

If cloudy days are not in the forecast, another option is to wait until dawn or dusk, before or after the sun is below the horizon and the sky is evenly lit. The problem is that this only allows a very short window for shooting.

Sometimes, we can’t help but take photos on sunny days. Before I talk about strategies for dealing with difficult exposures, I want to explain some of the problems direct sunlight can precipitate in light estimation methods: blown-out highlights, flare, and reflection.

Overexposed highlights

Overexposed or “blown-out” highlights is an issue of exposure settings and sensor limitations. When shooting into light, individual sensor cells can only record light up to a threshold. In my last post, I compared light collecting on camera sensor cells to an array of buckets in a field collecting raindrops. Using that analogy, think about sensor thresholds as the rim of the bucket. At some point, enough rain collects in the buckets that it overfills. After that point, you can record no more information about relative rainfall between buckets. In the camera, eventually too much light falls incident on a portion of the sensor and those pixels are maxed out and recorded as fully white (i.e. no information is coded in those cells). This leads to an underestimate of canopy closure because some pixels occupied by canopy will look like white sky after binarization. We can try correct our exposure to ensure we do not truncate those bright pixels, but compared to direct sun, blue sky directly overhead is relatively dark on sunny days, so this will almost certainly lead to a loss of information on the dark end of the spectrum, and we will then be overestimating canopy closure.

Unfortunately, there are no easy ways to deal with wide exposure ranges (other than avoiding sunny days). One solution is to shoot in RAW format which retains more information per pixel. With RAW photos one can attempt to recover highlights and boost shadows to some extent, but because the next processing step is binarization, this will only be effective if you can sufficiently expand the pixel value range at the binarization threshold. This also entails hand-calibrating each image, which reduces standardization and replicability, and may take a lot of time if you need to process many photos.

Flare

Flare is another problem and it emerges for a couple of reasons.

Hazy-looking “veiling flare” occurs when light scatters inside the glass optics of your lens. In normal photography, it is most prevalent when the sun is oblique to the front lens surface and light gets “trapped” bouncing around inside of the glass. It can also look like a halo of light bleeding into a solid object or streaks of light radiating from a point of light depending on your aperture settings (this is called Fraunhofer diffraction and can make for very cool effects…just not in hemispherical photos!). When these streaks appear to overlay solid canopy objects in our photos it will lead to underestimation of closure.

Ghosting flare looks like random orbs of light in photos and it occurs when light entering the lens highlights the inside of the optics close enough to focus on the sensor. Hemispherical lenses are incredibly prone to this type of flare because of the short focal distance of wide angle lenses.

If photos must be taken in sunlight, one alternative is to at least block the direct beams of sunlight by positioning the sun behind a natural sunblock or fashioning a shield. I’ve never tried the shield option myself, but I’ve seen photos of folks who have affixed a small disk on a semi-ridge wire on their tripod. The disk can be positioned such that it only blocks the sun. There are many problems with this option. First, the sunshield will be counted as canopy in the light calculations which will bias the estimates. One could exclude the blocked area from analysis by masking out the area of interest, but then that area will be excluded from the analysis. Another option is to spot-correct flare in each photo. This is most effective with RAW photos and can be accomplished in photo-editing applications by using a weak adjustment brush to reduce highlights, boost shadows, and increase contrast directly over the flare. Again, I don’t recommend editing individual photos, but sometimes this is the only option.

Reflection

Finally, direct sun reflecting on solid surfaces can lead to mischaracterization of pixels and overestimate openness. In this case, objects opposite the sun can be lit so well that they are brighter than the background. This is very common in forests dominated by light bark trees like aspen and birch. This also occurs just about any time there is snow in the frame, regardless of the lighting conditions. The only solution for this problem is darkening the solid objects in a photo-editing program. It is a painstaking task and increases the error in the final estimation, but sometimes is necessary.

Where.

Next you must decide where you want to take photos. The answer to this will depend on your research question. We can break it down into spatial/temporal sampling scale and relative position.

Hemispherical photos can fit into any standard spatial sampling scheme (e.g. transects, grid, opportunistic, clustered, etc.) depending on your downstream statistical analysis. However, because hemispherical photos capture such a wide angle of view, you must be careful of any analysis that assumes independence of observations if the viewshed overlaps between photos.

Generally, when we think about spatial sampling, we think in two dimensions (like in the figure below). However, it is also important to consider that canopy closure estimates integrate sun angle, and so it is critical that an even sampling scheme considers the third spatial dimension and include a representative sample of topographical aspect.

There is no perfect sampling strategy for any given project. To illustrate some considerations, I will outline the sampling for my work. For my project, I need to characterize the canopy closure above forested pond that range in size from a few meters to a hundred meters across. The most obvious strategy was to sample the intersections of a tightly spaced Cartesian grid over the entire surface of the pond. A previous research student tried this method on a handful of ponds. Using that information, we were then able to subsample those data to determine the spacing of the grid that would yield the most accurate estimates with the fewest photos. In this case, it turned out that every pond, regardless of size, could be characterized with 5 photos: 4 photos along the most distal shoreline in each cardinal direction and one photo in the center of the pond where the east-west and north-south lines intersect. An ancillary benefit of taking the same number of photos at each pond is that I can also calculate the variance within each pond, which gives me a sense of the homogeneity of the habitat. Keep in mind that measures of higher moments of the distribution of light values across habitats (like variance or kurtosis) may be extremely ecologically relevant and can be incorporated for more meaningful statistical analysis.

One final consideration in spatial sampling is the height at which photos are captured. By virtue of practicality, the most common capture height is about 1m from the ground since this is the height of most tripods. However, the study question might dictate taking photos above understory plants or at ground level. Regardless, the height of photos should be consistent, or recorded for each photo, and explicitly stated in published methods.

You will also need to consider the frequency of your sampling to ensure that you capture any relevant variation in the study system over time. In temperate forests, this usually means, at the very least, taking the same photos with deciduous leaves on and again after the leaves have fallen. On the other hand, phenological studies might need photos from many timepoints over shorter durations.

It is important to remember that canopy closure estimation integrates the sun’s path over a specific yearly window. We will define that window explicitly in the model, so it is important to ensure that the canopy structure in the photos accurately represents the sunpath window you define.

How.

In this section I will get into the nuts and bolts of taking photos in the field. I’ll cover camera settings and then camera operation.

Camera settings.

Most modern cameras are designed for ease of use and offer a variant of “automatic” settings. Automatic settings are great for snapping selfies and family photos, but awful for data collection. Manually adjusting the camera increases replicability and increases the accuracy of light estimates. Fortunately, there are only 4 parameters that we need to adjust for hemispherical photography: ISO, aperture, shutter speed, and focal distance.

ISO measures the sensitivity of a camera’s sensor to light. Higher ISO settings ( = greater sensitivity) allow for faster capture in lower light. However, high ISO leads to lots of noise and mischaracterization of pixels. In general, you should aim for the lowest ISO setting possible to produce better quality photos. More expensive cameras have better sensors and interpolation algorithms, so you can get away with higher ISO settings.

The aperture is the iris of a lens and controls the amount of light entering the camera. Aperture settings are given in f-numbers (which is the ratio of the lens focal length to the physical aperture width). Counterintuitively, a larger f-value (i.e. f22) is a smaller physical pupil, and therefore, less light than a smaller f-value (i.e. f2.8). Your aperture settings will be a balance between letting in enough light and getting crisp focus across the focal range (see focal distance below).

The shutter speed determines the duration of time that the sensor is exposed to light. Longer shutter speeds means more light resulting in brighter photos. However, the longer the shutter speed, the more any movement of the camera or the canopy will blur the image. If you are using a handheld system, I suggest at least 1/60sec shutter. With a tripod, shutter speeds can be longer, but only if the canopy is completely still. If there is ANY wind, I suggest at least 1/500sec shutter.

Focal distance is the simplest—just adjust the lens focus so that canopy edges are in sharp focus. This is easy when the canopy is a consistent distance from the lens, but can be difficult when capturing multi-layer structure. Lenses resolve greater depth of field (range of focal distances simultaneously in focus) when the aperture is smallest.

Since all four settings rely on all of the others, camera settings will be a balancing act. The end goal is to ensure that you have the best balance between overly white and overly black pixels and you can check this with your camera’s internal light meter. The big catch here is that we are actually not that interested in the exposure of the sky; in fact, we would like for the sky to be entirely white.

The most common exposure standardization technique is to first determine the exposure settings for open sky, then overexpose the image by 2-3 exposure values (EV) (Beckshäfer et al. 2013, Brown et al. 2000, Chianucci and Cutini 2012). In theory, this will ensure that a uniformly overcast sky is entirely white without blowing-out the canopy. The primary benefit is that this method uses the sky as a relative reference standard which is replicable.

It is easy to employ this method using your camera’s internal light meter. First, set your camera to meter from a single central point (you will probably need to look in your manual to figure out how to do this). If there is a large enough gap in the canopy overhead, you can point the meter spot there and take a reading then adjust your settings to get a 0 EV. (If the canopy has no gaps, you can set this in the open before going into the forest–just remember to take another reading if the conditions change). Now, reduce the shutter speed by 2 full stops (i.e. if 1/500 is 0 EV for the sky, set your shutter speed to 1/125; if 0 EV is 1/1600, set you speed to 1/400).

[Note, other authors (e.g. Beckshäfer et al. 2013) suggest adjusting for 2 EV overexposure. I don’t like using EV for anything other than the spot reference because all cameras use different methods of evaluating exposure. In contrast, shutter speed is invariant across all camera platforms.]

This may all seem like a confusing juggling act, but it is not that difficult in practice. Here is my general strategy:

• I set my ISO at 200 and my aperture at around f11.
• With the camera set to evaluate the central point of the image, I take a light meter reading of open sky.
• I adjust my shutter speed to an exposure value of 0 for open sky.
• Now, I re-adjust my shutter speed slower by 2 full stops.
• If my shutter speed is now too slow, I will increase my ISO one level or decrease my f-stop (aperture) by one stop and go back to step #2. I repeat until I find the balance.
• With the camera set, I can set up my camera and take images using these same settings; however, I must re-calibrate if the sky conditions change.

Taking photos.

At this point, shooting the photos is the easy part! A couple of helpful tips will make life easier.

Before shooting, you will need to orient the camera so that the sensor is perpendicular to the zenith angle (i.e. the camera lens is pointing directly up, opposite gravity). In my previous post covering hardware I mentioned that there are pre-fabricated leveling systems available or you can make a DIY version. With a tripod, you can manually level the camera.

For later analysis, you will need to know the compass orientation of the photos. Some pre-fab systems have light-up LEDs around the perimeter that are controlled by an internal compass and always light north. Otherwise, you can place a compass on your stabilizer or tripod and point the top of the image frame in a consistent direction (magnetic or true north is fine, just make sure you are consistent and write down which one you use).

It can be hard to take a hemispherical photo without unintentionally making self-portraits. With a tripod, you can use a remote to release the shutter from a distance or from behind a tree. Camera manufacturers make dedicated remotes, or if your camera has wifi capabilities, you can use an app from your phone. Most cameras also have a timer setting which can give you enough time to duck for cover.

Be sure to check out my other posts about canopy research that cover the theory, hardware, field sampling, and analysis pipelines for hemispherical photos.

Also, check out my new method of canopy photography with smartphones and my tips for taking spherical panoramas.

References

Beckschäfer, P., Seidel, D., Kleinn, C., and Xu, J. (2013). On the exposure of hemispherical photographs in forests. iForest 6, 228–237.

Brown, P. L., Doley, D., and Keenan, R. J. (2000). Estimating tree crown dimensions using digital analysis of vertical photographs. Agric. For. Meteorol. 100, 199–212.

Chianucci, F., and Cutini, A. (2012). Digital hemispherical photography for estimating forest canopy properties: Current controversies and opportunities. iForest – Biogeosciences and Forestry 5.

Collender, P. A., Kirby, A. E., Addiss, D. G., Freeman, M. C., and Remais, J. V. (2015). Methods for Quantification of Soil-Transmitted Helminths in Environmental Media: Current Techniques and Recent Advances. Trends Parasitol. 31, 625–639.