Challenge: In the past century, researchers have been studying a variety of birds in Australia to see how their bodies have changed as a result of global warming in order to determine how to adjust. In order to document the exact dimensions of thousands of beaks of 86 different species of birds in museums in a fast, accurate, and convenient manner, they needed a fast, accurate, and convenient method.
Solution: Artec Space Spider, Artec Studio
Results: By using the handheld 3D scanner Artec Space Spider, each bird can be scanned in submillimeter colour 3D in approximately two minutes. This makes it easy to scan anywhere from 30-50 birds in one museum visit. Scan processing takes just under six minutes for each bird.
One of the most startling impacts of global warming has taken place for decades now: multiple species of birds around the world have been reacting to rising temperatures by “shape-shifting,” changing their beaks, legs, and other appendages, in a desperate struggle to adapt and survive.
A little-known observation called “Allen’s rule” explains how this helps them cope with the heat. According to this biological rule, animals living in warmer climates generally have larger appendages, such as ears, beaks, tails, and limbs, which is why these animals are able to cope with the heat. It was first established in the 19th century.
Due to the fact that many appendages are not protected by fur or feathers, these anatomical structures are like a radiator, allowing heat to be dissipated and the animal to be kept at a more comfortable temperature.
The African elephant achieves this through the use of its ears, mice do it through the use of their tails, and birds accomplish it through the use of their beaks and legs.
Adapting the body temperature of birds is a complex process.
When we examine nature's way of equipping birds to accomplish this impressive thermoregulatory feat, we can see why we can't get enough of this strategy. The first thing that we should take into account is that the beak is one of the most efficient parts of a bird's body thermostat. If you look closely, it is possible that you would believe that birds' beaks are composed of dead, inert material, much like the bark on a tree, until you look closer.
Rather, they are living organs with a branching network of blood vessels, which are exceedingly vascularized, containing a rich network of blood vessels. It is interesting to note that, when birds are going to sleep, they will flood their beaks with additional blood, thus dispersing excess body heat, thereby bringing them down to a level where they are more at rest. This is a vivid example of this phenomenon.
This feat is obviously accomplished more efficiently by birds with large beaks relative to their body size, as compared to their smaller-beaked cousins who have tiny beaks.
What's behind the avian shape-shifting phenomenon and how does it work?
In the case of birds, these anatomical transformations occur over a short period of time and, in order for one to be able to determine how much shape-shifting is occurring, specimens of birds collected over the decades of the past century and now stored in museums have to be examined to measure the level of shape-shifting change.
It has been observed that this evolutionary process occurs within individual species of birds or within certain groups of birds in the past, although some research has focused on evidence to the contrary. The current research, however, provides insight into this rapidly developing branch of avian biology by examining nearly 6,000 birds representing 86 different species, spread across 10 orders.
As part of the research, which is led by PhD student Sara Ryding from Deakin University and her colleagues in Melbourne, Australia, this study focuses on the avian population of the Australian continent.
For Ryding’s supervisor, Dr Matthew Symonds, a 3D scanning technology was chosen as a solution to ensure that the highest level of accuracy could be achieved when measuring thousands of bird specimens necessary for this type of study.
After conducting careful research on all qualified 3D scanners on the market, Symonds contacted his local Artec partner Objective3D.
The company’s specialists introduced him to the Artec Space Spider, a metrology-grade, a handheld 3D scanner that’s an established favourite among researchers and other professionals with stringent requirements for the utmost accuracy and resolution.
The traditional way of detecting shape-shifting in birds demands the use of digital callipers to calculate the length, width, and depth of bird beaks. From there, these dimensions are plugged into an equation that gives researchers the surface area of a cone of the same size.
Capturing unabridged 3D shape data with Space Spider
Commenting on the fact that bird beaks come in a wide variety of complex shapes, Ryding said, “By reducing the measurements of a beak down to a simple cone shape, you’re going to be losing some geometry there, and that means missing out on important anatomical surface data that should be recorded.”
As she explained, “I am focusing my research on a wide variety of birds, including ducks, songbirds, and birds of prey...and when you study such a wide range of birds, it's inevitable that the beak shapes of these birds will vary greatly from species to species.” In my opinion, 3D scanning is the best method for capturing all the organic anatomy of a surface in this type of application since you are capturing all the organic features without leaving anything out.”
There is one more challenge associated with the manual measurement process: the potential for operator error. As a result of slightly different calliper placements between researchers, there can be significant variations in the measurements taken from researcher to researcher, which can have a significant effect on the results of the data even when the researchers have the best intentions and experience.
In seconds, you can make measurements down to the nanometer level, and scan after scan.
In Ryding’s words, “With the Artec Space Spider, you can reduce operator error to an absolute minimum, since almost every scan will be the same, regardless of who is scanning.” This is what every researcher aims for. In turn, this allows us to gain a better understanding of correlations and helps us come to our conclusions when the dataset is more accurate.
It has been found by Symond's research that the beaks of the birds being studied have grown approximately 4% to 10% larger in size over the past century as a result of breeding.
In terms of productivity, even with the COVID-19 lockdowns limiting her museum collection access to only sporadic visits, she still managed to scan more than 3,000 birds over the course of several months. Her ultimate target is 6,000 birds.
Ryding usually begins her scanning day by taking a number of specimens to the museum. With help from the curator, Ryding finds the trays with these specimens and begins searching through them, looking for the specimens that were collected for scanning, based on the year, location, etc. that the specimen was collected.
With smaller birds, she can scan about 40 or 50 in one afternoon. For larger birds, about 30 to 40 is a more realistic goal.
A typical scanning workflow by Ryding is to place a bird on a turntable, facing upwards, so the bird is lying on its back when it is scanned. After capturing the essential anatomy of the bird with Space Spider, she rotated the turntable slowly, capturing all the essential beak anatomy at the same time. In just two minutes, this process can be completed, and the result is a high-quality scan that is highly versatile.
Reliable 3D data that eclipses manual measurements.
In Ryding’s words, “Each scan gives me more than sufficient surface data for all of my analyses, and even enough for future research potentials, such as geometrical morphometrics. Thinking about the old way of doing this, there’s no way that a set of digital callipers could capture even a fraction of this highly-detailed surface data.”
She uses Artec Studio software to process the scans, whether she is doing it at her home or at her university. In total, from start to finish, each bird scan takes approximately six minutes from start to finish.
She went into detail about this step, “My scan processing workflow is as follows: I do a global registration, then outlier removal, followed by a sharp fusion, which keeps everything, even all the tiniest details, crystal clear. After that, I apply the texture, to make sure I can see where the feathers end and the beak begins.
As a result, I began the scanning process by trimming out all of the unnecessary parts, so that only the beak remained.
In order to verify the accuracy of Ryding's measurements, and to check them against the dimensions gauged with the digital callipers, Ryding then uses Artec Studio's measurement tool to obtain linear measurements of the beak as a type of control check.
As she explained, her next step is to do what digital callipers are incapable of doing, which is to measure the entire area of the beak, and not just its linear dimensions. I then do what digital callipers are unable to do: I measure the surface area of the beak.
“Space Spider captures every tiny sweep and curve of beak anatomy, which makes it possible to accurately determine the surface area of the beak, down below a millimetre.”
Furthermore, Ryding explained, “I take the measurements as is and I use them as is, but if I were to perform geometric or morphometric analyses with these Space Spider scans, which I or another researcher could do, I could just export the models into various applications and take them to accomplish the necessary tasks using PLY files.”
As far as expanding the scope of this research outside of Australia's borders goes, Ryding believes that a larger number of researchers will be able to add to this existing data pool. This will allow the researcher to accurately quantify and compare the shape-shifting that has occurred across regions, continents, and hemispheres in various species of birds (or other animals).
Research in biology is becoming increasingly dependent on the use of 3D scanning.
In her opinion, 3D scanning is a must-have for reliably achieving that goal: “If we want to facilitate our studies, from researcher to researcher, having directly comparable, accurate data is imperative. Manual measurements are no longer sufficient.”
The Space Spider, Ryding explained, could capture submillimeter surface data along with realistic texture details of the bird in just a few minutes per bird, which would enable us to produce every piece of data that we need to carry out our present and future projects."
For researchers with no access to effective 3D scanners, Ryding and her team are improving the existing formula (using geometry) for estimating beak size in birds, by comparing formula estimates with accurate 3D model measurements created with Space Spider.
Her method of doing this was to identify which of the eight separate measurements of the linear beaks are of the utmost importance. Ryding then devised a new formula for improving manual measurements of beak size by using a few of these measurements and comparing them with 3D models of the same specimens.
A lot of Ryding's research is still ongoing in this direction, and there are plans for expanding the coverage of more species and adding additional formulas to the collection.