Structure-from-Motion Photogrammetry for Modeling Coral Reefs

“Platygyra daedalea, sometimes known as the lesser valley coral, is a colonial species of stony coral in the family Merulinidae. It occurs on reefs in shallow water in the Indo-Pacific region. It is a common species and the International Union for Conservation of Nature has assessed its conservation status.' - Icunredlist ​ This brain coral was located on the southern side of the coral garden known as Siete Pecados off the coast of Coron, Philippines. The pictures (84) were obtained from a 4K HD video shot in wide mode using a GoPro Hero 3+; the video was corrected for barrel/fisheye distortion using GoPro Studios. The stills were removed using VideoLAN media player’s scene filter and then resized using Image Resizer.

With anthropomorphic climate change in the process of altering the status-quo of Earth’s environments, the destruction coral reefs are facing is finally obtaining the attention they have deserved from the general public. Coral reefs are not just aesthetically pleasing; the environments they create are biodiverse and provide country's fishing and tourism industries with millions of USDs of revenue a year. Where there are coral reefs, they act as barriers and first lines of defense against storm surges and help to mitigate flooding of coastal cities while also providing over 500 million humans with stable food and income. Coral reefs are invaluable to thousands of species of fish who use the area for reproduction and juvenile stages of life where 25% of marine life rely on reefs for survival, The importance of coral reefs to life on this planet is grossly understated while many of the public are only able to recognize coral reefs as colorful rock like structures in the ocean. The general unawareness of these creatures is exactly why marine scientists are pushing to educate the public of their necessity before it becomes too late. Coral reefs are massive organic structures large enough to be viewed from the International Space Station, yet they were created by simple, but extraordinary marine organisms. As the apex species on this planet, the sole responsibility of assisting these remarkable creatures rests on our shoulders. Even as non-scientists, individuals can educate themselves and others around them on ways to support marine scientists and conservationist in their mission to save the coral reefs.

Abstract ​ With the increase in usage of inanimate energy sources since the early-19th century, Earth’s atmosphere has accumulated more greenhouse gases (GHGs) as a byproduct of their combustion. As the volume of GHGs (notably CO2, CO, CH4, and N2O) in the atmosphere increases, the greater retention of heat energy blankets the planet altering the current climate. Global temperatures on average have risen by 1.4 degrees Celsius with models projecting 2 degrees by as early as 2064. Coral polyps are colorful individual marine organisms within the Cnidarian phylum that in large numbers, form colonies on top of calcium-carbonate structures known as coral. Polyps share a symbiotic relationship with a species of micro-algae called zooxanthellae and are highly temperamental to changes to their environment. Stress factors such as temperature changes can trigger polyps to bleach and expel zooxanthellae to ensure short term survival; if conditions persist, polyps eventually starve and the coral structure becomes overgrown with algae and begins to erode without fortification by polyps. For the past two decades, the frequency and severity of bleaching events have been on the rise; in 2015, the planet's coral reefs underwent the most severe global bleaching event on record. With 3D printers becoming more precise and economic, scientist and marine conservationist are now experimenting with printing coral structures to help repair and even build entire coral reefs. Within the open-source community, photogrammetric and 3D modeling software has become readily available to the public making it possible for untrained users to create sophisticated models without the need for specialized and costly equipment. This article attempts to provide a friendly workflow to assist in building 3D models of coral structures to proliferate the number of available models on the internet for marine scientists to experiment with.

Anatomy ​ Coral is often regarded as the colorful forests of the sea, saturated with all different kinds of hue, creating a spectacle for divers and those brave enough to venture into the unknown. But at a closer glance, coral is actually made up of a myriad of tiny, individual yet identical organisms known as polyps. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Hard branching coral (left) composed of calcium-carbonate consisting of thousands of individual polyps. Coral polyps (right) are invertebrate marine organisms with close relation to jellyfish (both species falling under the Cnidarian phylum). The shape of coral created by polyps is based on the species of polyps. Picture credit - Rottnest and Sanibel Sea School ​ These simple creatures consist of a mouth at the end of their cylindrical bodies with a symmetrical set of tentacles. During the day, polyps rely on the thousands of single-celled microalgae known as zooxanthellae to provide them with nutrients. These colorful autotrophic organisms using photosynthesis to provide nutrients to their host and help them survive in exchange for protection from predators. At night time, zooxanthellae cannot photosynthesize without sunlight and lay dormant while the polyps take over. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Although there are over a thousand different species of polyps, their basic anatomies are strikingly similar. Photo credit - Encyclopaedia Britannica ​ ​ Polyps use their moveable limbs containing stinging cells, much like stinging nettle, to impale, paralyze, and inject venom into small fish and other plankton. Prey that polyps catch are then consumed through their mouths and digested internally. They can then excrete the waste by releasing it through pores near the base of their bodies, or by regurgitating it back out through their mouth. Polyps are also able to share nutrients with other individuals within the colony through an intricate gastrointestinal network that links them together. Thanks to their symbiotic relationship and their ability to share food with others in the colony, polyps are high productive organisms who reside in nutrient poor water. The portion of the water column where shallow water corals are located is referred to as the euphotic zone and it provides photosynthetic bacteria, plankton, and algae like zooxanthellae with enough light to produce organic matter using photosynthesis. Not only is this portion of the water column important for the availability of light, it is also where there is some nutrients in the form of inorganic matter (carbon, nitrogen, phosphorus). In the euphotic zone, phytoplankton can find equilibrium where they obtain the most light and nutrients (inorganic materials) possible.

Life Cycle ​ Polyps can have genders or be hermaphroditic; because of this, coral can be made up of colonies containing all male, all female, mixed, or hermaphroditic polyps. Depending on their gender and species, they can reproduce asexually (budding, fragmentation) or sexually (broadcasting, brooding). Asexually, polyps can reproduce by budding which is the process where polyps of a coral begin splitting themselves in half to create identical copies. The second method of asexual reproduction is fragmentation, where an entire branch or portion of the colony breaks off (usually do to impact or erosion) and forms a new colony consisting of identical polyps. This is similar to how plants are cloned through asexual reproduction. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Coral polyps can reproduce asexually by either fragmentation or by budding. Through sexual reproduction polyps can use broadcasting or brooding (not shown in diagram). Picture credit - AmazingBiotechnology There are two methods of sexual reproduction: broadcasting and brooding. After reaching sexual maturity, male and female polyps begin making and accumulating the sperm and eggs they produce throughout the year and store them in sacks called gametes. During one night of the year, the species of coral within the area instinctively time the simultaneous release of their gametes within a single hour of each other. Scientists are still unsure of the mechanisms in which each individual knows to release their gametes but believe it involves chemical signaling. The buoyant gametes float towards the surface where the decrease in pressure causes them to burst open like a balloon entering higher atmosphere. Once released, the sperm cells seek out eggs of the same species and fertilize them to form a zygote, eventually morphing into the larva or planule. ​ Brooding is similar to broadcasting; the male polyp releases its sperm cells into the water column where they swim and attempt to locate a female of their species containing eggs. The sperm cell swims into the mouth of the female polyp where it attempts to fertilize the egg internally to form a zygote. In this method, the zygote is safe inside the female polyp until it reaches the larva stage where she will then expel the planule into the water column where it will seek to create a new colony. ​ At this stage the planulae is nektonic and is able to swim, however it has limited mobility and is similar to other types of plankton who rely on currents and surface area to move and stay within the water column. The planulae shows signs of phototaxis which allows it to identify the presence of light. Phototaxis helps to provide it with directions to swim towards in the water column and assist in finding a place to settle. Once the planulae finds an area of stable substrate, it anchors down permanently, relinquishing its ability for locomotion for the rest of its life and begins to take in zooxanthellae for nutrients and starts to grow a new colony.

Bleaching ​ Coral bleaching is the natural response in which coral polyps expel zooxanthellae and/or the pigment used by zooxantheallae to perform photosynthesis decreases. Coral polyps are close to transparent, while the zooxanthellae are the ones that contain the pigments creating vibrant colors. Corals appear white when bleached due to the polyp’s transparency and the white calcium-carbonate coral structure beneath them. ​ Corals are particularly finicky about their environment; if factors like temperature, salinity, UV light, or turbidity start to alter, corals begin to feel stressed and expel their symbiotic partner. The reasoning behind terminating this relationship is believed to be the polyp’s way of ensuring short-term survival. If environmental variables alter and zooxanthellae cannot provide the nutrients efficiently then polyps abort them. Some hypothesis propose that coral purposely bleach to rid themselves of zooxantheallae species that are not able to work as efficiently as needed and they allocate space for robust species capable of performing in a changing marine environment. This mechanism is analogous to a landlord removing tenants unable to provide payment to make room for more affluent residents. If the stress factor is mitigated, polyps can attain zooxantheallae in a matter of months, maybe weeks, regaining their vibrant colors as well. But, because the zooxantheallae provide up to 90% of the nutrients needed to keep polyps alive, if stress factors persist or worsen polyps, eventually starve to death leaving behind their organic tissue on the coral structure. At this time, algae will begin to attach to the coral structure to consume the tissue giving the coral a greenish-brownish color. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ The color of coral can give an indication on its current health: if coral is colorful then it contains healthy polyps with working zooxanthellae, if the coral is white then the polyps contain little to no zooxanthellae and is starving, while if the coral is covered with fuzzy brown organic matter, the polyps are likely dead and their tissue is being consumed by algae. At this point the coral is essentially dead and will begin to break apart and dissolve without polyps. Photo credit - GBRMPA ​ ​ Coral are shown to start bleaching when rapid changes in temperature occur; typically corals are more likely to bleach when temperatures increase rather than when they decrease. Coral have a lower tolerance for temperature increases, they have been reported to start bleaching with an increase of 2-3 degrees Fahrenheit, while able to sustain productivity in a decrease of 3-5 degrees. Increased shortwave solar radiance is also thought to have a negative effect on corals acting as a stress factor that can lead to bleaching. Ultraviolet light (280 - 400nm) is shortwave ionizing radiation that is partially blocked by the ozone (O3) layer of Earth’s atmosphere and, due to its high energy and frequency, dissipates quickly when traveling through water. However, changes in water level can reduce the volume of water shielding reefs from UV light, as well as inconsistencies and weakening of the ozone layer caused by chlorofluorocarbons (CFCs). Before the 1980's, each region of the world experienced minor bleaching, however they were isolated to each geographic region and were not a global phenomenon. Marine scientist first recorded their observations on the whitening of corals in specific regions, however it was not until a few years later they understood that it was likely a response to being over stressed due to increased exposure to ionizing UV-B radiation. During the 1980’s, marine scientists around the world start to notice an increase in the amount of bleaching, and the coincidental timing of other region's bleaching events. Less than a decade later in 1997-1998, the first global scale mass bleaching was recorded with the second hot on its heels occurring in 2010. The third global scale mass bleaching event was recognized in 2015, and at this time (2017), scientist believe it might be finally coming to an end. ​ ​ ​

Anthropomorphic Climate Change ​ Climate refers to the longtime trends of weather for a specific region. Climate, like weather is always changing, however at a much slower rate as it is defined as the average weather conditions over a long period of time (usually 10+ years). Gases like CO2, CH4, N2O, H20 are classified as greenhouse gases because their molecular size allows them to interact with light with wavelengths within the thermal band of the electromagnetic spectrum. With these molecules in our atmosphere, they act as a blanket trapping radiating heat that leaves Earth's surface for a period of time before escaping into space. This allows the temperature on the surface of the Earth to be habitable and conducive to life. ​ Earth's climate fluctuates through cyclical patterns over times periods of hundreds of thousands of years. These patterns are due to variations in Earth's orbit around the Sun and were theorized by Milutin Milankovitch in the early 20th century. The variations affect the orbit's eccentricity, obliquity and precession and deviate roughly every 400k, 40k, and 23k, years, respectively. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ The cartoon diagram illustrates the three variations in Earth's orbit around the Sun. The variations are what are believed to cause periods of warm and cold climates referred to as 'inter-glacial and glacial periods'. Earth is currently in an inter-glacial period after the last glacial maximum occurred roughly 22.5k years during the Pleistocene epoch and . Photo credit - Skeptical Scientists ​ ​ Currently the Earth is experiencing an increase in thermal energy retention within its atmosphere; a consensus of climate scientists agree that it is due to the burning of fossil fuels which release greenhouse gases as a byproduct. Since the Industrial Revolution, humans have been increasing the usage of inanimate energy sources to generate energy. Earth's climate has always, and will always change, it is the rate at which the Earth's average temperature is rising is the cause for concern. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ The iconic 'hockey-stick' line graph which depicts the northern hemisphere's average temperature for the past millennia. Photo credit - Penn State News The above graph shows that Earth's temperature regularly fluctuates but the cause for concern originates from how much the average temperature increased in such a short amount of time. As the amount of heat energy in the atmosphere increases, it is expected that extreme weather events will increase in severity and frequency, water levels will rise due to the melting of glacial ice and the thermal expansion of water molecules, and oceans will become more acidic as the atmospheric CO2 dissolves in seawater. ​ ​ Ocean Acidifciation ​ Calcium-carbonate is a molecule that used by certain species of plankton to create their porous shells which are known as tests. Other marine organisms like polyps also utilize this molecule to form their coral housing structures. Without calcium-carbonate many species of phytoplankton (coccolithophores and radiolarians) would not be able to form strong tests, reducing their ability to photosynthesis and create the oxygen animals depend on. A portion of the oceanic carbon cycle known as the 'Carbonate Pump' helps to explain how calcium-carbonate is recycled. Atmospheric CO2 is dissolved by surface waters, breaking down into carbonic acid, bicarbonate and then carbonate, while releasing hydrogen ions. The free carbonate ion can then be bonded with calcium ions in seawater within a creature’s tissue to form tests/coral. As the organism dies, the tests sink and begin to dissolve as they fall into deeper portions of the ocean. The pH level of deep ocean water is lower than that of surface water because it has accumulated more dissolved CO2 over long periods of time, increasing the carbonic acid concentration. Portions of the ocean that contain older water, and therefore more CO2, have higher carbonate-compensation depths (CCDs) and dissolve calcium-carbonate at shallower depths. This CO2 is eventually released back into the atmosphere by upwelling completing the cycle. Unfortunately, it is becoming increasingly difficult for organisms like coral polyps to utilize the carbonate ion to form calcium-carbonate due to the increase in hydrogen ions in the ocean. These hydrogen ions come from atmospheric CO2 dissolving into seawater and the breakdown of carbonic acid. For each CO2 molecule dissolved, essentially two hydrogen ions are being freed, causing a decrease in the ocean’s pH and making it more acidic. Because of the increase in hydrogen ions which bond with carbonate, marine organisms must expend more energy to remove the hydrogen ion from bicarbonate to utilize carbonate to bond with calcium. As fossil fuels continue to be burned, atmospheric CO2 continues to increase causing the partial pressure to also increase leading to dissolution in seawater in attempts to reach equilibrium.

Carbon-dioxide in the atmosphere dissolves in seawater through surface action as the atmospheric concentration increases as a result of burning fossil fuels to create energy. As it dissolves it combines with seawater to form carbonic-acid; this carbonic-acid breaks down further releasing two hydrogen ions that will bond with carbonate ions to form bicarbonate ions. Simply put, the more hydrogen ions in the water, the more acidic the water is resulting in coral polyps working harder to create their coral structures. Photo credit - Ocean Health Index

3D Printing Coral ​ As the severity and frequency of bleaching events increases around the world, marine scientist are attempting many different techniques to restore and rehabilitate coral reefs. Some scientists like Dr. David Vaughan are looking into artificial selection of polyps which involves mass producing robust and higher tolerant polyps inside a controlled environment using micro-fragmentation. Others like Dr. Kathryn Shamberger are studying specific species of polyps which grow in remote locations and are naturally resistant to low pH levels. A novel technique that is being tested by scientist and marine conservationists is the construction of coral using 3D printing technology. 3D printing, or additive manufacturing technology was first made in the 1980's but was not popularized until the past decade. 3D printers are now becoming more affordable and many companies are directing their products to the general public. 3D printers normally use filament that is composed of ABS, PLA, nylon, or even powdered materials (depending on the type of printer). As printing has become more mainstream, a variety of fields have adopted its use and are experimenting with the applications while big printing companies like MakerBot have been working on new inks to satisfy their requests. In 2015, MakerBot released a PLA composite filament containing Limestone, a sedimentary rock primarily composed of calcium-carbonate, the same molecule secreted by polyps to build coral. Using 3D printers, scientists are attempting to rebuild coral reefs by printing to scale models of coral structures that were reconstructed from images using photogrammetry software. Coral structures grow at rates of 2mm - 10cm per year depending on the species of polyps; as the ocean becomes more acidic, many species of polyps under stress are unable able to build strong structures as quickly as before. After the planule stage, polyps give up their ability to move and stay stranded on their coral in warming and acidic waters. With materials emulating the calcium-carbonate substance, scientist are using printers to create high resolution models and introducing them into different environments to see if they can attract planule. By providing polyps with vacant structures that mimic their own creations, scientist hope they can assist polyps in rebuilding entire coral reefs in areas better suited for their tolerance levels, in housing more resistant to ocean acidification! ​

Site Location ​ Using the methodology described below I was able to create accurate 3D models of underwater coral using open source software and inexpensive, consumer-grade cameras. For the project I utilized a GoPro Hero 3+ with the capture settings configured to 12M/Wide mode. I also grabbed stills from videos shot in the 4k HD/Wide mode using VideoLAN's Media Player's 'scene' filter; The video was corrected for barrel/fisheye distortion using GoPro’s Studio software. Normally when creating photogrammetric models, the environment should be controlled to reduce the changes in lighting and background; setting the camera to manual mode is advised so all images share the same quality. Taking images in an underwater environment restricts the user's ability to control natural lighting, distortion, and marine life obstructing views of the target. Due to the nature of an action camera, the GoPro has limited options for a 'manual mode' and does not allow the user to configure the settings to the same degree a DSLR would. Because of this, the camera's capture settings were set to automatic for all images.

A satellite image from Google Earth of the area surrounding south of Coron Town Proper (above). A veiw of Seite Pecaods coral garden (below). Photo credit - Coronislandtours and Budjetsetter

All photos were taken underwater at the Siete Pecados (“Isles of Seven Sins”) coral garden off the coast of Coron, Philippines. The garden is a cluster of seven karst isles located 2 kilometers south of Coron Town Proper and 300 meters off the coast of Busuanga. The area is a protected marine sanctuary and possibly the most visited location by tourists via island hopping excursions.

Photogrammetry Workflow

A workflow diagram I created describing the steps to create a watertight, 3D textured model using Image Resizer, VisualSFM and Meshlab. ​ The following methodology was implemented in the creation of the 3D models of coral shown below using open source photogrammetry software and consumer grade hardware. The programs used were Image Resizer for Windows, VisualSFM, Meshlab, and Blender (optional). ​ Image Resizer is a lightweight program made for the Windows operating system (a version for Mac is available as well) which reduces the size of images while still preserving it for photogrammetry by resampling the pixels. Simply said, resampling reduces the overall number of pixels in an image by averaging; every four pixel values will be averaged into one, reducing the length from 4000 pixels to 1000 pixels long. Although this potentially reduces the number of matches between images, it saves a tremendous amount of time and effort on your computer's RAM and processor. If images are not resampled before using VisualSFM, a project consisting of more than 75 images could easily take more than 24 hours to render a dense cloud. VisualSFM (structure from motion) is another open source program that is free to use and distribute. It was created by Wu Changchang during his postdoc while at the University of Washington Seattle. VisualSFM can take multiple images from different angles of an object or structure to generate sparse point clouds by using a similar technique that humans (and other animals with similar optics) use which allows the brain to understand the 3rd dimension of objects from our 2nd dimensional viewing prospective. VisualSFM is able to obtain the information needed to generate sparse dense clouds using a scale-invariant feature transform (SIFT) algorithm which essentially looks for specific commonalities between two or more images. It does this by scanning the pixel values that make up each image and searches for large gradients of contrast or great differences between neighboring pixels (see below). These areas are considered points of interest or, invariant local features, and are stored in .sift files which are assigned to every image in the queue. The algorithm essentially finds clusters of pixels whose values are much different than those around it and checks to see if other images also contain those pixels. It saves the values of the clusters of pixels along with information on their location, scale, and orientation in the .sift file and then attempts to match the clusters of pixels in all the remaining images in the queue. The program will compare every image with one another at least once, storing the information in the .sift files and creating a vast intricate web of connections through common pixels, between the uploaded images. ​ ​ ​ Examples of invariant local features, or, points of interest. Note the algorithm can detect the features regardless of the scale or orientation making the matching process robust to differences in angles and locations of the camera when capturing images. Photo credit - Piers Neal ​

To improve the amount of matches between images is straightforward: use a camera that contains a large sensor and is able to take high resolution images. As a quick review: the sensor, or charge-coupled device (CCD, or CMOS) is what determines how large the pixels are, while the resolution is total number of pixels the resulting image can have. The CCD is the device that uses transduction to convent photons into electrons; light travels as a wave/particle duality and is carried in packets called photons. The photons carrying visible light (390 – 700 nm) hit a small portion of the CCD and their energy is converted into charged electrons where the number of electrons will represent the intensity of light for that area. The voltage of the electrons are later converted into a value and stored in memory to be recompiled with the rest of the values later to form an image. A camera with a larger CCD (larger pixels) will able to store more light in each pixel opposed to a smaller CCD (see below). Having a greater range of pixel values increases the likelihood of invariant local features, leading to a higher number of matches between two images. The resolution (often measured in megapixels) refers to overall number of pixels in an image. A camera with 8 megapixel output produces an image with dimensions of roughly 4096 x 2048 pixels. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Although the camera manufactures may boast about their camera's resolution, make sure the camera's charged-couple device (CDD) or complimentary metal-oxide-semiconductor (CMOS) is up to par. Otherwise, the resulting images just have more pixels rather than crisper images with higher contrasts of colors. Photo credit - Panasonic ​ ​ ​ ​

If enough images are matched together through common invariant local features, a spare dense cloud can be generated. A point cloud is a collection of points in a 3-dimensional Cartesian coordinate system where each point has a definite x, y and z-value. The .sift file of each image contains the x and y values of the invariant local feature; because there are two or more images that also contain matching x,y-values representing the same invariant local feature, it is possible to use principles of trigonometry/parallax to calculate a z-value. The z value can be estimated following the assumption that the light ray reflected from the target towards the camera sensor traveled in a straight line with little to no distortion. Using a set of collinatory equations and metadata stored in the image at the time it was taken, the z-value can be calculated as the location in 3-dimensional space where the two light rays intersect: at the invariant local feature. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Calculating the z-value is a matter of trigonometry, it follows the same principle that scientists use today to calculate the distances of stars and planets. It’s also how Eratosthenes measured the circumference of the Earth in 250 BCE. Photo credit - Alshawabkeh Y. (et al) 2011 and Farnham

After creating a sparse point cloud, VisualSFM utilizes Yasutaka Furukawa's Clustering Views for Multi-view Stereo (CMVS) algorithm to generate a dense point cloud. When calculating the z-values for points to build a sparse point cloud, the algorithm also determines the location of the camera relative to the target when the image was taken. Knowing the camera’s location is what allows the CMVS software to construct a dense point cloud.

A sparse point cloud of a barrel sponge generated by VisualSFM's 'Compute Missing Matches' tool. The point cloud was generated using 76 images which were taken with a 12-megapixel camera, and resampled to to 1440 x 1080, roughly 1.5-megapixels.

Using Yasutaka Furukawa's Clustering Views for Multi-view Stereo (CMVS) algorithm to generate a dense point cloud in VisualSFM.

Once generated, the dense point cloud model can be cleaned of stray pixels and noise, and will be the basis of a 3D mesh in the program Meshlab. With Michael Kazhdan and Hugues Hoppes’ surface construction algorithm, a smooth, watertight surface can be generated from the dense point cloud. Using the Poisson equation as a function to estimate values, Kazhdan and Hoppes’ algorithm first finds the orientation of the points to differentiate the interior from the exterior of the point cloud. Once established, a sort of isoline is drawn to connect the points to create an isosurface; points far enough away from the boundary between interior and exterior are classified as noise and are not connected by the isoline to create the surface.

A diagram displaying the theory behind Michael Kazhdan and Hugues Hoppes’ Poisson surface reconstruction algorithm that generates surfaces using a dense point cloud (above). The application of the Poisson algorithm on the barrel sponge dense point cloud (below). Picture credit - Kazhadan and Hoppe

The algorithm can patch holes by interpolating values between known points of the dense cloud creating watertight model able to be 3D printed. The final step is to texture map the Poisson mesh using the images used to create the sparse and dense point cloud. Using the filter ‘Parameterzation + texture from registered rasters’, meshlab can take portions of the original images and apply them to surface of the Poisson mesh. The filter replaces values representing the surface by projecting fragments of the images.

A snapshot of the completed Poisson mesh with Parameterization texture mapping applied. Ain't it a beaut?

Completed Models ​ Below are some of the completed models created following the above workflow; to see the rest of them check out my Sketchfab page here.

This barrel sponge was located on the southern side of the coral garden known as Siete Pecados off the coast of Coron, Philippines. The pictures (76) were taken with a GoPro Hero 3+ with 12 megapixel/wide settings and were not corrected for their barrel/fisheye distortion. Not composed of coral polyps but still a neat looking model.

This brain coral was also located on the southern side of Siete Pecados ; the model is composed of 59 images shot using the GoPro Hero 3+'s 12-megapixel camera on wide mode. The texture mapping on this model turned out really well, however, the back side appear black due to the lack of light as the coral was close to one of kart isles which created an overhang.