Developing a USGS Digital Coral Growth Archive using Rotating X-Ray Computerized Tomography - The ACTS Project Active
The Archival Computed Tomography Scanning Project (ACTS) currently develops the USGS Coral Core Archive, housed at the Pacific and St. Petersburg Coastal and Marine Science Centers, that contains approximately 500 coral reef cores from U.S. jurisdictions worldwide. This archive, is one of the largest coral archives in the world and provides historical context for coral-reef science studies, including crucial data for modern coral calcification rates, reef erosion, and impacts on reef-lined coasts. The archive also offers unique opportunities to test hypotheses about environmental controls on coral growth and erosion.
In 2019, PCMSC invested in a Geotek core-imaging system, capable of using computed tomography (CT) to create high-resolution, three-dimensional reconstructions of density patterns in coral cores. CT, commonly used in the medical world to acquire x-ray scans for diagnostic purposes, is now considered to be a valuable tool when determining yearly growth rates and the density of corals which can in turn be used to determine the calcification, or constructive process responsible for reef growth.
Relevance
Coral reefs serve as a first line of defense against storm-related hazards in coastal communities. Indeed, a recent USGS study (Storlazzi et al., 2019) found the flood risk reduction provided by U.S. coral reefs protects ~18,000 lives and saves more than $1.8 billion annually. The ability of reefs to continue to buffer the impacts of waves on shorelines depends on the maintenance of a structurally complex reef surface and continued coral growth and reef accretion, particularly as sea-level rise accelerates in the future. Unfortunately, the reef-building capacity of corals has been significantly diminished in recent years as coral populations have experienced dramatic declines around the world as a result of climate change and other human impacts. A recent acceleration of reef restoration efforts by federal and state agencies (e.g., NOAA, DARPA, FWC) as well as academic researchers and NGOs (e.g., TNC) are seeking to reverse this trend; however, the efficacy of these efforts relies on setting realistic restoration targets based on natural baselines of coral growth and erosion. The records of historical coral growth and erosion contained within the USGS coral core archives have the potential to provide invaluable science-based guidance for setting those targets.
The Challenge
Corals have presented unique challenges in developing consistent protocols and methods for determining bulk density due to high porosity of the skeletal carbonate structure. To date there is no standard coral CT scanning methodology and little practical information on accurately translating RXCT numbers (an approximation of the material's linear attenuation coefficient) to actual density. Our methodology development addresses key issues such as creating and scanning density standards, implementing packaging filters, as well as post-reconstruction filtering to minimize quantum noise effects as well as segmenting object data from the surrounding medium.
Beam Hardening
As a polychromatic x-ray beam travels through an object, lower-energy X-rays are attenuated more easily than higher-energies. This results in a “hardened” X-ray beam with an increased average energy. Beam hardening causes the center of an X-ray CT image to be darker than the edges of the image, an artifact referred to as a cupping effect. Consequently, CT values will differ based upon the location in the image even if the material has a uniform density. To gain uniform values throughout the sample, filters and packing material can be used to pre-harden the beam and achieve uniform X-ray energies throughout the sample.
Packing aids in the reduction of beam hardening effects but contributes to an increase in X-ray attenuation. As X-ray beams travel through matter, they are absorbed or deflected and scattered. This scattering leads to a decreased intensity as the beam travels further into the sample. Packing material enclosing a sample will increase x-ray attenuation and lead to artifacts and increased noise in the image.
X-ray Attenuation
X-ray attenuation is the process wherein X-rays interact with matter, leading to a reduction in their intensity. This interaction is influenced by the density of the material; denser substances attenuate X-rays more effectively thus allowing for detailed visualization of internal structures based on their differing absorption properties. However, as x-ray beams travel through matter, they are absorbed or deflected and scattered. This scattering leads to a decreased intensity as the beam travels further into the sample. Packing material are required to be uniform and without air gaps to increase x-ray attenuation without leading to artifacts and increased noise in an image.
Density Offsets
To convert CT values to real-world densities and quantify the uncertainty in reconstructed density as a result of offsets, a set of carbonate standards are included in every scan that represent a range of coral species with different densities. With optimal sample packaging and CT settings, differences between CT gray values and true bulk densities approach matching values (R2= 0.999).
Final Products
The developed standardized RXCT methodology was applied to the entire USGS Core Archive containing approximately 500 coral and reef cores. The resulting CT imagery will be compiled in one of the largest permanent, high-resolution, publicly accessible digital coral archives in the world. The coral archive is produced at a maximum Voxel/Pixel resolution of ~ 50 µm, which resulted in a total archive volume of more than 35 terabytes. Examples of the data density can be viewed in the animated GIFs below. The data will become publicly available through to researchers at USGS and external institutions to increase scientific understanding for decades to come.
Coral Reef Project
The Archival Computed Tomography Scanning Project (ACTS) currently develops the USGS Coral Core Archive, housed at the Pacific and St. Petersburg Coastal and Marine Science Centers, that contains approximately 500 coral reef cores from U.S. jurisdictions worldwide. This archive, is one of the largest coral archives in the world and provides historical context for coral-reef science studies, including crucial data for modern coral calcification rates, reef erosion, and impacts on reef-lined coasts. The archive also offers unique opportunities to test hypotheses about environmental controls on coral growth and erosion.
In 2019, PCMSC invested in a Geotek core-imaging system, capable of using computed tomography (CT) to create high-resolution, three-dimensional reconstructions of density patterns in coral cores. CT, commonly used in the medical world to acquire x-ray scans for diagnostic purposes, is now considered to be a valuable tool when determining yearly growth rates and the density of corals which can in turn be used to determine the calcification, or constructive process responsible for reef growth.
Relevance
Coral reefs serve as a first line of defense against storm-related hazards in coastal communities. Indeed, a recent USGS study (Storlazzi et al., 2019) found the flood risk reduction provided by U.S. coral reefs protects ~18,000 lives and saves more than $1.8 billion annually. The ability of reefs to continue to buffer the impacts of waves on shorelines depends on the maintenance of a structurally complex reef surface and continued coral growth and reef accretion, particularly as sea-level rise accelerates in the future. Unfortunately, the reef-building capacity of corals has been significantly diminished in recent years as coral populations have experienced dramatic declines around the world as a result of climate change and other human impacts. A recent acceleration of reef restoration efforts by federal and state agencies (e.g., NOAA, DARPA, FWC) as well as academic researchers and NGOs (e.g., TNC) are seeking to reverse this trend; however, the efficacy of these efforts relies on setting realistic restoration targets based on natural baselines of coral growth and erosion. The records of historical coral growth and erosion contained within the USGS coral core archives have the potential to provide invaluable science-based guidance for setting those targets.
The Challenge
Corals have presented unique challenges in developing consistent protocols and methods for determining bulk density due to high porosity of the skeletal carbonate structure. To date there is no standard coral CT scanning methodology and little practical information on accurately translating RXCT numbers (an approximation of the material's linear attenuation coefficient) to actual density. Our methodology development addresses key issues such as creating and scanning density standards, implementing packaging filters, as well as post-reconstruction filtering to minimize quantum noise effects as well as segmenting object data from the surrounding medium.
Beam Hardening
As a polychromatic x-ray beam travels through an object, lower-energy X-rays are attenuated more easily than higher-energies. This results in a “hardened” X-ray beam with an increased average energy. Beam hardening causes the center of an X-ray CT image to be darker than the edges of the image, an artifact referred to as a cupping effect. Consequently, CT values will differ based upon the location in the image even if the material has a uniform density. To gain uniform values throughout the sample, filters and packing material can be used to pre-harden the beam and achieve uniform X-ray energies throughout the sample.
Packing aids in the reduction of beam hardening effects but contributes to an increase in X-ray attenuation. As X-ray beams travel through matter, they are absorbed or deflected and scattered. This scattering leads to a decreased intensity as the beam travels further into the sample. Packing material enclosing a sample will increase x-ray attenuation and lead to artifacts and increased noise in the image.
X-ray Attenuation
X-ray attenuation is the process wherein X-rays interact with matter, leading to a reduction in their intensity. This interaction is influenced by the density of the material; denser substances attenuate X-rays more effectively thus allowing for detailed visualization of internal structures based on their differing absorption properties. However, as x-ray beams travel through matter, they are absorbed or deflected and scattered. This scattering leads to a decreased intensity as the beam travels further into the sample. Packing material are required to be uniform and without air gaps to increase x-ray attenuation without leading to artifacts and increased noise in an image.
Density Offsets
To convert CT values to real-world densities and quantify the uncertainty in reconstructed density as a result of offsets, a set of carbonate standards are included in every scan that represent a range of coral species with different densities. With optimal sample packaging and CT settings, differences between CT gray values and true bulk densities approach matching values (R2= 0.999).
Final Products
The developed standardized RXCT methodology was applied to the entire USGS Core Archive containing approximately 500 coral and reef cores. The resulting CT imagery will be compiled in one of the largest permanent, high-resolution, publicly accessible digital coral archives in the world. The coral archive is produced at a maximum Voxel/Pixel resolution of ~ 50 µm, which resulted in a total archive volume of more than 35 terabytes. Examples of the data density can be viewed in the animated GIFs below. The data will become publicly available through to researchers at USGS and external institutions to increase scientific understanding for decades to come.