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Dendroid stony corals build highly complex colonies that develop from a single coral polyp sitting in a cup-like skeleton, called corallite, by asexual reproduction, resulting in a tree-like branching pattern of its skeleton. Despite their beauty and ecological importance as reef builders in tropical shallow-water reefs as well as in cold-water coral mounds in the deep ocean, systematic studies investigating the ontogenetic morphological development of such coral colonies are largely missing. One reason for this is the sheer number of corallites – up to several thousands in a single coral colony. Another limiting factor, especially for the analysis of dendroid cold-water corals, is the existence of many secondary joints in the ideally tree-like structure that make a reconstruction of the skeleton tree extremely tedious.
Herein, we present CoDA, the Coral Dendroid structure Analyzer, a visual analytics suite that allows for the first time to investigate the ontogenetic morphological development of complex dendroid coral colonies, exemplified on three important framework-forming dendroid cold-water corals: Lophelia pertusa (Linnaeus, 1758), Madrepora oculata (Linnaeus, 1758), and Goniocorella dumosa (Alcock, 1902). Input to CoDA is an initial instance segmentation of the coral polyp cavities (calices), from which it estimates the skeleton tree of the colony and extracts classical morphological measurements and advanced shape features of the individual corallites. CoDA also works as a proofreading and error correction tool by helping to identify wrong parts in the skeleton tree and providing tools to quickly correct these errors. The final skeleton tree enables the derivation of additional information about the calices/corallite instances that otherwise could not be obtained, including their ontogenetic generation and branching patterns – the basis of a fully quantitative statistical analysis of the coral colony morphology. Part of CoDA is CoDA.Graph, a feature-rich link-and-brush user interface for visualizing the extracted features and 2D graph layouts of the skeleton tree, enabling the real-time exploration of complex coral colonies and their building blocks, the individual corallites and branches.
In the future, we expect CoDA to greatly facilitate the analysis of large stony corals of different species and morphotypes, as well as other dendroid structures, enabling new insights into the influence of genetic and environmental factors on their ontogenetic morphological development.
Polyp-Cavity Segmentation of Cold-Water Corals guided by Ambient Occlusion and Ambient Curvature
(2022)
The segmentation of cavities in three-dimensional images of arbitrary objects is a difficult problem since the cavities are usually connected to the outside of the object without any difference in image intensity. Hence, the information whether a voxel belongs to a cavity or the outside needs to be derived from the ambient space. If a voxel is enclosed by object material, it is very likely that this voxel belongs to a cavity. However, there are dense structures where a voxel might still belong to the outside even though it is surrounded to a large degree by the object. This is, for example, the case for coral colonies. Therefore, additional information needs to be considered to distinguish between those cases. In this paper, we introduce the notion of ambient curvature, present an efficient way to compute it, and use it to segment coral polyp cavities by integrating it into the ambient occlusion framework. Moreover, we combine the ambient curvature with other ambient information in a Gaussian mixture model, trained from a few user scribbles, resulting in a significantly improved cavity segmentation. We showcase the superiority of our approach using four coral colonies of very different morphological types. While in this paper we restrict ourselves to coral data, we believe that the concept of ambient curvature is also useful for other data. Furthermore, our approach is not restricted to curvature but can be easily extended to exploit any properties given on an object's surface, thereby adjusting it to specific applications.
During the last decades, X-ray (micro-)computed tomography has gained increasing attention for the description of porous skeletal and shell structures of various organism groups. However, their quantitative analysis is often hampered by the difficulty to discriminate cavities and pores within the object from the surrounding region. Herein, we test the ambient occlusion (AO) algorithm and newly implemented optimisations for the segmentation of cavities (implemented in the software Amira). The segmentation accuracy is evaluated as a function of (i) changes in the ray length input variable, and (ii) the usage of AO (scalar) field and other AO-derived (scalar) fields. The results clearly indicate that the AO field itself outperforms all other AO-derived fields in terms of segmentation accuracy and robustness against variations in the ray length input variable. The newly implemented optimisations improved the AO field-based segmentation only slightly, while the segmentations based on the AO-derived fields improved considerably. Additionally, we evaluated the potential of the AO field and AO-derived fields for the separation and classification of cavities as well as skeletal structures by comparing them with commonly used distance-map-based segmentations. For this, we tested the zooid separation within a bryozoan colony, the stereom classification of an ophiuroid tooth, the separation of bioerosion traces within a marble block and the calice (central cavity)-pore separation within a dendrophyllid coral. The obtained results clearly indicate that the ideal input field depends on the three-dimensional morphology of the object of interest. The segmentations based on the AO-derived fields often provided cavity separations and skeleton classifications that were superior to or impossible to obtain with commonly used distance- map-based segmentations. The combined usage of various AO-derived fields by supervised or unsupervised segmentation algorithms might provide a promising target for future research to further improve the results for this kind of high-end data segmentation and classification. Furthermore, the application of the developed segmentation algorithm is not restricted to X-ray (micro-)computed tomographic data but may potentially be useful for the segmentation of 3D volume data from other sources.
During the last decades, X-ray (micro-)computed tomography has gained increasing attention for the description of porous skeletal and shell structures of various organism groups. However, their quantitative analysis is often hampered by the difficulty to discriminate cavities and pores within the object from the surrounding region. Herein, we test the ambient occlusion (AO) algorithm and newly implemented optimisations for the segmentation of cavities (implemented in the software Amira). The segmentation accuracy is evaluated as a function of (i) changes in the ray length input variable, and (ii) the usage of AO (scalar) field and other AO-derived (scalar) fields. The results clearly indicate that the AO field itself outperforms all other AO-derived fields in terms of segmentation accuracy and robustness against variations in the ray length input variable. The newly implemented optimisations improved the AO field-based segmentation only slightly, while the segmentations based on the AO-derived fields improved considerably. Additionally, we evaluated the potential of the AO field and AO-derived fields for the separation and classification of cavities as well as skeletal structures by comparing them with commonly used distance-map-based segmentations. For this, we tested the zooid separation within a bryozoan colony, the stereom classification of an ophiuroid tooth, the separation of bioerosion traces within a marble block and the calice (central cavity)-pore separation within a dendrophyllid coral. The obtained results clearly indicate that the ideal input field depends on the three-dimensional morphology of the object of interest. The segmentations based on the AO-derived fields often provided cavity separations and skeleton classifications that were superior to or impossible to obtain with commonly used distance- map-based segmentations. The combined usage of various AO-derived fields by supervised or unsupervised segmentation algorithms might provide a promising target for future research to further improve the results for this kind of high-end data segmentation and classification. Furthermore, the application of the developed segmentation algorithm is not restricted to X-ray (micro-)computed tomographic data but may potentially be useful for the segmentation of 3D volume data from other sources.
Biological erosion is a key process for the recycling of carbonate and the formation of calcareous sediments in the oceans. Experimental studies showed that bioerosion is subject to distinct temporal variability, but previous long-term studies were restricted to tropical waters. Here, we present results from a 14-year bioerosion experiment that was carried out along the rocky limestone coast of the island of Rhodes, Greece, in the Eastern Mediterranean Sea, in order to monitor the pace at which bioerosion affects carbonate substrate and the sequence of colonisation by bioeroding organisms. Internal macrobioerosion was visualised and quantified by micro-computed tomography and computer-algorithm-based segmentation procedures. Analysis of internal macrobioerosion traces revealed a dominance of bioeroding sponges producing eight types of characteristic Entobia cavity networks, which were matched to five different clionaid sponges by spicule identification in extracted tissue. The morphology of the entobians strongly varied depending on the species of the producing sponge, its ontogenetic stage, available space, and competition by other bioeroders. An early community developed during the first 5 years of exposure with initially very low macrobioerosion rates and was followed by an intermediate stage when sponges formed large and more diverse entobians and bioerosion rates increased. After 14 years, 30 % of the block volumes were
occupied by boring sponges, yielding maximum bioerosion rates of 900 g m^−2 yr^−1. A high spatial variability in macrobioerosion prohibited clear conclusions about the onset of macrobioerosion equilibrium conditions. This highlights the necessity of even longer experimental exposures and higher replication at various factor levels in order to better understand and quantify temporal patterns of macrobioerosion in marine carbonate environments.
Many natural objects contain pores and cavities that are filled with the same material that also surrounds the object. When such objects are imaged using, for example, computed tomography, the pores and cavities cannot be distinguished from the surrounding material by considering gray values and texture properties of the image. In this case, morphological operations are often used to fill the inner region. This is efficient, if the pore and cavity structures are small compared to the overall size of the object and if the object’s shape is mainly convex. If this is not the case, the segmentation might be very difficult and may result in a lot of noise. We propose the usage of ambient occlusion for the segmentation of pores and cavities. One nice property of ambient occlusion is that it generates smooth scalar fields. Due to this smoothness property, a segmentation based on those fields will result in smooth boundaries at the pore and cavity openings. This is often desired, particularly when dealing with natural objects.