A Semi-Automatic Method to Extract Canal Pathways in 3D Micro-CT Images of Octocorals

Abstract

The long-term goal of our study is to understand the internal organization of the octocoral stem canals, as well as their physiological and functional role in the growth of the colonies, and finally to assess the influence of climatic changes on this species. Here we focus on imaging tools, namely acquisition and processing of three-dimensional high-resolution images, with emphasis on automated extraction of canal pathways. Our aim was to evaluate the feasibility of the whole process, to point out and solve – if possible – technical problems related to the specimen conditioning, to determine the best acquisition parameters and to develop necessary image-processing algorithms. The pathways extracted are expected to facilitate the structural analysis of the colonies, namely to help observing the distribution, formation and number of canals along the colony. Five volumetric images of Muricea muricata specimens were successfully acquired by X-ray computed tomography with spatial resolution ranging from 4.5 to 25 micrometers. The success mainly depended on specimen immobilization. More than of the canals were successfully detected and tracked by the image-processing method developed. Thus obtained three-dimensional representation of the canal network was generated for the first time without the need of histological or other destructive methods. Several canal patterns were observed. Although most of them were simple, i.e. only followed the main branch or “turned” into a secondary branch, many others bifurcated or fused. A majority of bifurcations were observed at branching points. However, some canals appeared and/or ended anywhere along a branch. At the tip of a branch, all canals fused into a unique chamber. Three-dimensional high-resolution tomographic imaging gives a non-destructive insight to the coral ultrastructure and helps understanding the organization of the canal network. Advanced image-processing techniques greatly reduce human observer's effort and provide methods to both visualize and quantify the structures of interest.

Diversity and Evolution of Octocoral Animal Forests at Both Sides of Tropical America

“…Colony growth in gorgonians is a complex yet self-organized process (Sanchez et al 2004;Sanchez 2004), in which other modules in addition to the polyps (twigs and branchlets) have determinate growth (Lasker et al 2003) but the sum of the parts follows an adaptive growth program (Lasker and Sánchez 2002). The development of a gorgonian colony (astogeny) has arranged relationships between global (whole colony) and local properties (main stem and holdfast), e.g., the number of total branches correlate with the number of stem canals, which suggests that the adaptive colonial growth has a coordinated integration Morales Pinzon et al 2014;Sánchez and Lasker 2004). Consequently, integrated colonial features, such as the main stem, together with seasonal productivity pulses, can provide a demographic record of the colony (Goffredo and Lasker 2006), which has been successfully used as an age proxy to develop individual-based models of population growth and response to clipping (Goffredo and Lasker 2008).…”

Micro‐CT reconstruction reveals the colony pattern regulations of four dominant reef‐building corals

“…They provide limited evidence due to their non‐transparent coral skeletons, which restrict the direct observation of the structures and related parameters in coral colonies (Marfenin, 2015 ). In recent years, computed tomography (CT) has been applied to study reef‐building coral skeletons (Beuck et al, 2007 ; Gutiérrez‐Heredia et al, 2015 ; Knackstedt et al, 2006 ; Kruszyński et al, 2007 ; Kruszynski et al, 2006 ; Pinzón et al, 2014 ). With the development and popularization of high‐resolution micro‐computed tomography (HRCT), research on coral skeletons has revealed the morphological and internal structures of coral branchlets, and also investigated coral skeletal structures (Ivankina et al, 2020 ; Sentoku et al, 2015 ; Sentoku et al, 2015 ; Urushihara et al, 2016 ) and exogenous influences on coral skeletons, including water currents (Chindapol et al, 2013 ), the marine environment (Iwasaki et al, 2016 ), and ocean acidification (Enochs et al, 2016 ; Fordyce et al, 2020 ).…”

Three-dimensional reconstruction of high latitude bamboo coral via X-ray microfocus Computed Tomography

“…Techniques used to investigate the microstructure of coral skeletons, such as scanning electron microscopy (SEM) and the grinding of sections, have relied on methods that require high workloads, strict operability and destructive preparation work 9 . Recent imaging methods, such as high-resolution micro-focus computed tomography (µCT) removes these constraints and, as it allows quantitative analyses of coral skeletal microarchitecture, is emerging as a growing area of scientific focus 10,11 for contemporary investigations of reef-building coral skeletons [12][13][14][15][16] .…”