Towards the analysis of coral skeletal density-banding using deep learning

AbstractX-ray micro–computed tomography (µCT) is increasingly used to record the skeletal growth banding of corals. However, the wealth of data generated is time consuming to analyse for growth rates and colony age. Here we test an artificial intelligence (AI) approach to assist the expert identification of annual density boundaries in small colonies of massive Porites spanning decades. A convolutional neural network (CNN) was trained with µCT images combined with manually labelled ground truths to learn banding-related features. The CNN successfully predicted the position of density boundaries in independent images not used in training. Linear extension rates derived from CNN-based outputs and the traditional method were consistent. In the future, well-resolved 2D density boundaries from AI can be used to reconstruct density surfaces and enable studies focused on variations in rugosity and growth gradients across colony 3D space. We recommend the development of a community platform to share annotated images for AI.

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Growth Interruptions in Arctic Rhodoliths Correspond to Water Depth and Rhodolith Morphology

Minerals ◽

10.3390/min11050538 ◽

2021 ◽

Vol 11 (5) ◽

pp. 538

Author(s):

Moritz Schlüter ◽

Ines Pyko ◽

Max Wisshak ◽

Christian Schulbert ◽

Sebastian Teichert

Keyword(s):

Light Availability ◽

Growth Patterns ◽

Skeletal Growth ◽

Coralline Algae ◽

Ambient Light ◽

Micro Computed Tomography ◽

Svalbard Archipelago ◽

X Ray ◽

Algal Thalli ◽

Environmental Proxies

Coralline algae that form rhodoliths are widespread globally and their skeletal growth patterns have been used as (paleo-) environmental proxies in a variety of studies. However, growth interruptions (hiati) within their calcareous skeletons are regarded as problematic in this context. Here we investigated how hiati in the growth of Arctic rhodoliths from the Svalbard archipelago correspond to their environment and morphology. Using X-ray micro-computed tomography and stepwise model selections, we found that rhodoliths from deeper waters are subject to more frequent hiatus formation. In addition, rhodoliths with a higher sphericity (i.e., roundness) are less often affected by such growth interruptions. We conclude that these correlations are mainly regulated by hydrodynamics, because, in deeper waters, rhodoliths are not turned frequently enough to prevent a dieback of coralline algal thalli forming on the underside of the rhodolith. In this coherence, spheroidal rhodoliths are turned more easily, therefore shortening the amount of time between turnover events. Moreover, the incidence of light is more advantageous in shallower waters where rhodoliths exhibit a greater share of their surface to diffused ambient light, thus enabling thallus growth also on the down-facing surface of the rhodoliths. In consequence, information on the frequency of hiatus formation combined with rhodolith morphology might serve as a valuable proxy for (paleo-)environmental reconstructions in respect to light availability and the hydrodynamic regime.

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Determinate growth is predominant and likely ancestral in squamate reptiles

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2020.2737 ◽

2020 ◽

Vol 287 (1941) ◽

pp. 20202737

Author(s):

Petra Frýdlová ◽

Jana Mrzílková ◽

Martin Šeremeta ◽

Jan Křemen ◽

Jan Dudák ◽

...

Keyword(s):

Growth Pattern ◽

Growth Arrest ◽

Complete Loss ◽

Skeletal Growth ◽

Ancestral State ◽

Micro Computed Tomography ◽

X Ray ◽

Squamate Reptiles ◽

Adult Growth ◽

Determinate Growth

Body growth is typically thought to be indeterminate in ectothermic vertebrates. Indeed, until recently, this growth pattern was considered to be ubiquitous in ectotherms. Our recent observations of a complete growth plate cartilage (GPC) resorption, a reliable indicator of arrested skeletal growth, in many species of lizards clearly reject the ubiquity of indeterminate growth in reptiles and raise the question about the ancestral state of the growth pattern. Using X-ray micro-computed tomography (µCT), here we examined GPCs of long bones in three basally branching clades of squamate reptiles, namely in Gekkota, Scincoidea and Lacertoidea. A complete loss of GPC, indicating skeletal growth arrest, was the predominant finding. Using a dataset of 164 species representing all major clades of lizards and the tuataras, we traced the evolution of determinate growth on the phylogenetic tree of Lepidosauria. The reconstruction of character states suggests that determinate growth is ancestral for the squamate reptiles (Squamata) and remains common in the majority of lizard lineages, while extended (potentially indeterminate) adult growth evolved several times within squamates. Although traditionally associated with endotherms, determinate growth is coupled with ectothermy in this lineage. These findings combined with existing literature suggest that determinate growth predominates in both extant and extinct amniotes.

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Identification of Fibrotic Thickening as Early Marker of Aortic Valve Stenosis Using X-Ray Micro Computed Tomography and Optical Coherence Tomography

The Thoracic and Cardiovascular Surgeon ◽

10.1055/s-0036-1571661 ◽

2016 ◽

Vol 64 (S 01) ◽

Author(s):

A. Jannasch ◽

C. Schnabel ◽

M. Santini ◽

S. Fest-Santini ◽

M. Lorenzi ◽

...

Keyword(s):

Computed Tomography ◽

Optical Coherence Tomography ◽

Aortic Valve ◽

Aortic Valve Stenosis ◽

Optical Coherence ◽

Micro Computed Tomography ◽

X Ray ◽

Early Marker

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Morphology and Affinities of Ampelocissites Seeds (Vitaceae: Ampelopsis clade) from the Paleogene of Texas, USA

Systematic Botany ◽

10.1600/036364420x15935294613400 ◽

2020 ◽

Vol 45 (3) ◽

pp. 478-482

Author(s):

Steven R. Manchester

Keyword(s):

Computed Tomography ◽

Cross Sections ◽

Seed Coat ◽

Ct Scanning ◽

Seed Morphology ◽

Early Eocene ◽

Micro Computed Tomography ◽

X Ray ◽

Fossil Seeds ◽

Fossil Genus

Abstract—The type material on which the fossil genus name Ampelocissites was established in 1929 has been reexamined with the aid of X-ray micro-computed tomography (μ-CT) scanning and compared with seeds of extant taxa to assess the relationships of these fossils within the grape family, Vitaceae. The specimens were collected from a sandstone of late Paleocene or early Eocene age. Although originally inferred by Berry to be intermediate in morphology between Ampelocissus and Vitis, the newly revealed details of seed morphology indicate that these seeds represent instead the Ampelopsis clade. Digital cross sections show that the seed coat maintains its thickness over the external surfaces, but diminishes quickly in the ventral infolds. This feature, along with the elliptical chalaza and lack of an apical groove, indicate that Ampelocissites lytlensis Berry probably represents Ampelopsis or Nekemias (rather than Ampelocissus or Vitis) and that the generic name Ampelocissites may be useful for fossil seeds with morphology consistent with the Ampelopsis clade that lack sufficient characters to specify placement within one of these extant genera.

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