Invertible Orientation Scores of 3D Images

The enhancement and detection of elongated structures in noisy image data is relevant for many biomedical applications. To handle complex crossing structures in 2D images, 2D orientation scores were introduced, which already showed their use in a variety of applications. Here we extend this work to 3D orientation scores. First, we construct the orientation score from a given dataset, which is achieved by an invertible coherent state type of transform. For this transformation we introduce 3D versions of the 2D cake-wavelets, which are complex wavelets that can simultaneously detect oriented structures and oriented edges. For efficient implementation of the different steps in the wavelet creation we use a spherical harmonic transform. Finally, we show some first results of practical applications of 3D orientation scores.Comment: ssvm 2015 published version in LNCS contains a mistake (a switch notation spherical angles) that is corrected in this arxiv versio

Characteristics and sinking behavior of typical microplastics including the potential effect of biofouling : implications for remediation

Microplastics are ubiquitous pollutants within the marine environment, predominantly (>90%) accumulating in sediments worldwide. Despite the increasing global concern regarding these anthropogenic pollutants, research into the remediation of microplastics is lacking. Here, we examine those characteristics of microplastics that are essential to adequately evaluate potential remediation techniques such as sedimentation and (air) flotation techniques. We analyzed the sinking behavior of typical microplastics originating from real plastic waste samples and identified the best-available drag model to quantitatively describe their sinking behavior. Particle shape is confirmed to be an important parameter strongly affecting the sinking behavior of microplastics. Various common shape descriptors were experimentally evaluated on their ability to appropriately characterize frequently occurring particle shapes of typical microplastics such as spheres, films, and fibers. This study is the first in this field to include film particles in its experimental design, which were found to make up a considerable fraction of marine pollution and are shown to significantly affect the evaluation of shape-dependent drag models. Circularity χ and sphericity Φ are found to be appropriate shape descriptors in this context. We also investigated the effect of biofouling on the polarity of marine plastics and estimated its potential contribution to the settling motion of initially floating microplastics based on density-modification. It is found that biofouling alters the polarity of plastics significantly; this is from (near) hydrophobic (i.e., water contact angles from 70 to 100°) to strong hydrophilic (i.e., water contact angles from 30 to 40°) surfaces, rendering them more difficult to separate from sediment based on polarity as a primary separation factor. Thus, besides providing a better understanding of the fate and behavior of typical marine microplastics, these findings serve as a fundamental stepping-stone to the development of the first large-scale sediment remediation technique for microplastics to address the global microplastic accumulation issue

Metabarcoding of marine zooplankton communities in the North Sea using nanopore sequencing

Zooplankton are crucial organisms both in terms of biodiversity and their unique position in aquatic food webs. As such, it is crucial that we improve our insights into how anthropogenic and natural factors may affect these pelagic organisms. Although easily collected in large numbers, the subsequent processing and identification of specimens has usually been a barrier to large-scale biodiversity assessments. DNA barcoding, the use of standardized short gene regions to discriminate species, has been increasingly used by non-taxonomists to identify species. Here, we measured the diversity and community composition of zooplankton in the Belgian part of the North Sea over the course of one year. We identified zooplankton using both a traditional approach, based on morphological characteristics, and by metabarcoding of a 650 bp fragment of the 18S rRNA gene using the MinION™, a portable nanopore-based DNA sequencing platform. We established a method for characterizing zooplankton communities in marine samples using nanopore sequencing. We were able to identify several taxa at the species level, across a broad taxonomic scale and we thus could obtain several diversity metrics, allowing comparisons of diversity and community composition