Benthic Habitats and the Effects of Fishing

2005 ◽  
Keyword(s):  
New Hampshire ◽  
Ground Truth ◽  
Habitat Characteristics ◽  
Benthic Habitat ◽  
Automated Segmentation ◽  
Habitat Types ◽  
Benthic Habitats ◽  
Substrate Composition ◽  
Biological Features ◽  
Ground Truthing

<strong><em>Abstract. </em></strong>Subtidal benthic habitats from the Piscataqua River, New Hampshire and Maine, have been delineated by an automated segmentation technique using bathymetry derived from multibeam echo sounder data. The map, produced by segmentation of seafloor textures, represents a hypothetical benthic habitat map that requires ground-truthing. Video mosaics are being used to ground-truth substrate composition and transitions apparent in the bathymetry data map and to describe biological features and organism occurrences and densities. Here, we describe the utility of video mosaics for ground-truthing benthic habitat characteristics and present two examples of their use. Video mosaics acquired along two transects in the Piscataqua River were used to detect substrate transitions apparent in the bathymetry that were identified as distinct hypothetical habitat types and to quantitatively assess coverages of distinct sediment conditions, density of megafaunal organisms (lobsters), and bioturbational features (crab feeding pits).

scholarly journals Assessing biases, relaxing moralism: On ground-truthing practices in machine learning design and application

2021 ◽  
Vol 8 (1) ◽  
pp. 205395172110135
Author(s):  
Florian Jaton
Keyword(s):  
Machine Learning ◽  
William James ◽  
A Priori ◽  
Learning Algorithms ◽  
Three Dimensional ◽  
Ground Truth ◽  
Machine Learning Algorithms ◽  
Ground Truthing ◽  
Set Up ◽  
The Moment

This theoretical paper considers the morality of machine learning algorithms and systems in the light of the biases that ground their correctness. It begins by presenting biases not as a priori negative entities but as contingent external referents—often gathered in benchmarked repositories called ground-truth datasets—that define what needs to be learned and allow for performance measures. I then argue that ground-truth datasets and their concomitant practices—that fundamentally involve establishing biases to enable learning procedures—can be described by their respective morality, here defined as the more or less accounted experience of hesitation when faced with what pragmatist philosopher William James called “genuine options”—that is, choices to be made in the heat of the moment that engage different possible futures. I then stress three constitutive dimensions of this pragmatist morality, as far as ground-truthing practices are concerned: (I) the definition of the problem to be solved (problematization), (II) the identification of the data to be collected and set up (databasing), and (III) the qualification of the targets to be learned (labeling). I finally suggest that this three-dimensional conceptual space can be used to map machine learning algorithmic projects in terms of the morality of their respective and constitutive ground-truthing practices. Such techno-moral graphs may, in turn, serve as equipment for greater governance of machine learning algorithms and systems.

Scale-dependent relationships between benthic habitat characteristics and abundances of blacklip abalone, Haliotis rubra (Leach)

2010 ◽  
Vol 61 (11) ◽  
pp. 1227 ◽  
Author(s):  
Elisabeth M. A. Strain ◽  
Craig R. Johnson
Keyword(s):  
Spatial Scale ◽  
Red Algae ◽  
Positive Relationship ◽  
Spatial Scales ◽  
Habitat Characteristics ◽  
Benthic Habitat ◽  
Sessile Invertebrates ◽  
Haliotis Rubra ◽  
The Relationship ◽  
Biotic Characteristics

Habitat characteristics can influence marine herbivore densities at a range of spatial scales. We examined the relationship between benthic habitat characteristics and adult blacklip abalone (Haliotis rubra) densities across local scales (0.0625–16 m2), at 2 depths, 4 sites and 2 locations, in Tasmania, Australia. Biotic characteristics that were highly correlated with abalone densities included cover of non-calcareous encrusting red algae (NERA), non-geniculate coralline algae (NCA), a matrix of filamentous algae and sediment, sessile invertebrates, and foliose red algae. The precision of relationships varied with spatial scale. At smaller scales (0.0625–0.25 m2), there was a positive relationship between NERA and ERA, and negative relationships between sediment matrix, sessile invertebrates and abalone densities. At the largest scale (16 m2), there was a positive relationship between NERA and abalone densities. Thus, for some biotic characteristics, the relationship between NERA and abalone densities may be scalable. There was very little variability between depths and sites; however, the optimal spatial scale differed between locations. Our results suggest a dynamic interplay between the behavioural responses of H. rubra to microhabitat and/or to abalone maintaining NERA free of algae, sediment, and sessile invertebrates. This approach could be used to describe the relationship between habitat characteristics and species densities at the optimal spatial scales.

scholarly journals Die plantgemeenskappe van die Ba-landtipe in die Mooirivieropvanggebied, Transvaal

1991 ◽  
Vol 10 (2) ◽  
pp. 85-92 ◽  
Author(s):  
H. Bezuidenhout
Keyword(s):  
Nature Conservation ◽  
Plant Communities ◽  
Soil Type ◽  
Habitat Characteristics ◽  
Clear Distinction ◽  
Conservation Practices ◽  
Numerical Classification ◽  
Habitat Types ◽  
Land Type ◽  
Vegetation Gradients

The aim of this study was to identify, characterize and interpret ecologically, by using habitat characteristics, the major vege­tation units and their variations of the Ba land type. Six plant communities were successfully distinguished through applying a numerical classification (TWINSPAN) and Braun-Blanquet procedures. The plant communities could easily be correlated with specific habitat types. A clear distinction could be made between plant communities of the upland and lowland areas. Vegetation gradients and associated gradients in habitat were identified by using an ordination technique (DECORANA). The studv emphasized the importance of topography and soil type for the delimitation of management units for farming or nature conservation practices.

scholarly journals Plantegroeiklassifikasie van die A-landtipe van die Mooirivier - opvanggebied, Transvaal

1991 ◽  
Vol 10 (1) ◽  
pp. 4-10
Author(s):  
H. Bezuidenhout
Keyword(s):  
Nature Conservation ◽  
Plant Communities ◽  
Soil Type ◽  
Habitat Characteristics ◽  
Clear Distinction ◽  
Conservation Practices ◽  
Numerical Classification ◽  
Habitat Types ◽  
Land Type ◽  
Vegetation Gradients

The aim of this study was to identify, characterize and interpret ecologically, by using habitat characteristics, the major vege­tation units and their variations of the A land type. Five plant communities were successfully distinguished by applying a numerical classification and Braun-Blanquet procedures. The plant communities could easily be correlated with specific habitat types. A clear distinction could be made between plant communities of the upland and lowland areas. Vegetation gradients and associated gradients in habitat were identified by using an ordination technique. The study emphasized the importance of topography and soil type for the delimitation of management units for farming or nature conservation practices.

Benthic Habitats and the Effects of Fishing

2005 ◽  
Keyword(s):  
Habitat Type ◽  
High Energy ◽  
Benthic Habitat ◽  
Commercial Fishing ◽  
Placopecten Magellanicus ◽  
Benthic Species ◽  
Habitat Types ◽  
Closed Area ◽  
Sea Scallops ◽  
Moderate Complexity

<strong><em>Abstract. </em></strong>In late 1994, substantial portions of Georges Bank were closed to commercial fishing to assist with stock rebuilding. These areas were Closed Area I (CAI), located on the western portion of the bank, and Closed Area II (CAII), on the eastern portion. After about 5 years of closure, the southern portion of CAII and the central portion of CAI, having exhibited substantial increases in biomass and density of sea scallops <em>Placopecten magellanicus</em>, were reopened to scallop fishing. Before the industry was allowed entry, we conducted surveys to monitor the recovery of benthic habitat and fauna inside both areas. Sampling sites were selected in a paired station design for an inside–outside comparison representative of major habitat types in each closed area; other stations were chosen to survey the remainder of the closed areas. At each station, we examined a suite of biotic and abiotic variables ranging from substrate type to benthos to nekton. Our results suggest few differences between the inside–outside paired stations in both closed areas for nekton and benthic species composition and species richness. Fish abundance and biomass were similar inside and outside the closed areas. However, individuals of species such as skates (<em>Raja </em>spp.), haddock <em>Melanogrammus aeglefinus</em>, and flounders (Pleuronectiformes) were generally larger inside than outside the closed areas. Additionally, habitat type was important in determining the distribution, abundance, biomass, size, and feeding ecology for some of the more benthic-oriented species studied. In CAI, the differences we observed in the suite of biotic metrics are likely a result of the high diversity of habitat types, with many of the habitat types composed of higher-relief material (e.g., cobble, gravel, etc.) in the region. The seabed in the southern portion of CAII is a relatively high-energy sand habitat of low to moderate complexity and has a relatively low vulnerability to trawling and dredging, which may explain why there were less pronounced differences in abundance or biomass across habitat types in that closed area as compared to CAI. Other parts of closed areas on the northeastern shelf may exhibit more obvious changes in the same biological metrics due to the presence of more complex habitats and increased vulnerability to bottom tending fishing gear. Those differences we observed for CAI and CAII may have implications for the population dynamics of commercially valuable benthic species, yet that question remains a major challenge.

Benthic Habitats and the Effects of Fishing

2005 ◽  
Keyword(s):  
Fisheries Management ◽  
Large Scale ◽  
Scale Effects ◽  
Ecosystem Processes ◽  
Fishing Effort ◽  
Habitat Types ◽  
Benthic Habitats ◽  
Management Actions ◽  
Ecosystem Effects ◽  
Ecosystem Based Fisheries Management

<strong><em>Abstract. </em></strong>We review the impacts of towed gears on benthic habitats and communities and predict the consequences of these impacts for ecosystem processes. Our emphasis is on the additive and synergistic large-scale effects of fishing, and we assess how changes in the distribution of fishing activity following management action are likely to affect production, turnover time, and nutrient fluxes in ecosystems. Analyses of the large-scale effects of fishing disturbance show that the initial effects of fishing on a habitat have greater ecosystem consequences than repeated fishing in fished areas. As a result, patchy fishing effort distributions have lower total impacts on the ecosystem than random or uniform effort distributions. In most fisheries, the distribution of annual fishing effort within habitats is more patchy than random, and patterns of effort are maintained from year to year. Our analyses suggest that many vulnerable species and habitats have only persisted in heavily fished ecosystems because effort is patchy. Ecosystem-based fisheries management involves taking account of the ecosystem effects of fishing when setting management objectives. One step that can be taken toward ecosystem-based fisheries management is to make an a priori assessment of the ecosystem effects of proposed management actions such as catch controls, effort controls, and technical measures. We suggest a process for predicting the ecosystem consequences of management action. This requires information on habitat distributions, models to predict changes in the spatial distribution of fleets following management action, and models of the impacts of trawling disturbance on ecosystem processes. For each proposed management action, the change in disturbance affecting different habitat types would be predicted and used to forecast the consequences for the ecosystem. These simulations would be used to produce a decision table, quantifying the consequences of alternative management actions. Actions that minimize the ecosystem effects of fishing could then be identified. In data-poor situations, we suggest that management strategies that maintain or maximize the patchiness of effort within habitat types are more consistent with the precautionary approach than those that lead to more uniform fishing effort distributions.

scholarly journals LUMINOUS database: lumbar multifidus muscle segmentation from ultrasound images

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Clyde J. Belasso ◽  
Bahareh Behboodi ◽  
Habib Benali ◽  
Mathieu Boily ◽  
Hassan Rivaz ◽  
...  
Keyword(s):  
Ground Truth ◽  
Ease Of Use ◽  
Automated Segmentation ◽  
Manual Segmentation ◽  
Clinical Implementation ◽  
Multifidus Muscle ◽  
Lumbar Multifidus ◽  
The Us ◽  
Segmentation Algorithms ◽  
And Function

Abstract Background Among the paraspinal muscles, the structure and function of the lumbar multifidus (LM) has become of great interest to researchers and clinicians involved in lower back pain and muscle rehabilitation. Ultrasound (US) imaging of the LM muscle is a useful clinical tool which can be used in the assessment of muscle morphology and function. US is widely used due to its portability, cost-effectiveness, and ease-of-use. In order to assess muscle function, quantitative information of the LM must be extracted from the US image by means of manual segmentation. However, manual segmentation requires a higher level of training and experience and is characterized by a level of difficulty and subjectivity associated with image interpretation. Thus, the development of automated segmentation methods is warranted and would strongly benefit clinicians and researchers. The aim of this study is to provide a database which will contribute to the development of automated segmentation algorithms of the LM. Construction and content This database provides the US ground truth of the left and right LM muscles at the L5 level (in prone and standing positions) of 109 young athletic adults involved in Concordia University’s varsity teams. The LUMINOUS database contains the US images with their corresponding manually segmented binary masks, serving as the ground truth. The purpose of the database is to enable development and validation of deep learning algorithms used for automatic segmentation tasks related to the assessment of the LM cross-sectional area (CSA) and echo intensity (EI). The LUMINOUS database is publicly available at http://data.sonography.ai. Conclusion The development of automated segmentation algorithms based on this database will promote the standardization of LM measurements and facilitate comparison among studies. Moreover, it can accelerate the clinical implementation of quantitative muscle assessment in clinical and research settings.

Acoustic remote sensing monitoring of morphological and sedimentological seabed evolution of small and medium-scale French estuaries

2020 ◽  
Author(s):  
Guillaume Michel ◽  
Sophie Le Bot ◽  
Sandric Lesourd ◽  
Robert Lafite
Keyword(s):  
Remote Sensing ◽  
Benthic Habitat ◽  
Physical Factors ◽  
Seabed Sediment ◽  
Medium Scale ◽  
Quality Health ◽  
Acoustic Remote Sensing ◽  
Ground Truthing ◽  
Mapping Techniques ◽  
Seabed Evolution

&lt;p&gt;Estuarine benthic habitat quality health is integrated within the framework of the EU Water Directive and Marine Strategy Framework Directive. The long-term monitoring of small and medium-scale estuarine benthic habitat is based on recurrent observation of several factors, mainly bathymetry and seabed nature. Numerous studies have already addressed the performance and limitations of acoustic remote sensing and mapping techniques. However, most of these studies are limited to the marine and coastal domains and do not include the estuarine domain. Estuaries are considered as transitional domains, with various seabed morphologies (from rocky reefs to hydraulic dunes with anthropic modification overlap) and subtle granulometric variations of the seabed nature.&lt;/p&gt;&lt;p&gt;The objectives of our study are to explore the mapping performance of several acoustic remote sensing techniques and to determine which physical factors are the most representative of morphological and sedimentological characteristics of subtidal estuarine environment and of its evolution. The exploration of these cartographic variables has been performed for three small and medium-scale French estuaries: the Orne estuary, the Baie de Somme and the Belon estuary. These estuaries have been chosen to cover different morphological and sedimentological estuarine contexts.&lt;/p&gt;&lt;p&gt;Firstly, we evaluate the capacity of the main variables derived from bathymetry (slope, curvature, ruggedness) to map seabed morphology. We extend the variable exploration to the &amp;#8220;Terrain Variable&amp;#8221; GIS category and BTM (Benthic Terrain Modeler Toolbox) as well. Secondly, we explore the capacity of several cartographic variables, extracted from bathymetric, seabed acoustic backscatter and acoustic ground discrimination system (i.e. RoxAnn&amp;#169;), to map seabed sediment characteristics and variations. The seabed nature mapping is validated with ground truthing data, namely grab samples and seabed video profiles. Moreover, quantitative (D90, roughness, sorting) and qualitive information (apparent roughness of the seabed, benthic habitat) are extracted from the grab samples and seabed video profiles, respectively. The capacity of these variables to produce seabed nature maps is also explored.&lt;/p&gt;&lt;p&gt;Mapping results on the three areas are compared, in terms of mapping precision and reproducibility, and transposed into recommendations for small and medium-scale estuaries monitoring. The next step of the AUPASED project is he exploration of image analysis and machine learning classifications and their comparison to manual morphological and sedimentological maps produced.&lt;/p&gt;&lt;p&gt;The AUPASED project is funded by the AFB (French Agency for Biodiversity) as part of a convention between the AFB and the CNRS (UMR 6143, M2C).&lt;/p&gt;

scholarly journals Quantifying Variability of Manual Annotation in Cryo-Electron Tomograms

2016 ◽  
Vol 22 (3) ◽  
pp. 487-496 ◽  
Author(s):  
Corey W. Hecksel ◽  
Michele C. Darrow ◽  
Wei Dai ◽  
Jesús G. Galaz-Montoya ◽  
Jessica A. Chin ◽  
...  
Keyword(s):  
Confidence Level ◽  
Electron Tomography ◽  
Ground Truth ◽  
Automated Segmentation ◽  
Manual Annotation ◽  
Algorithm Development ◽  
Automated Annotation ◽  
Cryo Electron Tomography ◽  
Segmentation Algorithms ◽  
Tomography Data

AbstractAlthough acknowledged to be variable and subjective, manual annotation of cryo-electron tomography data is commonly used to answer structural questions and to create a “ground truth” for evaluation of automated segmentation algorithms. Validation of such annotation is lacking, but is critical for understanding the reproducibility of manual annotations. Here, we used voxel-based similarity scores for a variety of specimens, ranging in complexity and segmented by several annotators, to quantify the variation among their annotations. In addition, we have identified procedures for merging annotations to reduce variability, thereby increasing the reliability of manual annotation. Based on our analyses, we find that it is necessary to combine multiple manual annotations to increase the confidence level for answering structural questions. We also make recommendations to guide algorithm development for automated annotation of features of interest.

scholarly journals Assessing the ecological importance of red tree coral thickets in the eastern Gulf of Alaska

2014 ◽  
Vol 72 (3) ◽  
pp. 900-915 ◽  
Author(s):  
Robert P. Stone ◽  
Michele M. Masuda ◽  
John F. Karinen
Keyword(s):  
North Pacific Ocean ◽  
Fish Habitat ◽  
Keystone Species ◽  
Gulf Of Alaska ◽  
Habitat Characteristics ◽  
Benthic Habitat ◽  
Logistic Regression Models ◽  
Small Areas ◽  
Bottom Contact ◽  
The North

Abstract Red tree corals (Primnoa pacifica), the largest structure-forming gorgonians in the North Pacific Ocean, form dense thickets in some areas. These thickets are a dominant benthic habitat feature in the Gulf of Alaska (GOA), yet little is known about the ecosystems they support. In 2005, we used a submersible to study the ecology of thickets inside or near five small areas of the eastern GOA later designated in 2006 as habitat areas of particular concern (HAPCs)―areas closed to all bottom contact fishing. We show that red tree corals are keystone species in habitats where they form thickets (mean density 0.52 corals m−2)—the densest and largest thickets documented anywhere. Measured sponge densities (2.51 sponges m−2) were also among the highest documented anywhere. The corals and sponges in the study areas provide essential fish habitat for some fish species, and we show with logistic regression models modified with a scaled binomial variance that bedrock, while important habitat for some fish, is even more important when paired with corals and sponges. Red tree corals were not equally distributed with regard to habitat characteristics, and we show that their presence was correlated with bedrock substrate, moderate to high seabed roughness, and slope &gt;10°. Most corals and sponges are vulnerable to disturbance from longlining, the principal bottom contact fishing in this region, but the larger corals and sponges are the most vulnerable. We observed evidence of infrequent recruitment events and a strong pulse of predation, apparently from fishing gear-induced trauma, that could exacerbate slow recovery of red tree corals from disturbance. Some red tree coral thickets are provided protection within designated HAPCs and some are not. Modifications to longline gear and an expanded network of HAPCs could help preserve these keystone species and the ecosystems they support.

Sign in / Sign up

Export Citation Format

Share Document