Domain-inspired image processing and computer vision to support deep-sea benthic ecology

Optical imagery is a necessary methodological tool for ecological research within marine environments, particularly in deeper waters. For benthic (seafloor) surveys, interpretation of image data is crucial to creating high-resolution maps of seabed habitats. This is fundamental to marine spatial planning and mitigating long-term damage of anthropogenic stressors such as growing resource demand, climate change and pollution. However there are numerous, and significant, issues in extracting a reliable ground-truth from imagery to support this process. Analysis of benthic images is difficult, due in part to the extreme variation and inconsistency in image quality - caused by complex interactions between light and water. It is also time-consuming. This thesis is dedicated to providing solutions to manage these challenges, from a strong perspective of the end-user. Specifically, we aim to improve the annotation of benthic habitats from imagery in terms of quality, consistency and efficiency. Throughout, we consider the purpose the imagery serves and work closely with end-users to best optimize our solutions. First, and for the majority of this thesis, we investigate image processing techniques to improve the appearance of image features important for habitat classification. We find that tone mapping is an effective and simple (and thus accessible) method through which to improve image quality for interpretation. We describe beneficial (expert-informed) properties for brightness distributions in underwater images and introduce a novel tone-mapping algorithm, Weibull Tone Mapping (WTM), to enhance benthic images. WTM theory operates within general constraints that model image requirements (properties) specified by image analysts, yet possesses a suitable degree of flexibility and customisation. As a tool, WTM provides analysts with a fast and ‘user-friendly’ method to improve benthic habitat classification. Second, we consider computer vision methods that could automatically identify benthic habitats in imagery, relieving the analysis bottleneck. We find that baseline transfer learning of machine learning models, with limited optimization, will better facilitate adoption by novice users, yet still provides a powerful means to swiftly extract and assess benthic data

Chromatic Weibull Tone Mapping for Underwater Image Enhancement

Image enhancement is often used to alleviate the low contrast, blurring and colour reduction effects, common in underwater imagery. Tone Mapping, a particularly simple yet elegant enhancement technique improves image quality by modifying image histograms to a more desirable tonal distribution. In previous work, we presented our novel chromaticity-preserving algorithm, Weibull Tone Mapping (WTM), that can simplify custom tonal manipulations, to increase conspicuousness of image features. In this paper, we present a natural non-chromaticity preserving counterpart, in which the WTM tone map is applied to all colour channels (R,G,B). We demonstrate, as before, that user's prefer WTM to unenhanced images. However, contrary to prior work, our non-chromaticity preserving WTM is less preferred to custom tonal manipulations. Thus, how we map the colour aspect of images (given a brightness only tonal adjustment) has a significant impact on users' subjective preference judgements

Weibull Tone Mapping for Underwater Imagery

Imagery is a preferred tool for environmental surveys within marine environments, particularly in deeper waters, as it is non-destructive compared to traditional sampling methods. However, underwater illumination effects limit its use by causing extremely varied and inconsistent image quality. Therefore, it is often necessary to pre-process images to improve visibility of image features and textures, and standardize their appearance. Tone mapping is a simple and effective technique to improve contrast and manipulate the brightness distributions of images. Ideally, such tone mapping would be automated, however we found that existing techniques are inferior when compared to custom manipulations by image annotators (biologists). Our own work begins with the observation that these user-defined tonal manipulations are quite variable, though on average, are fairly smooth, gentle waving operations. To predict user-defined tone maps we found it sufficed to approximate the brightness distributions of input and user adjusted images by Weibull distributions and then solve for the tone curve which matched these distributions from input to output. Experiments demonstrate that our Weibull Tone Mapping (WTM) method is strongly preferred over traditional automated tone mappers and weakly preferred over the users' own tonal adjustments

How do practitioners characterize land tenure security?

Improving land tenure security (LTS) is a significant challenge for sustainable development. The Sustainable Development Goals and other recent global initiatives have renewed and increased the need to improve LTS to address climate change, biodiversity loss, food security, poverty reduction, and other challenges. At the same time, policymakers are increasingly interested in evidence- based policies and decisions, creating urgency for practitioners and researchers to work together. Yet, incongruent characterizations of LTS (identifying the key components of LTS) by practitioners and researchers can limit collaboration and information flows necessary for research and effective policymaking. While there are systematic reviews of how LTS is characterized in the academic literature, no prior study has assessed how practitioners characterize LTS. We address this gap using data from 54 interviews of land tenure practitioners working in 10 countries of global importance for biodiversity and climate change mitigation. Practitioners characterize LTS as complex and multifaceted, and a majority of practitioners refer to de jure terms (e.g., titling) when characterizing it. Notably, in our data just one practitioner characterized LTS in terms of perceptions of the landholder, contrasting the recent emphasis in the academic literature on landholder perceptions in LTS characterizations. Researchers should be aware of incongruence in how LTS is characterized in the academic literature when engaging practitioners.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/155485/1/csp2186.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/155485/2/csp2186_am.pd

A framework for the development of a global standardised marine taxon reference image database (SMarTaR-ID) to support image-based analyses

Video and image data are regularly used in the field of benthic ecology to document biodiversity. However, their use is subject to a number of challenges, principally the identification of taxa within the images without associated physical specimens. The challenge of applying traditional taxonomic keys to the identification of fauna from images has led to the development of personal, group, or institution level reference image catalogues of operational taxonomic units (OTUs) or morphospecies. Lack of standardisation among these reference catalogues has led to problems with observer bias and the inability to combine datasets across studies. In addition, lack of a common reference standard is stifling efforts in the application of artificial intelligence to taxon identification. Using the North Atlantic deep sea as a case study, we propose a database structure to facilitate standardisation of morphospecies image catalogues between research groups and support future use in multiple front-end applications. We also propose a framework for coordination of international efforts to develop reference guides for the identification of marine species from images. The proposed structure maps to the Darwin Core standard to allow integration with existing databases. We suggest a management framework where high-level taxonomic groups are curated by a regional team, consisting of both end users and taxonomic experts. We identify a mechanism by which overall quality of data within a common reference guide could be raised over the next decade. Finally, we discuss the role of a common reference standard in advancing marine ecology and supporting sustainable use of this ecosystem

Weibull Tone Mapping (WTM) for the Enhancement of Underwater Imagery

Domain experts prefer interactive and targeted control-point tone mapping operations (TMOs) to enhance underwater image quality and feature visibility; though this comes at the expense of time and training. In this paper, we provide end-users with a simpler and faster interactive tone-mapping approach. This is built upon Weibull Tone Mapping (WTM) theory; introduced in previous work as a preferred tool to describe and improve domain expert TMOs. We allow end-users to easily shape brightness distributions according to the Weibull distribution, using two parameter sliders which modify the distribution peak and spread. Our experiments showed that 10 domain experts found the two-slider Weibull manipulation sufficed to make a desired adjustment in >80% of images in a large dataset. For the remaining ∼20%, observers opted for a control-point TMO which can, broadly, encompass many global tone mapping algorithms. Importantly, 91% of these control-point TMOs can actually be visually well-approximated by our Weibull slider manipulation, despite users not identifying slider parameters themselves. Our work stresses the benefit of the Weibull distribution and significance of image purpose in underwater image enhancement

Extensive loss of Wnt genes in Tardigrada

Background: Wnt genes code for ligands that activate signaling pathways during development in Metazoa. Through the canonical Wnt (cWnt) signaling pathway, these genes regulate important processes in bilaterian development, such as establishing the anteroposterior axis and posterior growth. In Arthropoda, Wnt ligands also regulate segment polarity, and outgrowth and patterning of developing appendages. Arthropods are part of a lineage called Panarthropoda that includes Onychophora and Tardigrada. Previous studies revealed potential roles of Wnt genes in regulating posterior growth, segment polarity, and growth and patterning of legs in Onychophora. Unlike most other panarthropods, tardigrades lack posterior growth, but retain segmentation and appendages. Here, we investigated Wnt genes in tardigrades to gain insight into potential roles that these genes play during development of the highly compact and miniaturized tardigrade body plan. Results: We analyzed published genomes for two representatives of Tardigrada, Hypsibius exemplaris and Ramazzottius varieornatus. We identified single orthologs of Wnt4, Wnt5, Wnt9, Wnt11, and WntA, as well as two Wnt16 paralogs in both tardigrade genomes. We only found a Wnt2 ortholog in H. exemplaris. We could not identify orthologs of Wnt1, Wnt6, Wnt7, Wnt8, or Wnt10. We identified most other components of cWnt signaling in both tardigrade genomes. However, we were unable to identify an ortholog of arrow/Lrp5/6, a gene that codes for a Frizzled co-receptor of Wnt ligands. Additionally, we found that some other animals that have lost several Wnt genes and are secondarily miniaturized, like tardigrades, are also missing an ortholog of arrow/Lrp5/6. We analyzed the embryonic expression patterns of Wnt genes in H. exemplaris during developmental stages that span the establishment of the AP axis through segmentation and leg development. We detected expression of all Wnt genes in H. exemplaris besides one of the Wnt16 paralogs. During embryo elongation, expression of several Wnt genes was restricted to the posterior pole or a region between the anterior and posterior poles. Wnt genes were expressed in distinct patterns during segmentation and development of legs in H. exemplaris, rather than in broadly overlapping patterns. Conclusions: Our results indicate that Wnt signaling has been highly modified in Tardigrada. While most components of cWnt signaling are conserved in tardigrades, we conclude that tardigrades have lost Wnt1, Wnt6, Wnt7, Wnt8, and Wnt10, along with arrow/Lrp5/6. Our expression data may indicate a conserved role of Wnt genes in specifying posterior identities during establishment of the AP axis. However, the loss of several Wnt genes and the distinct expression patterns of Wnt genes during segmentation and leg development may indicate that combinatorial interactions among Wnt genes are less important during tardigrade development compared to many other animals. Based on our results, and comparisons to previous studies, we speculate that the loss of several Wnt genes in Tardigrada may be related to a reduced number of cells and simplified development that accompanied miniaturization and anatomical simplification in this lineage

Can static habitat protection encompass critical areas for highly mobile marine top predators? Insights from coastal East Africa

© 2015 Pérez-Jorge et al. Along the East African coast, marine top predators are facing an increasing number of anthropogenic threats which requires the implementation of effective and urgent conservation measures to protect essential habitats. Understanding the role that habitat features play on the marine top predator' distribution and abundance is a crucial step to evaluate the suitability of an existing Marine Protected Area (MPA), originally designated for the protection of coral reefs. We developed species distribution models (SDM) on the IUCN data deficient Indo-Pacific bottlenose dolphin (Tursiops aduncus) in southern Kenya. We followed a comprehensive ecological modelling approach to study the environmental factors influencing the occurrence and abundance of dolphins while developing SDMs. Through the combination of ensemble prediction maps, we defined recurrent, occasional and unfavourable habitats for the species. Our results showed the influence of dynamic and static predictors on the dolphins' spatial ecology: dolphins may select shallow areas (5-30 m), close to the reefs (< 500 m) and oceanic fronts (< 10 km) and adjacent to the 100m isobath (< 5 km).We also predicted a significantly higher occurrence and abundance of dolphins within the MPA. Recurrent and occasional habitats were identified on large percentages on the existing MPA (47% and 57% using presence-absence and abundance models respectively). However, the MPA does not adequately encompass all occasional and recurrent areas and within this context, we propose to extend the MPA to incorporate all of them which are likely key habitats for the highly mobile species. The results from this study provide two key conservation and management tools: (i) an integrative habitat modelling approach to predict key marine habitats, and (ii) the first study evaluating the effectiveness of an existing MPA for marine mammals in the Western Indian Ocean. Copyright:ML was funded by a Juan de la Cierva postdoctoral contract (JCI-2010-07639, Spanish Ministry of Science and Innovation - http://www.idi.mineco.gob.es/) and a Ramón y Cajal postdoctoral contract (RYC-2012-09897). Funds were partially provided by a grant from the Spanish Ministry of Economy - http://www.idi.mineco.gob.es/ (CGL2013-42203-R)Peer Reviewe

Report on the Marine Imaging Workshop 2022

Imaging is increasingly used to capture information on the marine environment thanks to the improvements in imaging equipment, devices for carrying cameras and data storage in recent years. In that context, biologists, geologists, computer specialists and end-users must gather to discuss the methods and procedures for optimising the quality and quantity of data collected from images. The 4th Marine Imaging Workshop was organised from 3-6 October 2022 in Brest (France) in a hybrid mode. More than a hundred participants were welcomed in person and about 80 people attended the online sessions. The workshop was organised in a single plenary session of presentations followed by discussion sessions. These were based on dynamic polls and open questions that allowed recording of the imaging community’s current and future ideas. In addition, a whole day was dedicated to practical sessions on image analysis, data standardisation and communication tools. The format of this edition allowed the participation of a wider community, including lower-income countries, early career scientists, all working on laboratory, benthic and pelagic imaging.This article summarises the topics addressed during the workshop, particularly the outcomes of the discussion sessions for future reference and to make the workshop results available to the open public