Individualized Models of Colour Differentiation through Situation-Specific Modelling

In digital environments, colour is used for many purposes: for example, to encode information in charts, signify missing field information on websites, and identify active windows and menus. However, many people have inherited, acquired, or situationally-induced Colour Vision Deficiency (CVD), and therefore have difficulties differentiating many colours. Recolouring tools have been developed that modify interface colours to make them more differentiable for people with CVD, but these tools rely on models of colour differentiation that do not represent the majority of people with CVD. As a result, existing recolouring tools do not help most people with CVD. To solve this problem, I developed Situation-Specific Modelling (SSM), and applied it to colour differentiation to develop the Individualized model of Colour Differentiation (ICD). SSM utilizes an in-situ calibration procedure to measure a particular user’s abilities within a particular situation, and a modelling component to extend the calibration measurements into a full representation of the user’s abilities. ICD applies in-situ calibration to measuring a user’s unique colour differentiation abilities, and contains a modelling component that is capable of representing the colour differentiation abilities of almost any individual with CVD. This dissertation presents four versions of the ICD and one application of the ICD to recolouring. First, I describe the development and evaluation of a feasibility implementation of the ICD that tests the viability of the SSM approach. Second, I present revised calibration and modelling components of the ICD that reduce the calibration time from 32 minutes to two minutes. Next, I describe the third and fourth ICD versions that improve the applicability of the ICD to recolouring tools by reducing the colour differentiation prediction time and increasing the power of each prediction. Finally, I present a new recolouring tool (ICDRecolour) that uses the ICD model to steer the recolouring process. In a comparative evaluation, ICDRecolour achieved 90% colour matching accuracy for participants – 20% better than existing recolouring tools – for a wide range of CVDs. By modelling the colour differentiation abilities of a particular user in a particular environment, the ICD enables the extension of recolouring tools to helping most people with CVD, thereby reducing the difficulties that people with CVD experience when using colour in digital environments

Live Video and Image Recolouring for Colour Vision Deficient Patients

Colour Vision Deficiency (CVD) is an important issue for a significant population across the globe. There are several types of CVD\u27s, such as monochromacy, dichromacy, trichromacy, and anomalous trichromacy. Each of these categories contain specific other subtypes. The aim of this research is to device a scheme to address CVD by using variations in pixel plotting of colours to capture colour disparities and perform colour compensation. The proposed scheme recolours the video and images by colour contrast variation of each colour for CVD patients, and depending on the type of deficiency, it is able to provide live results. Different types of CVD’s can be identified and cured by changing the particular colour related to it and based upon the type of diseases, it performs RGB (Red, Green, and Blue) to LMS (Long, Medium, and Short) transformation. This helps in colour identification and also adjustments of colour contrasts. The processing and rendering of recoloured video and images, allows the affected patients with CVD to see perfect shades in the recoloured frames of video or images and other modes of files. In this thesis, we propose an efficient recolouring algorithm with a strong focus on real-time applications that is capable of providing different recoloured outputs based on specific types of CVD

Imperfect camouflage: how to hide in a variable world?

Camouflage is an important anti-predator strategy for many animals and is traditionally thought of as being tightly linked to a specific visual background. While much work focuses on optimizing camouflage against one background, this may not be relevant for many species and contexts, as animals may encounter many different habitats throughout their lives due to temporal and spatial variation in their environment. How should camouflage be optimized when an animal or object is seen against multiple visual backgrounds? Various solutions may exist, including colour change to match new environments or use of behaviour to maintain crypsis by choosing appropriate substrates. Here, we focus on a selection of approaches under a third alternative strategy: animals may adopt (over evolution) camouflage appearances that represent an optimal solution against multiple visual scenes. One approach may include a generalist or compromise strategy, where coloration matches several backgrounds to some extent, but none closely. A range of other camouflage types, including disruptive camouflage, may also provide protection in multiple environments. Despite detailed theoretical work determining the plausibility of compromise camouflage and elucidating the conditions under which it might evolve, there is currently mixed experimental evidence supporting its value and little evidence of it in natural systems. In addition, there remain many questions including how camouflage strategies should be defined and optimized, and how they might interact with other types of crypsis and defensive markings. Overall, we provide a critical overview of our current knowledge about how camouflage can enable matching to multiple backgrounds, discuss important challenges of working on this question and make recommendations for future research

A quantitative and qualitative approach to cuttlefish (Sepia officinalis) body patterning

Cuttlefish are renowned for their ability to quickly alter the colour and texture of their skin, for camouflage and communication. This is due to the presence of thousands of pigment-filled sacs, known as chromatophores, which are distributed across the skin. The chromatophores are innervated by motoneurons, which dilate the chromatophores to create the spots, stripes, and other markings, known as chromatic components. There are 34 recognized chromatic components, and it is an interesting question how cuttlefish coordinate the expression of these components to camouflage and communicate. The digital age has introduced new, powerful algorithms and methods to tease out subtle features in the coloration patterns, by means of image registration, segmentation, and identification, as well as methods for modeling the underlying control systems. These tools offer major new insights into the mechanisms of visual perception. In addition, powerful techniques have recently been developed that have yet to be applied to this complex visual motor control system. These methods have large potential in helping discover what features between the pattern and the environment are necessary to prevent detection. Here I present four laboratory experiments, that for the first time use machine learning models, to investigate cuttlefish pattern formation, implementation, and information. The first two experimental chapters investigate how cuttlefish orchestrate their chromatic components for camouflage patterns, and what strategies they employ on diverse backgrounds. I demonstrate that components are expressed more independently than previously believed, finding that the range of patterns expressed lie on a continuum, allowing us to suggest a revised classification scheme for cuttlefish body patterns. The diversity of patterns seem to imply that a cuttlefish could use its repertoire flexibly to display the maximally cryptic pattern for a given background, however I show that cuttlefish to not in fact select a single (possibly optimal) camouflage pattern, continually alter their appearance on a given background, and that the frequency of change increases in relation to the size of the objects in the environment. My third chapter investigated the language-like properties of cuttlefish communication using human speech recognition models. From our subset of cuttlefish patterns, I discovered cuttlefish utilize a lexicon of 10 patterns, with language-like properties such as: they obeyed Zipf’s law, contained around 1.6 bits per display, and interestingly, while 2 patterns were visually similar, they were displayed in separate contexts. By implementing a regression onto the patterns, I introduce a basic dictionary of cuttlefish terms and their meaning. From my investigations into cuttlefish intraspecific signaling, I discovered two previously undocumented patterns, used in agonistic encounters between cuttlefish. My final chapter describes these patterns and the contexts they are displayed

Ecological and molecular insights into the function of colourful signals in aquatic environments

Discovering the processes that drive the emergence of new species and connecting it to biodiversity in its past, present, and future form has been one of the central questions of natural scientists for over a century. Two ways in which we can start to unravel the mechanisms that have created such diversity is to investigate: 1) the selective pressures that can initiate/drive and 2) the molecular capacities allowing evolutionary changes to happen. A convenient approach to study how environmental cues and molecular processes are linked to appearance is by investigating the emergence of similar phenotypes, whether they evolve in response to likewise selective pressures and/or in response to molecular or developmental constraints. Here, mimics because they imitate unrelated species (the model), are a classical example in which to study phenotypic convergence. CHAPTER1 (Published in Current Biology, 2015); Using a combination of behavioural, cell histological, neurophysiological and molecular approaches, the first chapter of my PhD thesis aimed to uncover the triggers for colour change in a small coral reef fish mimic, the dottyback, Pseudochromis fuscus. Yellow morphs are mainly found on live coral in association with yellow damselfish species such as the ambon- (Pomacentrus amboinensis) and the lemon damselfish (P. moluccensis), while brown morphs occur mainly on coral rubble in association with brown damselfishes such as the whitetail damselfish (P. chrysurus). Potential environmental cues that could be associated with colour change therefore included: i) aggressive mimicry, dottyback morphs associate with similarly coloured damselfishes to increase foraging success by preventing detection by juvenile fish prey; ii) social mimicry, differently coloured morphs hide among similarly coloured damselfish to reduce detection and predation risk from their own predators; and iii) crypsis, different coloured morphs match the colour of their background habitat to prevent detection from predators or potential prey. CHAPTER 2 (Published in The Journal of Experimental Biology, 2016); The second chapter aimed at investigating the triggers for ontogenetic colour changes and how these interrelate to the development of the visual system in dottybacks. Although adult dottybacks were found to be aggressive mimics that change colour to impersonate the colouration of the prevalent damselfish community, little was known about the early life stages of this fish. Using a developmental time series in combination with wild caught dottyback specimens I show multiple colour changes during dottyback ontogeny and link them to crucial life history transitions of dottybacks. Moreover, changes in the visual system were found to precede ontogenetic colour changes, and theoretical fish visual models were subsequently used to investigate the potential benefits of this pattern. CHAPTER 3 (Published in PNAS, 2015); Work for chapter 3 was done in collaboration with Dr. Zuzana Musilová at the University of Basel and was based on the discovery of multiple novel visual genes (opsins) in the dottyback (Chapter 2), which arose through gene duplications. One of these novel gene duplicates was found in the violet-blue opsin sub-family (SWS2); however, initial reconstruction of the SWS2 phylogeny suggested a much older, non- dottyback specific origin of the duplication event. Therefore, in chapter three we performed a thorough investigation of SWS2 by exploring the evolutionary history of this family in close to 100 fish species representing most fish lineages across the modern fish phylogeny

Pattern Recognition

Pattern recognition is a very wide research field. It involves factors as diverse as sensors, feature extraction, pattern classification, decision fusion, applications and others. The signals processed are commonly one, two or three dimensional, the processing is done in real- time or takes hours and days, some systems look for one narrow object class, others search huge databases for entries with at least a small amount of similarity. No single person can claim expertise across the whole field, which develops rapidly, updates its paradigms and comprehends several philosophical approaches. This book reflects this diversity by presenting a selection of recent developments within the area of pattern recognition and related fields. It covers theoretical advances in classification and feature extraction as well as application-oriented works. Authors of these 25 works present and advocate recent achievements of their research related to the field of pattern recognition

Patterns of visual adaptation in tropical mimetic butterflies

Species diversity within an ecosystem can be supported by favouring microhabitat specialisation. In complex habitats, like tropical rainforests, spatial and temporal segregation across microhabitats can expose species to distinct sensory realms. For many animals, visual systems serve as the primary conduit for perceiving biologically relevant sensory information, and the structural and functional variety of eyes and sensory brain regions reflects their critical role in diverse animal behaviours. However, little is known of their role in mediating niche segregation across subtle ecological scales, particularly in terrestrial environments. I explore the role of microhabitat partitioning in driving predictable patterns of adaptive visual system evolution within two diverse radiations of mimetic Neotropical butterfly, the Heliconius and Ithomiini. By taking a comparative approach, I investigate whether dual patterns of habitat divergence and convergence is manifested in the visual system at the perceptual, processing, and molecular level. I find extensive evidence of heritable, habitat-associated visual system variation, particularly for neural processing structures, hinting at the evolutionary lability of these systems to rapidly accommodate local adaptations to visual ecologies. My research also empirically demonstrates, for the first time, how variation in forest structure can give rise to distinct photic environments, highlighting the role of spectral variation as a major driver of adaptive community assemblage within a terrestrial forest radiation. In addition, evidence of visual morphological convergence offers a mechanistic insight into the evolvability of visual adaptations when confronted with similar ecological challenges, shedding light on their significance in promoting ecological diversification and speciation