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1.  WWW design code – a new tool for colour estimation in animal studies 
Background
The colour of animals' skin, fur, feathers or cuticula has been estimated in a large number of studies. The methods used to do so are diverse, with some being costly and not available to all researchers. In a study to measure plumage colour in a bird species, a new method of creating a colour chart was developed. While colour-charts have their own limitations, these can be minimised when they have the following properties: 1) being readily available to the majority of biologists, 2) containing a large array of colours to allow accurate recording and differentiation of subtle colour differences, 3) low cost, 4) adhering to a world-wide standard, and 5) being available in both hard-copy and digital formats to allow for various analytical methods. The method described below satisfies all of these requirements.
Results
Colour charts estimated to fit the range of the species' plumage colours were created on the computer screen using web software that allowed for HTML-coding (in this case Dreamweaver™). The charts were adjusted using feathers from dead specimens until a satisfying range of darker and lighter colours were found. The resulting chart was printed out and was successfully used in the field to determine the plumage colour of hand-held birds.
Conclusion
Access to a computer and printer, and the software to enable the creation of a chart, is within the reach of the vast majority of biologists. The numbers of colours that can be generated should suit most studies, with the advantage of the method being that the chart can be individually tailored to the species under study. HTML colour coding is a worldwide standard, thus the colours used in studies can be described in the methods section of journal articles using the six-digit alphanumeric code. We believe this method is very useful as a low-tech method for future estimation of individual colour.
doi:10.1186/1742-9994-1-2
PMCID: PMC544934  PMID: 15679904
2.  From spectral information to animal colour vision: experiments and concepts 
Many animals use the spectral distribution of light to guide behaviour, but whether they have colour vision has been debated for over a century. Our strong subjective experience of colour and the fact that human vision is the paradigm for colour science inevitably raises the question of how we compare with other species. This article outlines four grades of ‘colour vision’ that can be related to the behavioural uses of spectral information, and perhaps to the underlying mechanisms. In the first, even without an (image-forming) eye, simple organisms can compare photoreceptor signals to locate a desired light environment. At the next grade, chromatic mechanisms along with spatial vision guide innate preferences for objects such as food or mates; this is sometimes described as wavelength-specific behaviour. Here, we compare the capabilities of di- and trichromatic vision, and ask why some animals have more than three spectral types of receptors. Behaviours guided by innate preferences are then distinguished from a grade that allows learning, in part because the ability to learn an arbitrary colour is evidence for a neural representation of colour. The fourth grade concerns colour appearance rather than colour difference: for instance, the distinction between hue and saturation, and colour categorization. These higher-level phenomena are essential to human colour perception but poorly known in animals, and we suggest how they can be studied. Finally, we observe that awareness of colour and colour qualia cannot be easily tested in animals.
doi:10.1098/rspb.2009.2118
PMCID: PMC2871852  PMID: 20164101
colour vision; phototaxis; colour preference; colour learning; colour categorization; chromaticity
3.  Quantifying Plant Colour and Colour Difference as Perceived by Humans Using Digital Images 
PLoS ONE  2013;8(8):e72296.
Human perception of plant leaf and flower colour can influence species management. Colour and colour contrast may influence the detectability of invasive or rare species during surveys. Quantitative, repeatable measures of plant colour are required for comparison across studies and generalisation across species. We present a standard method for measuring plant leaf and flower colour traits using images taken with digital cameras. We demonstrate the method by quantifying the colour of and colour difference between the flowers of eleven grassland species near Falls Creek, Australia, as part of an invasive species detection experiment. The reliability of the method was tested by measuring the leaf colour of five residential garden shrub species in Ballarat, Australia using five different types of digital camera. Flowers and leaves had overlapping but distinct colour distributions. Calculated colour differences corresponded well with qualitative comparisons. Estimates of proportional cover of yellow flowers identified using colour measurements correlated well with estimates obtained by measuring and counting individual flowers. Digital SLR and mirrorless cameras were superior to phone cameras and point-and-shoot cameras for producing reliable measurements, particularly under variable lighting conditions. The analysis of digital images taken with digital cameras is a practicable method for quantifying plant flower and leaf colour in the field or lab. Quantitative, repeatable measurements allow for comparisons between species and generalisations across species and studies. This allows plant colour to be related to human perception and preferences and, ultimately, species management.
doi:10.1371/journal.pone.0072296
PMCID: PMC3748102  PMID: 23977275
4.  A New Colorimetrically-Calibrated Automated Video-Imaging Protocol for Day-Night Fish Counting at the OBSEA Coastal Cabled Observatory 
Sensors (Basel, Switzerland)  2013;13(11):14740-14753.
Field measurements of the swimming activity rhythms of fishes are scant due to the difficulty of counting individuals at a high frequency over a long period of time. Cabled observatory video monitoring allows such a sampling at a high frequency over unlimited periods of time. Unfortunately, automation for the extraction of biological information (i.e., animals' visual counts per unit of time) is still a major bottleneck. In this study, we describe a new automated video-imaging protocol for the 24-h continuous counting of fishes in colorimetrically calibrated time-lapse photographic outputs, taken by a shallow water (20 m depth) cabled video-platform, the OBSEA. The spectral reflectance value for each patch was measured between 400 to 700 nm and then converted into standard RGB, used as a reference for all subsequent calibrations. All the images were acquired within a standardized Region Of Interest (ROI), represented by a 2 × 2 m methacrylate panel, endowed with a 9-colour calibration chart, and calibrated using the recently implemented “3D Thin-Plate Spline” warping approach in order to numerically define color by its coordinates in n-dimensional space. That operation was repeated on a subset of images, 500 images as a training set, manually selected since acquired under optimum visibility conditions. All images plus those for the training set were ordered together through Principal Component Analysis allowing the selection of 614 images (67.6%) out of 908 as a total corresponding to 18 days (at 30 min frequency). The Roberts operator (used in image processing and computer vision for edge detection) was used to highlights regions of high spatial colour gradient corresponding to fishes' bodies. Time series in manual and visual counts were compared together for efficiency evaluation. Periodogram and waveform analysis outputs provided very similar results, although quantified parameters in relation to the strength of respective rhythms were different. Results indicate that automation efficiency is limited by optimum visibility conditions. Data sets from manual counting present the larger day-night fluctuations in comparison to those derived from automation. This comparison indicates that the automation protocol subestimate fish numbers but it is anyway suitable for the study of community activity rhythms.
doi:10.3390/s131114740
PMCID: PMC3871094  PMID: 24177726
coastal fishes; cables observatories; OBSEA; automated video-imaging; colorimetric calibration; swimming rhythms; 3D Thin-Plate Spline warping
5.  Chromatic Illumination Discrimination Ability Reveals that Human Colour Constancy Is Optimised for Blue Daylight Illuminations 
PLoS ONE  2014;9(2):e87989.
The phenomenon of colour constancy in human visual perception keeps surface colours constant, despite changes in their reflected light due to changing illumination. Although colour constancy has evolved under a constrained subset of illuminations, it is unknown whether its underlying mechanisms, thought to involve multiple components from retina to cortex, are optimised for particular environmental variations. Here we demonstrate a new method for investigating colour constancy using illumination matching in real scenes which, unlike previous methods using surface matching and simulated scenes, allows testing of multiple, real illuminations. We use real scenes consisting of solid familiar or unfamiliar objects against uniform or variegated backgrounds and compare discrimination performance for typical illuminations from the daylight chromaticity locus (approximately blue-yellow) and atypical spectra from an orthogonal locus (approximately red-green, at correlated colour temperature 6700 K), all produced in real time by a 10-channel LED illuminator. We find that discrimination of illumination changes is poorer along the daylight locus than the atypical locus, and is poorest particularly for bluer illumination changes, demonstrating conversely that surface colour constancy is best for blue daylight illuminations. Illumination discrimination is also enhanced, and therefore colour constancy diminished, for uniform backgrounds, irrespective of the object type. These results are not explained by statistical properties of the scene signal changes at the retinal level. We conclude that high-level mechanisms of colour constancy are biased for the blue daylight illuminations and variegated backgrounds to which the human visual system has typically been exposed.
doi:10.1371/journal.pone.0087989
PMCID: PMC3929610  PMID: 24586299
6.  Effects of memory colour on colour constancy for unknown coloured objects 
i-Perception  2012;3(3):190-215.
The perception of an object's colour remains constant despite large variations in the chromaticity of the illumination—colour constancy. Hering suggested that memory colours, the typical colours of objects, could help in estimating the illuminant's colour and therefore be an important factor in establishing colour constancy. Here we test whether the presence of objects with diagnostical colours (fruits, vegetables, etc) within a scene influence colour constancy for unknown coloured objects in the scene. Subjects matched one of four Munsell papers placed in a scene illuminated under either a reddish or a greenish lamp with the Munsell book of colour illuminated by a neutral lamp. The Munsell papers were embedded in four different scenes—one scene containing diagnostically coloured objects, one scene containing incongruent coloured objects, a third scene with geometrical objects of the same colour as the diagnostically coloured objects, and one scene containing non-diagnostically coloured objects (eg, a yellow coffee mug). All objects were placed against a black background. Colour constancy was on average significantly higher for the scene containing the diagnostically coloured objects compared with the other scenes tested. We conclude that the colours of familiar objects help in obtaining colour constancy for unknown objects.
doi:10.1068/i0461
PMCID: PMC3485846  PMID: 23145282
Colour constancy; memory colours; object colour; colour appearance
7.  Pterin pigment granules are responsible for both broadband light scattering and wavelength selective absorption in the wing scales of pierid butterflies 
A small but growing literature indicates that many animal colours are produced by combinations of structural and pigmentary mechanisms. We investigated one such complex colour phenotype: the highly chromatic wing colours of pierid butterflies including oranges, yellows and patterns which appear white to the human eye, but strongly absorb the ultraviolet (UV) wavelengths visible to butterflies. Pierids produce these bright colours using wing scales that contain collections of minute granules. However, to date, no work has directly characterized the molecular composition or optical properties of these granules. We present results that indicate these granules contain pterin pigments. We also find that pterin granules increase light reflection from single wing scales, such that wing scales containing denser granule arrays reflect more light than those with less dense granule collections. As male wing scales contain more pterin granules than those of females, the sexual dichromatism found in many pierid species can be explained by differences in wing scale pterin deposition. Additionally, the colour pattern elements produced by these pterins are known to be important during mating interactions in a number of pierid species. Therefore, we discuss the potential relevance of our results within the framework of sexual selection and colour signal evolution.
doi:10.1098/rspb.2006.3730
PMCID: PMC1702378  PMID: 17164199
animal coloration; nano-optics; trait evolution; pierid butterflies; structural colour; pterin pigments
8.  Filling schemes at submicron scale: Development of submicron sized plasmonic colour filters 
Scientific Reports  2014;4:6435.
The pixel size imposes a fundamental limit on the amount of information that can be displayed or recorded on a sensor. Thus, there is strong motivation to reduce the pixel size down to the nanometre scale. Nanometre colour pixels cannot be fabricated by simply downscaling current pixels due to colour cross talk and diffraction caused by dyes or pigments used as colour filters. Colour filters based on plasmonic effects can overcome these difficulties. Although different plasmonic colour filters have been demonstrated at the micron scale, there have been no attempts so far to reduce the filter size to the submicron scale. Here, we present for the first time a submicron plasmonic colour filter design together with a new challenge - pixel boundary errors at the submicron scale. We present simple but powerful filling schemes to produce submicron colour filters, which are free from pixel boundary errors and colour cross- talk, are polarization independent and angle insensitive, and based on LCD compatible aluminium technology. These results lay the basis for the development of submicron pixels in displays, RGB-spatial light modulators, liquid crystal over silicon, Google glasses and pico-projectors.
doi:10.1038/srep06435
PMCID: PMC4170198  PMID: 25242695
9.  Field-Portable Pixel Super-Resolution Colour Microscope 
PLoS ONE  2013;8(9):e76475.
Based on partially-coherent digital in-line holography, we report a field-portable microscope that can render lensfree colour images over a wide field-of-view of e.g., >20 mm2. This computational holographic microscope weighs less than 145 grams with dimensions smaller than 17×6×5 cm, making it especially suitable for field settings and point-of-care use. In this lensfree imaging design, we merged a colorization algorithm with a source shifting based multi-height pixel super-resolution technique to mitigate ‘rainbow’ like colour artefacts that are typical in holographic imaging. This image processing scheme is based on transforming the colour components of an RGB image into YUV colour space, which separates colour information from brightness component of an image. The resolution of our super-resolution colour microscope was characterized using a USAF test chart to confirm sub-micron spatial resolution, even for reconstructions that employ multi-height phase recovery to handle dense and connected objects. To further demonstrate the performance of this colour microscope Papanicolaou (Pap) smears were also successfully imaged. This field-portable and wide-field computational colour microscope could be useful for tele-medicine applications in resource poor settings.
doi:10.1371/journal.pone.0076475
PMCID: PMC3785454  PMID: 24086742
10.  Synaesthetic Colour in the Brain: Beyond Colour Areas. A Functional Magnetic Resonance Imaging Study of Synaesthetes and Matched Controls 
PLoS ONE  2010;5(8):e12074.
Background
In synaesthesia, sensations in a particular modality cause additional experiences in a second, unstimulated modality (e.g., letters elicit colour). Understanding how synaesthesia is mediated in the brain can help to understand normal processes of perceptual awareness and multisensory integration. In several neuroimaging studies, enhanced brain activity for grapheme-colour synaesthesia has been found in ventral-occipital areas that are also involved in real colour processing. Our question was whether the neural correlates of synaesthetically induced colour and real colour experience are truly shared.
Methodology/Principal Findings
First, in a free viewing functional magnetic resonance imaging (fMRI) experiment, we located main effects of synaesthesia in left superior parietal lobule and in colour related areas. In the left superior parietal lobe, individual differences between synaesthetes (projector-associator distinction) also influenced brain activity, confirming the importance of the left superior parietal lobe for synaesthesia. Next, we applied a repetition suppression paradigm in fMRI, in which a decrease in the BOLD (blood-oxygenated-level-dependent) response is generally observed for repeated stimuli. We hypothesized that synaesthetically induced colours would lead to a reduction in BOLD response for subsequently presented real colours, if the neural correlates were overlapping. We did find BOLD suppression effects induced by synaesthesia, but not within the colour areas.
Conclusions/Significance
Because synaesthetically induced colours were not able to suppress BOLD effects for real colour, we conclude that the neural correlates of synaesthetic colour experience and real colour experience are not fully shared. We propose that synaesthetic colour experiences are mediated by higher-order visual pathways that lie beyond the scope of classical, ventral-occipital visual areas. Feedback from these areas, in which the left parietal cortex is likely to play an important role, may induce V4 activation and the percept of synaesthetic colour.
doi:10.1371/journal.pone.0012074
PMCID: PMC2919410  PMID: 20711467
11.  Genetic determinants of hair and eye colours in the Scottish and Danish populations 
BMC Genetics  2009;10:88.
Background
Eye and hair colour is highly variable in the European population, and is largely genetically determined. Both linkage and association studies have previously been used to identify candidate genes underlying this variation. Many of the genes found were previously known as underlying mutant mouse phenotypes or human genetic disease, but others, previously unsuspected as pigmentation genes, have also been discovered.
Results
We assayed the hair of a population of individuals of Scottish origin using tristimulus colorimetry, in order to produce a quantitative measure of hair colour. Cluster analysis of this data defined two groups, with overlapping borders, which corresponded to visually assessed dark versus red/light hair colour. The Danish population was assigned into categorical hair colour groups. Both cohorts were also assessed for eye colour. DNA from the Scottish group was genotyped at SNPs in 33 candidate genes, using 384 SNPs identified by HapMap as representatives of each gene. Associations found between SNPs and colorimetric hair data and eye colour categories were replicated in a cohort of the Danish population. The Danish population was also genotyped with SNPs in 4 previously described pigmentation genes. We found replicable associations of hair colour with the KITLG and OCA2 genes. MC1R variation correlated, as expected, with the red dimension of colorimetric hair colour in Scots. The Danish analysis excluded those with red hair, and no associations were found with MC1R in this group, emphasising that MC1R regulates the colour rather than the intensity of pigmentation. A previously unreported association with the HPS3 gene was seen in the Scottish population. However, although this replicated in the smaller cohort of the Danish population, no association was seen when the whole study population was analysed.
Conclusions
We have found novel associations with SNPs in known pigmentation genes and colorimetrically assessed hair colour in a Scottish and a Danish population.
doi:10.1186/1471-2156-10-88
PMCID: PMC2810292  PMID: 20042077
12.  Individual quality explains association between plumage colouration, arrival dates and mate acquisition in yellow warblers (Setophaga petechia) 
BMC Ecology  2014;14:13.
Background
In many bird species colour traits influence social dominance and breeding success. In our study we first evaluated whether the colour of the basic plumage (tail feathers grown at the end of the breeding season), that provides an index of individual quality, influenced winter habitat use by yellow warblers. We then evaluated whether winter habitat use (inferred using δ13C and δ15N signatures of winter grown greater-coverts) influenced alternate plumage colouration, after controlling for individual quality using basic plumage colouration. Finally, we investigated whether basic and alternate plumage colouration influenced arrival dates, mate acquisition, breeding phenology and reproductive success of yellow warblers breeding in southern (Revelstoke, B.C.) and arctic (Inuvik, N.W.T.) Canada.
Results
The colour (chroma and hue) of tail feathers, grown on the breeding grounds, was not related to subsequent winter habitat use. Greater covert and tail feather colour (chroma and hue) were correlated, suggesting genetics and/or individual quality played a role in pigment deposition. After controlling for individual difference in tail colour, δ13C values did not explain any variation in greater covert colour, but birds with high δ15N signatures had greater coverts with higher chroma. Male arrival dates varied with tail chroma in Revelstoke and tail hue in Inuvik. Males that arrived early paired with older and/or more colourful mates that initiated clutches earlier, and at one site (Revelstoke) were more likely to fledge young. In addition, in Revelstoke (but not Inuvik) males with high tail hue also acquired more colourful mates. In contrast, after controlling for individual differences in tail colour, greater covert colour did not affect male arrival date, the quality of the mate obtained or reproductive success in either population.
Conclusions
Our results suggest that plumage colour effects on breeding phenology and mate acquisition result from differences in the intrinsic quality of individuals rather than a carry-over effect of winter habitat use.
doi:10.1186/1472-6785-14-13
PMCID: PMC4024118  PMID: 24886073
Carry-over effects; Seasonal interactions; Breeding phenology; Plumage colour; Carotenoid-based colouration; Yellow warbler; American redstart
13.  Coloration using higher order optical interference in the wing pattern of the Madagascan sunset moth 
Colour patterns of animals' bodies are usually produced by the spatial distribution of pigments with different colours. However, some animals use the spatial variation of colour-producing microstructures. We have studied one distinctive example of such structurally produced colour patterns, the wing of the Madagascan sunset moth, to clarify the physical rules that underlie the colour variation. It is known that the iridescent wing scale of the sunset moth has the alternate air–cuticle multilayer structure that causes optical interference. The microscopic and optical investigations of various parts of the wing have confirmed that the thickness of the cuticle layers within the scale largely varies to produce the colour pattern. However, it varies in very different ways between the dorsal and ventral sides of the hind wing; the thickness gradually varies on the dorsal side from scale to scale, while the abrupt changes are found on the ventral side to form distinctive borders between differently coloured areas. It is also revealed that an unusual coloration mechanism is involved in the green part of the ventral hind wing: the colour is caused by higher order optical interference of the highly non-ideal multilayer structure. The physical mechanism of the colour pattern formation is briefly discussed with the several mathematical models proposed so far.
doi:10.1098/rsif.2007.1268
PMCID: PMC2607392  PMID: 17999945
wing pattern; pattern formation; iridescence; structural colour; reaction–diffusion
14.  Selection for Social Signalling Drives the Evolution of Chameleon Colour Change 
PLoS Biology  2008;6(1):e25.
Rapid colour change is a remarkable natural phenomenon that has evolved in several vertebrate and invertebrate lineages. The two principal explanations for the evolution of this adaptive strategy are (1) natural selection for crypsis (camouflage) against a range of different backgrounds and (2) selection for conspicuous social signals that maximise detectability to conspecifics, yet minimise exposure to predators because they are only briefly displayed. Here we show that evolutionary shifts in capacity for colour change in southern African dwarf chameleons (Bradypodion spp.) are associated with increasingly conspicuous signals used in male contests and courtship. To the chameleon visual system, species showing the most dramatic colour change display social signals that contrast most against the environmental background and amongst adjacent body regions. We found no evidence for the crypsis hypothesis, a finding reinforced by visual models of how both chameleons and their avian predators perceive chameleon colour variation. Instead, our results suggest that selection for conspicuous social signals drives the evolution of colour change in this system, supporting the view that transitory display traits should be under strong selection for signal detectability.
Author Summary
The ability to change colour has evolved in numerous vertebrate and invertebrate groups, the most well-known of which are chameleons and cephalopods (octopuses and their relatives). There is great variation among species, however, in the apparent capacity for colour change, ranging from limited changes in brightness to dramatic changes in hue. What drives the evolution of this remarkable strategy? We addressed this question by using a combination of field-based behavioural trials in which we quantified colour change, models of colour perception, and our knowledge of phylogenetic relationships for 21 distinct lineages of southern African dwarf chameleons. We show that evolutionary changes in the capacity for colour change are consistently associated with the use of social signals that are highly conspicuous to the visual system of chameleons. Moreover, capacity for colour change is unrelated to variation in the environmental backgrounds that chameleons must match in order to be camouflaged. Overall, our results suggest that the evolution of the ability to exhibit striking changes in colour evolved as a strategy to facilitate social signalling and not, as popularly believed, camouflage.
In dwarf chameleons, evolutionary shifts in the capacity for colour change are associated with increasingly conspicuous signals used in contests and courtship rather than by the need to match different backgrounds.
doi:10.1371/journal.pbio.0060025
PMCID: PMC2214820  PMID: 18232740
15.  Female-specific colouration, carotenoids and reproductive investment in a dichromatic species, the upland goose Chloephaga picta leucoptera 
Behavioral Ecology and Sociobiology  2010;64(11):1779-1789.
Although studies on the evolution and function of female ornaments have become more numerous in the last years, the majority of these studies were carried out in cases where female ornaments were a smaller and duller version of the ornaments found in males. There are substantially fewer studies on species with female-specific ornaments. However, no study so far investigated the potential of female-specific colouration as a quality signal in birds with conventional sex roles. We studied female-specific ornamentation in a strongly sexually dichromatic species, the upland goose Chloephaga picta leucoptera, in two consecutive years. Male upland geese have white head and breast feathers and black legs, whereas females have reddish-brown head and breast feathers and conspicuous yellow-orange legs. We found that female-specific colouration in upland geese can reliably indicate different aspects of female phenotypic quality. Females with more orange coloured legs and more red-like head colours had higher clutch and egg volumes than females with a paler leg and head colouration, and a more reddish plumage colouration was related to a higher body condition. These relationships provide the theoretic possibility for males to assess female phenotypic quality on the basis of colouration. Furthermore, the females with a more orange-like tarsus colouration had higher plasma carotenoid levels. Both tarsus colouration and carotenoid concentrations of individual females were highly correlated across years, indicating that tarsus colour is a stable signal. Despite this correlation, small individual differences in plasma carotenoid concentrations between the two study years were related to differences in tarsus colouration. We thus show for the first time in a wild bird and under natural conditions that carotenoid-based integument colouration remains consistent between individuals in consecutive years and is also a dynamic trait reflecting individual changes in carotenoid levels. In this species, where pairs form life-long bonds, the honesty of the carotenoid-based integument colouration suggests that it may be a sexually selected female ornament that has evolved through male mate choice.
Electronic supplementary material
The online version of this article (doi:10.1007/s00265-010-0990-4) contains supplementary material, which is available to authorized users.
doi:10.1007/s00265-010-0990-4
PMCID: PMC2952766  PMID: 20976290
Upland goose; Chloephaga picta leucoptera; Female-specific colouration; Signalling; Carotenoids; Individual quality
16.  An experimental test of the contributions and condition dependence of microstructure and carotenoids in yellow plumage coloration 
A combination of structural and pigmentary components is responsible for many of the colour displays of animals. Despite the ubiquity of this type of coloration, neither the relative contribution of structures and pigments to variation in such colour displays nor the relative effects of extrinsic factors on the structural and pigment-based components of such colour has been determined. Understanding the sources of colour variation is important because structures and pigments may convey different information to conspecifics. In an experiment on captive American goldfinches Carduelis tristis, we manipulated two parameters, carotenoid availability and food availability, known to affect the expression of carotenoid pigments in a full-factorial design. Yellow feathers from these birds were then analysed in two ways. First, we used full-spectrum spectrometry and high-performance liquid chromatography to examine the extent to which variation in white structural colour and total carotenoid content was associated with variation in colour properties of feathers. The carotenoid content of yellow feathers predicted two colour parameters (principal component 1—representing high values of ultraviolet and yellow chroma and low values of violet–blue chroma—and hue). Two different colour parameters (violet–blue and yellow chroma) from white de-pigmented feathers, as well as carotenoid content, predicted reflectance measurements from yellow feathers. Second, we determined the relative effects of our experimental manipulations on white structural colour and yellow colour. Carotenoid availability directly affected yellow colour, while food availability affected it only in combination with carotenoid availability. None of our manipulations had significant effects on the expression of white structural colour. Our results suggest that the contribution of microstructures to variation in the expression of yellow coloration is less than the contribution of carotenoid content, and that carotenoid deposition is more dependent on extrinsic variability than is the production of white structural colour.
doi:10.1098/rspb.2006.3675
PMCID: PMC1639519  PMID: 17015356
American goldfinch; Carduelis tristis; carotenoid pigmentation; diet; honest signalling; sexual selection
17.  Automatic colorimetric calibration of human wounds 
BMC Medical Imaging  2010;10:7.
Background
Recently, digital photography in medicine is considered an acceptable tool in many clinical domains, e.g. wound care. Although ever higher resolutions are available, reproducibility is still poor and visual comparison of images remains difficult. This is even more the case for measurements performed on such images (colour, area, etc.). This problem is often neglected and images are freely compared and exchanged without further thought.
Methods
The first experiment checked whether camera settings or lighting conditions could negatively affect the quality of colorimetric calibration. Digital images plus a calibration chart were exposed to a variety of conditions. Precision and accuracy of colours after calibration were quantitatively assessed with a probability distribution for perceptual colour differences (dE_ab). The second experiment was designed to assess the impact of the automatic calibration procedure (i.e. chart detection) on real-world measurements. 40 Different images of real wounds were acquired and a region of interest was selected in each image. 3 Rotated versions of each image were automatically calibrated and colour differences were calculated.
Results
1st Experiment: Colour differences between the measurements and real spectrophotometric measurements reveal median dE_ab values respectively 6.40 for the proper patches of calibrated normal images and 17.75 for uncalibrated images demonstrating an important improvement in accuracy after calibration. The reproducibility, visualized by the probability distribution of the dE_ab errors between 2 measurements of the patches of the images has a median of 3.43 dE* for all calibrated images, 23.26 dE_ab for all uncalibrated images. If we restrict ourselves to the proper patches of normal calibrated images the median is only 2.58 dE_ab! Wilcoxon sum-rank testing (p < 0.05) between uncalibrated normal images and calibrated normal images with proper squares were equal to 0 demonstrating a highly significant improvement of reproducibility. In the second experiment, the reproducibility of the chart detection during automatic calibration is presented using a probability distribution of dE_ab errors between 2 measurements of the same ROI.
Conclusion
The investigators proposed an automatic colour calibration algorithm that ensures reproducible colour content of digital images. Evidence was provided that images taken with commercially available digital cameras can be calibrated independently of any camera settings and illumination features.
doi:10.1186/1471-2342-10-7
PMCID: PMC2850874  PMID: 20298541
18.  Class Separation Improvements in Pixel Classification Using Colour Injection 
Sensors (Basel, Switzerland)  2010;10(8):7803-7842.
This paper presents an improvement in the colour image segmentation in the Hue Saturation (HS) sub-space. The authors propose to inject (add) a colour vector in the Red Green Blue (RGB) space to increase the class separation in the HS plane. The goal of the work is the development of an algorithm to obtain the optimal colour vector for injection that maximizes the separation between the classes in the HS plane. The chromatic Chrominace-1 Chrominance-2 sub-space (of the Luminance Chrominace-1 Chrominance-2 (YC1C2) space) is used to obtain the optimal vector to add. The proposal is applied on each frame of a colour image sequence in real-time. It has been tested in applications with reduced contrast between the colours of the background and the object, and particularly when the size of the object is very small in comparison with the size of the captured scene. Numerous tests have confirmed that this proposal improves the segmentation process, considerably reducing the effects of the variation of the light intensity of the scene. Several tests have been made in skin segmentation in applications for sign language recognition via computer vision, where an accurate segmentation of hands and face is required.
doi:10.3390/s100807803
PMCID: PMC3231167  PMID: 22163628
pixel classification; colour clustering; colour segmentation; class separation; colour sub-spaces; colour injection
19.  Rockpool Gobies Change Colour for Camouflage 
PLoS ONE  2014;9(10):e110325.
Camouflage is found in a wide range of species living in numerous habitat types, offering protection from visually guided predators. This includes many species from the intertidal zone, which must cope with background types diverse in appearance and with multiple predator groups foraging at high and low tide. Many animals are capable of either relatively slow (hours, days, weeks) or rapid (seconds and minutes) colour change in order to better resemble the background against which they are found, but most work has been restricted to a few species or taxa. It is often suggested that many small intertidal fish are capable of colour change for camouflage, yet little experimental work has addressed this. Here, we test rock gobies (Gobius paganellus) for colour change abilities, and whether they can tune their appearance to match the background. In two experiments, we place gobies on backgrounds of different brightness (black or white), and of different colours (red and blue) and use digital image analysis and modelling of predator (avian) vision to quantify colour and luminance (perceived lightness) changes and camouflage. We find that gobies are capable of rapid colour change (occurring within one minute), and that they can change their luminance on lighter or darker backgrounds. When presented on backgrounds of different colours, gobies also change their colour (hue and saturation) while keeping luminance the same. These changes lead to predicted improvements in camouflage match to the background. Our study shows that small rockpool fish are capable of rapid visual change for concealment, and that this may be an important mechanism in many species to avoid predation, especially in complex heterogeneous environments.
doi:10.1371/journal.pone.0110325
PMCID: PMC4198244  PMID: 25333382
20.  Why do seals have cones? Behavioural evidence for colour-blindness in harbour seals 
Animal Cognition  2014;18:551-560.
All seals and cetaceans have lost at least one of two ancestral cone classes and should therefore be colour-blind. Nevertheless, earlier studies showed that these marine mammals can discriminate colours and a colour vision mechanism has been proposed which contrasts signals from cones and rods. However, these earlier studies underestimated the brightness discrimination abilities of these animals, so that they could have discriminated colours using brightness only. Using a psychophysical discrimination experiment, we showed that a harbour seal can solve a colour discrimination task by means of brightness discrimination alone. Performing a series of experiments in which two harbour seals had to discriminate the brightness of colours, we also found strong evidence for purely scotopic (rod-based) vision at light levels that lead to mesopic (rod–cone-based) vision in other mammals. This finding speaks against rod–cone-based colour vision in harbour seals. To test for colour-blindness, we used a cognitive approach involving a harbour seal trained to use a concept of same and different. We tested this seal with pairs of isoluminant stimuli that were either same or different in colour. If the seal had perceived colour, it would have responded to colour differences between stimuli. However, the seal responded with “same”, providing strong evidence for colour-blindness.
Electronic supplementary material
The online version of this article (doi:10.1007/s10071-014-0823-3) contains supplementary material, which is available to authorized users.
doi:10.1007/s10071-014-0823-3
PMCID: PMC4320766  PMID: 25452008
Rod–cone-based colour vision; Colour-blindness; Spectral sensitivity; Marine mammals; Harbour seals
21.  Disruptive Colouration and Perceptual Grouping 
PLoS ONE  2014;9(1):e87153.
Camouflage is the primary defence of many animals and includes multiple strategies that interfere with figure-ground segmentation and object recognition. While matching background colours and textures is widespread and conceptually straightforward, less well explored are the optical ‘tricks’, collectively called disruptive colouration, that exploit perceptual grouping mechanisms. Adjacent high contrast colours create false edges, but this is not sufficient for an object’s shape to be broken up; some colours must blend with the background. We test the novel hypothesis that this will be particularly effective when the colour patches on the animal appear to belong to, not merely different background colours, but different background objects. We used computer-based experiments where human participants had to find cryptic targets on artificial backgrounds. Creating what appeared to be bi-coloured foreground objects on bi-coloured backgrounds, we generated colour boundaries that had identical local contrast but either lay within or between (illusory) objects. As predicted, error rates for targets matching what appeared to be different background objects were higher than for targets which had otherwise identical local contrast to the background but appeared to belong to single background objects. This provides evidence for disruptive colouration interfering with higher-level feature integration in addition to previously demonstrated low-level effects involving contour detection. In addition, detection was impeded in treatments where targets were on or in close proximity to multiple background colour or tone boundaries. This is consistent with other studies which show a deleterious influence of visual ‘clutter’ or background complexity on search.
doi:10.1371/journal.pone.0087153
PMCID: PMC3899390  PMID: 24466337
22.  The Reproducibility and Applicability of an EFD® Dispenser in the Prosthetic Technology of Maxillofacial Prostheses 
A reproducible method of dosing pigments can be beneficial and more efficient in the current colour matching procedure in maxillofacial prosthetics. In this study the reproducibility and applicability for pigment dosing of a commercial available EFD® dispenser were tested. The reproducibility of a Performus™ II type EFD® dispenser was tested by repeating dosing experiments with a set of eight syringes filled with pigment pastes (Factor 2; Flagstaff, USA). To evaluate conventional colour matching, four conventionally colour matched samples were polymerized and compared to the original ones. To investigate the reproducibility of the dispenser in practice, a fifth recipe was dispensed 10 times and colour differences were evaluated visually and as well calculated from measurements with a colour and translucency meter (CTM, PBSensortechnology bv). All dispensed amounts of pigment pastes showed a coefficient of variation in weight of less than 10 %. Evaluating the reproductions of four skin batches compared to the original batches, a ∆E2000 colour difference of 3–7 was measured. Evaluating ten reproductions of one skin coloured batch made with the dispenser, color difference ∆E2000 values compared to the average L*a*b* values, were less than 2 and no visual colour differences could be estimated. Conform these results, low colour differences could be measured with the CTM, indicating no visually observable consequences. Despite the estimated coefficient of variation, the reproducibility of the EFD® dispenser in terms of colour difference ∆E2000 of successive dispensing is applicable for colour reproduction in facial prosthetics. Segregation of the current color pastes in due time needs to be taken into consideration.
doi:10.1007/s13191-013-0291-5
PMCID: PMC3732728  PMID: 24431737
Maxillofacial prosthetics; Colour matching; Pigments; Dispenser; Spectrophotometer
23.  How to measure image quality in tissue-based diagnosis (diagnostic surgical pathology) 
Diagnostic Pathology  2008;3(Suppl 1):S11.
Background
Automated image analysis, measurements of virtual slides, and open access electronic measurement user systems require standardized image quality assessment in tissue-based diagnosis.
Aims
To describe the theoretical background and the practical experiences in automated image quality estimation of colour images acquired from histological slides.
Theory, material and measurements
Digital images acquired from histological slides should present with textures and objects that permit automated image information analysis. The quality of digitized images can be estimated by spatial independent and local filter operations that investigate in homogenous brightness, low peak to noise ratio (full range of available grey values), maximum gradients, equalized grey value distribution, and existence of grey value thresholds. Transformation of the red-green-blue (RGB) space into the hue-saturation-intensity (HSI) space permits the detection of colour and intensity maxima/minima. The feature distance of the original image to its standardized counterpart is an appropriate measure to quantify the actual image quality. These measures have been applied to a series of H&E stained, fluorescent (DAPI, Texas Red, FITC), and immunohistochemically stained (PAP, DAB) slides. More than 5,000 slides have been measured and partly analyzed in a time series.
Results
Analysis of H&E stained slides revealed low shading corrections (10%) and moderate grey value standardization (10 – 20%) in the majority of cases. Immunohistochemically stained slides displayed greater shading and grey value correction. Fluorescent stained slides are often revealed to high brightness. Images requiring only low standardization corrections possess at least 5 different statistically significant thresholds, which are useful for object segmentation. Fluorescent images of good quality only posses one singular intensity maximum in contrast to good images obtained from H&E stained slides that present with 2 – 3 intensity maxima.
Conclusion
Evaluation of image quality and creation of formally standardized images should be performed prior to automatic analysis of digital images acquired from histological slides. Spatial dependent and local filter operations as well as analysis of the RGB and HSI spaces are appropriate methods to reproduce evaluated formal image quality.
doi:10.1186/1746-1596-3-S1-S11
PMCID: PMC2500119  PMID: 18673499
24.  Adaptive Colour Contrast Coding in the Salamander Retina Efficiently Matches Natural Scene Statistics 
PLoS ONE  2013;8(10):e79163.
The visual system continually adjusts its sensitivity to the statistical properties of the environment through an adaptation process that starts in the retina. Colour perception and processing is commonly thought to occur mainly in high visual areas, and indeed most evidence for chromatic colour contrast adaptation comes from cortical studies. We show that colour contrast adaptation starts in the retina where ganglion cells adjust their responses to the spectral properties of the environment. We demonstrate that the ganglion cells match their responses to red-blue stimulus combinations according to the relative contrast of each of the input channels by rotating their functional response properties in colour space. Using measurements of the chromatic statistics of natural environments, we show that the retina balances inputs from the two (red and blue) stimulated colour channels, as would be expected from theoretical optimal behaviour. Our results suggest that colour is encoded in the retina based on the efficient processing of spectral information that matches spectral combinations in natural scenes on the colour processing level.
doi:10.1371/journal.pone.0079163
PMCID: PMC3813611  PMID: 24205373
25.  Iridescence: a functional perspective 
Journal of the Royal Society Interface  2009;6(Suppl 2):S115-S132.
In animals, iridescence is generated by the interaction of light with biological tissues that are nanostructured to produce thin films or diffraction gratings. Uniquely among animal visual signals, the study of iridescent coloration contributes to biological and physical sciences by enhancing our understanding of the evolution of communication strategies, and by providing insights into physical optics and inspiring biomimetic technologies useful to humans. Iridescent colours are found in a broad diversity of animal taxa ranging from diminutive marine copepods to terrestrial insects and birds. Iridescent coloration has received a surge of research interest of late, and studies have focused on both characterizing the nanostructures responsible for producing iridescence and identifying the behavioural functions of iridescent colours. In this paper, we begin with a brief description of colour production mechanisms in animals and provide a general overview of the taxonomic distribution of iridescent colours. We then highlight unique properties of iridescent signals and review the proposed functions of iridescent coloration, focusing, in particular, on the ways in which iridescent colours allow animals to communicate with conspecifics and avoid predators. We conclude with a brief overview of non-communicative functions of iridescence in animals. Despite the vast amount of recent work on animal iridescence, our review reveals that many proposed functions of iridescent coloration remain virtually unexplored, and this area is clearly ripe for future research.
doi:10.1098/rsif.2008.0395.focus
PMCID: PMC2706478  PMID: 19336344
iridescence; behaviour; function; communication; sexual selection; predation

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