Use of commercial off-the-shelf digital cameras for scientific data acquisition and scene-specific color calibration

Author Posting. © Optical Society of America, 2014. This article is posted here by permission of Optical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Optical Society of America A: Optics, Image Science, and Vision 31 (2014): 312-321, doi:10.1364/JOSAA.31.000312.Commercial off-the-shelf digital cameras are inexpensive and easy-to-use instruments that can be used for quantitative scientific data acquisition if images are captured in raw format and processed so that they maintain a linear relationship with scene radiance. Here we describe the image-processing steps required for consistent data acquisition with color cameras. In addition, we present a method for scene-specific color calibration that increases the accuracy of color capture when a scene contains colors that are not well represented in the gamut of a standard color-calibration target. We demonstrate applications of the proposed methodology in the fields of biomedical engineering, artwork photography, perception science, marine biology, and underwater imaging.T. Treibitz is an Awardee of the Weizmann Institute of Science—National Postdoctoral Award Program for Advancing Women in Science and was supported by NSF grant ATM-0941760. D. Akkaynak, J. Allen, and R. Hanlon were supported by NSF grant 1129897 and ONR grants N0001406-1-0202 and N00014-10-1-0989 and U. Demirci by grants R01AI093282, R01AI081534, and NIH U54EB15408. J. Allen is grateful for support from a National Defense Science and Engineering Graduate Fellowship

Application of metric photography in building using the conventional digital camera: a case study applied to archaeological heritage

El análisis estratigráfico constituye una herramienta de diagnosis indispensable en obras de arqueología, que permite descifrar a arqueólogos, historiadores y antropólogos la disposición e interrelación entre los diferentes estratos y la ordenación cronológica de los restos hallados. En este campo, la fotogrametría realizada con cámara digital convencional y software de amplia difusión constituye una alternativa versátil, eficiente y asequible frente a las técnicas convencionales de representación, basadas en procedimientos artesanales y cargadas de subjetividad, cuyas principales limitaciones son analizadas. En este artículo se establecen una sencilla metodología y un modelo sistemático para la documentación y preservación de unidades estratigráficas en excavaciones arqueológicas, compatibles con la técnica de análisis estratigráfico basada en la matriz Harris. La validez y posibilidades del método han sido constatadas en el proyecto de intervención arqueológica desarrollado en la Capilla Real de la Catedral de Sevilla.The stratigraphic analysis constitutes an essential diagnostic tool in archelogy works, which allows the archaeologists, historians and anthropologists to decipher the arrangement and interrelation between the different strata and the chronological ordering of the remains found. In this field, the photogrammetry realized with conventional digital camera and software of wide diffusion constitutes a versatile alternative, efficient and affordable in front of the conventional techniques of representation, based on artisan and loaded procedures of subjectivity, whose main limitations are analyzed. This article establishes a simple methodology and a systematic model for the documentation and preservation of stratigraphic units in archaeological excavations, compatible with the technique of stratigraphic analysis based on the Harris matrix. The validity and possibilities of the method have been verified in the project of archaeological intervention developed in the Royal Chapel of the Cathedral of Seville

Image calibration and analysis toolbox: a free software suite for objectively measuring reflectance, colour and pattern

Article"This is the pre-peer reviewed version of the following article: Image Calibration and Analysis Toolbox – a free software suite for objectively measuring reflectance, colour and pattern, which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12439/abstract. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving."1.Quantitative measurements of colour, pattern, and morphology are vital to a growing range of disciplines. Digital cameras are readily available and already widely used for making these measurements, having numerous advantages over other techniques, such as spectrometry. However, off-the-shelf consumer cameras are designed to produce images for human viewing, meaning that their uncalibrated photographs cannot be used for making reliable, quantitative measurements. Many studies still fail to appreciate this, and of those scientists who are aware of such issues, many are hindered by a lack usable tools for making objective measurements from photographs. 2.We have developed an image processing toolbox that generates images that are linear with respect to radiance from the RAW files of numerous camera brands, and can combine image channels from multispectral cameras, including additional ultraviolet photographs. Images are then normalised using one or more grey standards to control for lighting conditions. This enables objective measures of reflectance and colour using a wide range of consumer cameras. Furthermore, if the camera's spectral sensitivities are known, the software can convert images to correspond to the visual system (cone-catch values) of a wide range of animals, enabling human and non-human visual systems to be modelled. The toolbox also provides image analysis tools that can extract luminance (lightness), colour, and pattern information. Furthermore, all processing is performed on 32-bit floating point images rather than commonly used 8-bit images. This increases precision and reduces the likelihood of data loss through rounding error or saturation of pixels, while also facilitating the measurement of objects with shiny or fluorescent properties. 3.All cameras tested using this software were found to demonstrate a linear response within each image and across a range of exposure times. Cone-catch mapping functions were highly robust, converting images to several animal visual systems and yielding data that agreed closely with spectrometer-based estimates. 4.Our imaging toolbox is freely available as an addition to the open source ImageJ software. We believe that it will considerably enhance the appropriate use of digital cameras across multiple areas of biology, in particular researchers aiming to quantify animal and plant visual signals

MALE REPRODUCTIVE STRATEGIES IN WILD NORTHERN PIG-TAILED MACAQUES (MACACA LEONINA): TESTING THE PRIORITY-OF-ACCESS MODEL

Among multi-male, multi-female primate groups, males engage in direct contest competition for access to mates. The priority-of-access model (PoA model) generally predicts that male reproductive success increases with male dominance rank, but the strength of this relationship is expected to decrease with increasing female reproductive synchrony, particularly in seasonally breeding primates. Genetic paternity studies support the model’s predictions, having found a positive relationship between male dominance rank and reproductive success. However, in addition to dominance status and female reproductive synchrony, a number of proximate factors also impact males’ ability to sire offspring, which have not been considered in studies of male reproductive strategies.By integrating behavioral, genetic, morphological, and hormonal analysis as more direct measures of reproductive success in individual males, this dissertation investigated the relationship between male dominance rank and reproductive success and including the proximate factors affecting this relationship in wild northern pig-tailed macaques (Macaca leonina). The main objectives of this study are: 1) to identify the relationships between male dominance rank, male mating success, and male reproductive success, and assess to what extent female synchrony affects these relationships; 2) to identify the proximate factors that may reduce the reproductive success of the top-ranking male and assess variation in male mating tactics related to dominance rank and migration status (i.e., resident males vs. extra-group males); and 3) to evaluate the function of males’ red ornaments that may be used to signal male dominance status (male-male competition) to attract females (female mate choice) or both. The study was conducted at Khao Yai National Park, northeastern Thailand. Systematic data collection on CH group occurred from September 2015-June 2017. The group composition was recorded daily as well as births, deaths, individual emigrations and immigrations, females’ parity status, and the presence of extra-group males (EGMs). Sociosexual data and male-female interactions (i.e., copulations, ejaculatory copulations, consortships, grooming, female proceptive behaviors and receptive behaviors) were recorded during females’ receptive periods. To assess male reproductive success, genetic paternity analyses were conducted on fecal DNA samples collected from 18 adult and subadult males, 22 adult females, and 25 juveniles and infants. To measure red skin coloration of males, hindquarter images were collected non-invasively for seven adult males. From those images, skin color and luminance were computationally quantified to assess variation in male anogenital reflectance. Lastly, fecal samples were collected from nine adult males to assess monthly levels of fecal testosterone by microtitreplate enzyme immunoassay. The distribution of births and matings suggested that northern pig-tailed macaques, at least in this group, are best categorized as moderate seasonal breeders. Indeed, 33-67% of births occurred within a three-month period. Copulation data revealed a positive relationship between male dominance rank and mating success, supporting the predictions of the PoA model. However, the distribution of male reproductive success indicated that: 1) high-ranking males controlled a proportion of paternity much lower than predicted by the PoA model; 2) middle-ranking males controlled a proportion of paternity higher than predicted by the model; and 3) EGMs, not considered in the PoA model, controlled a surprisingly large proportion of paternity despite a low observed mating success. When females were simultaneously receptive, lower-ranking and subadult males engaged in opportunistic and surreptitious copulation and avoided direct competition with higher-ranking males, and most females approached and mated with EGMs out of the resident adult males’ sight. However, one EGM also mated in full sight of resident adult males. This is the first study to report mating and successful paternity by EGMs in a moderately seasonally breeding species.Four male mating tactics were identified: 1) the top-ranking resident male tactic, in which the male competes for the alpha male position to control priority of access to receptive females through long consortships and copulations; 2) the lower-ranking resident male tactic, in which the male copulates opportunistically and surreptitiously out of sight of higher-ranking males mostly during the mating peak; 3) the subordinate EGM tactic, in which the male lives semi-solitarily and copulates opportunistically and surreptitiously, mostly during the mating peaks; and 4) the super-dominant EGM tactic, in which the EGM copulates irrespective of the presence of other males and in full sight of even the highest-ranking resident male. In addition, I found support for female mate choice. Darker and redder males had more mating partners, received more female proceptive behaviors, and were engaged in more consortships and grooming with receptive females. Furthermore, males became redder and darker as female reproductive synchrony increased. Together, these results suggest that male red ornaments exhibited in the male’s anogenital area is attractive to females. Furthermore, behavioral evidence of female mate choice towards EGMs was found. This dissertation provides a comprehensive picture of the complex male mating tactics of northern pig-tailed macaques. To achieve reproductive success, males engage in a diversity of mating tactics, strongly influenced by male dominance rank and the degree of female reproductive synchrony. However, mate-guarding costs, surreptitious copulations by lower-ranking males and EGMs, and female mate choice, need to be included in an extended version of the PoA model to provide stronger predictions of the distribution of male reproductive success in primates

The form and function of warning signals in Lepidoptera, with a special focus on burnet moths (Zygaenidae)

Many species use visual features to avoid predation by several methods, such as concealing themselves, deceiving predators and hindering capture. One of the most striking strategies is aposematism, or warning coloration, in which prey use conspicuous visual signals to advertise chemical or physical defences, and thereby deter predators from attacking. My thesis focuses on the form of these warning signals, namely which elements of visual patterns might be most effective in generating predator avoidance, as well as how these different visual features relate to defence levels and ultimately to prey survival in the wild. To address these issues, I studied the warning signals of Lepidoptera and in particular burnet moths (Zygaenidae: Zygaeninae), day-flying moths with distinctive red and black wings and the remarkable ability to both synthesise defensive compounds and sequester them from their host plants. Technological advances and a growing understanding of animal vision mean that animal signals can be studied in an increasingly precise and ecologically-relevant way. Throughout this thesis, I use sophisticated methods to quantify both the defensive chemicals and wing coloration of burnet moths, as perceived by their avian predators. I examine the key features of day-flying defended Lepidoptera, then focus on the potential for quantitative signal honesty in burnet moths. I explore the relationship between defence levels and measures of coloration, both within the six-spot burnet moth, Zygaena filipendulae, and across species in the Zygaenidae, then test the effects of variation in warning signals on predation risk for artificial burnet-like prey in the field. My work highlights some of the complicating factors that should be accounted for in the study of warning coloration, especially when investigating the potential for quantitative signal honesty. I hope my thesis will provide a basis for future research on the defensive strategies of day-flying moths and inspire others to pursue investigations into aposematism in the Zygaenidae.BBSR

A computational approach to the quantification of animal camouflage

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2014Evolutionary pressures have led to some astonishing camouflage strategies in the animal kingdom. Cephalopods like cuttlefish and octopus mastered a rather unique skill: they can rapidly adapt the way their skin looks in color, texture and pattern, blending in with their backgrounds. Showing a general resemblance to a visual background is one of the many camouflage strategies used in nature. For animals like cuttlefish that can dynamically change the way they look, we would like to be able to determine which camouflage strategy a given pattern serves. For example, does an inexact match to a particular background mean the animal has physiological limitations to the patterns it can show, or is it employing a different camouflage strategy (e.g., disrupting its outline)? This thesis uses a computational and data-driven approach to quantify camouflage patterns of cuttlefish in terms of color and pattern. First, we assess the color match of cuttlefish to the features in its natural background in the eyes of its predators. Then, we study overall body patterns to discover relationships and limitations between chromatic components. To facilitate repeatability of our work by others, we also explore ways for unbiased data acquisition using consumer cameras and conventional spectrometers, which are optical imaging instruments most commonly used in studies of animal coloration and camouflage. This thesis makes the following contributions: (1) Proposes a methodology for scene-specific color calibration for the use of RGB cameras for accurate and consistent data acquisition. (2) Introduces an equation relating the numerical aperture and diameter of the optical fiber of a spectrometer to measurement distance and angle, quantifying the degree of spectral contamination. (3) Presents the first study assessing the color match of cuttlefish (S. officinalis) to its background using in situ spectrometry. (4) Develops a computational approach to pattern quantification using techniques from computer vision, image processing, statistics and pattern recognition; and introduces Cuttlefish72x5, the first database of calibrated raw (linear) images of cuttlefish.Funding was provided by the National Science Foundation, Office of Naval Research, NIH-NEI, and the Woods Hole Oceanographic Institution Academic Programs Office

An Empirical Camera Model for Internet Color Vision

Images harvested from the Web are proving to be useful for many visual tasks, including recognition, geo-location, and three-dimensional reconstruction. These images are captured under a variety of lighting conditions by consumer-level digital cameras, and these cameras have color processing pipelines that are diverse, complex, and scenedependent. As a result, the color information contained in these images is difficult to exploit. In this paper, we analyze the factors that contribute to the color output of a typical camera, and we explore the use of parametric models for relating these output colors to meaningful scenes properties. We evaluate these models using a database of registered images captured with varying camera models, camera settings, and lighting conditions. The database is available online a