PT  - JOURNAL ARTICLE
AU  - Cedric P. van den Berg
AU  - Jolyon Troscianko
AU  - John A. Endler
AU  - N. Justin Marshall
AU  - Karen L. Cheney
TI  - Quantitative Colour Pattern Analysis (QCPA): A Comprehensive Framework for the Analysis of Colour Patterns in Nature
AID  - 10.1101/592261
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 592261
4099  - http://biorxiv.org/content/early/2019/03/29/592261.short
4100  - http://biorxiv.org/content/early/2019/03/29/592261.full
AB  - To understand the function of colour signals in nature, we require robust quantitative analytical frameworks to enable us to estimate how animal and plant colour patterns appear against their natural background as viewed by ecologically relevant species. Due to the quantitative limitations of existing methods, colour and pattern are rarely analysed in conjunction with one another, despite a large body of literature and decades of research on the importance of spatiochromatic colour pattern analyses. Furthermore, key physiological limitations of animal visual systems such as spatial acuity, spectral sensitivities, photoreceptor abundances and receptor noise levels are rarely considered together in colour pattern analyses.Here, we present a novel analytical framework, called the ‘Quantitative Colour Pattern Analysis’ (QCPA). We have overcome many quantitative and qualitative limitations of existing colour pattern analyses by combining calibrated digital photography and visual modelling. We have integrated and updated existing spatiochromatic colour pattern analyses, including adjacency, visual contrast and boundary strength analysis, to be implemented using calibrated digital photography through the ‘Multispectral Image Analysis and Calibration’ (MICA) Toolbox.This combination of calibrated photography and spatiochromatic colour pattern analyses is enabled by the inclusion of psychophysical colour and luminance discrimination thresholds for image segmentation, which we call ‘Receptor Noise Limited Clustering’, used here for the first time. Furthermore, QCPA provides a novel psycho-physiological approach to the modelling of spatial acuity using convolution in the spatial or frequency domains, followed by ‘Receptor Noise Limited Ranked Filtering’ to eliminate intermediate edge artefacts and recover sharp boundaries following smoothing. We also present a new type of colour pattern analysis, the ‘Local Edge Intensity Analysis’ (LEIA) as well as a range of novel psycho-physiological approaches to the visualisation of spatiochromatic data.QCPA combines novel and existing pattern analysis frameworks into what we hope is a unified, user-friendly, free and open source toolbox and introduce a range of novel analytical and data-visualisation approaches. These analyses and tools have been seamlessly integrated into the MICA toolbox providing a dynamic and user-friendly workflow.QCPA is a framework for the empirical investigation of key theories underlying the design, function and evolution of colour patterns in nature. We believe that it is compatible with, but more thorough than, other existing colour pattern analyses.