Quantitative Colour Pattern Analysis (QCPA): A Comprehensive Framework for the Analysis of Colour Patterns in Nature

Abstract

11 1. To understand the function of colour signals in nature, we require robust quantitative 12 analytical frameworks to enable us to estimate how animal and plant colour patterns appear 13 against their natural background as viewed by ecologically relevant species. Due to the 14 quantitative limitations of existing methods, colour and pattern are rarely analysed in 15 conjunction with one another, despite a large body of literature and decades of research on 16 the importance of spatiochromatic colour pattern analyses. Furthermore, key physiological 17 limitations of animal visual systems such as spatial acuity, spectral sensitivities, photoreceptor 18 abundances and receptor noise levels are rarely considered together in colour pattern 19 analyses. 20 2. Here, we present a novel analytical framework, called the 'Quantitative Colour Pattern 21 Analysis' (QCPA). We have overcome many quantitative and qualitative limitations of existing 22 image segmentation, which we call 'Receptor Noise Limited Clustering', used here for the first 30 time. Furthermore, QCPA provides a novel psycho-physiological approach to the modelling of 31 spatial acuity using convolution in the spatial or frequency domains, followed by 'Receptor 32 Noise Limited Ranked Filtering' to eliminate intermediate edge artefacts and recover sharp 33 boundaries following smoothing. We also present a new type of colour pattern analysis, the 34 'Local Edge Intensity Analysis' (LEIA) as well as a range of novel psycho-physiological 35 approaches to the visualisation of spatiochromatic data.36 4. QCPA combines novel and existing pattern analysis frameworks into what we hope is a unified, 37 user-friendly, free and open source toolbox and introduce a range of novel analytical and data-38 visualisation approaches. These analyses and tools have been seamlessly integrated into the 39 MICA toolbox providing a dynamic and user-friendly workflow. 40 5. QCPA is a framework for the empirical investigation of key theories underlying the design, 41 function and evolution of colour patterns in nature. We believe that it is compatible with, but 42 more thorough than, other existing colour pattern analyses. 43 44 Keywords: colour pattern analysis, colour perception, image analysis, visual modelling, receptor noise 45 limited model, animal colouration, colour space 46 47 65

Generalist camouflage can be more successful than microhabitat specialisation in natural environments

“…Each image included a Classic ColorChecker® chart (X-Rite Inc., Grand Rapids, USA) to enable normalisation with respect to light levels and provide a scale bar. Camera calibration and all image analyses were carried out with the Image Calibration and Analysis toolbox-MicaToolbox [ 63 , 64 ] in ImageJ [ 65 ]. Cone catch models for human vision were created based on photographs of the colour chart, following custom plugins in the toolbox.…”

Achromatic plumage variation between and within hybridizing Black‐capped and Mountain chickadees

“…We did not collect either supercilium or flight feathers from live birds in our study because the small areas they cover make these regions challenging to accurately measure with a spectrophotometer. In museum specimens, contour feathers and remiges (including the supercilium and white wing bars) were outlined in photographs and analyzed using the Quantitative Colour and Pattern Analysis framework (QCPA; van den Berg et al 2020).…”

“…We obtained feather color data from photographs using the Quantitative Colour and Pattern Analysis framework (QCPA; van den Berg et al 2020) from the micaToolbox (V2 & QCPA; Troscianko and Stevens 2015) plugin in ImageJ (1.52o). For all orientations (dorsal, ventral, and left and right lateral) for each individual, we assembled a multispectral image stack using the ultraviolet and visible images of adequate exposure (one visible and one ultraviolet image per stack).…”

“…We characterized plumage variation between and within Black‐capped and Mountain chickadees using two complementary methods: digital photography of museum specimens and spectrophotometry of feathers from wild birds. Specifically, we measured (1) overall plumage color and the size of throat and cheek patches from photographs of museum specimens using both the Quantitative Colour and Pattern Analysis framework (QCPA; van den Berg et al 2020) and manual patch tracing, and (2) plumage color using reflectance curves obtained using a spectrophotometer of feathers collected from live birds. Our objectives were to determine if Black‐capped and Mountain chickadees in Colorado (1) differ in plumage coloration from a songbird perspective, (2) differ in the size of cheek and throat patches, and (3) are sexually dimorphic (i.e., plumage color and patch size) from a songbird perspective.…”

Camouflage in arid environments: the case of Sahara-Sahel desert rodents

“…For example, some rodents may specialize on specific micro-habitats and integration of colour quantification methods may prove useful in revealing habitat specialization and intracommunity interactions. Recent methodological advances enable the measurement of animal-tobackground matching more objectively (Troscianko & Stevens 2015, Van Den Berg et al 2019 and the quantification of how camouflage may deceive ecologically relevant sensory systems.…”