References: Belleghem, S.M. Van, Papa, R., Ortiz-zuazaga, H., Hendrickx, F., Jiggins, C.D., Mcmillan, W.O., et al. 2017. Patternize : An R package for quantifying color pattern variation. Chan, I.Z.W., Stevens, M. & Todd, P.A. 2018. PAT‐ GEOM: A Software Package for
Particle Analysis
Particle analysis provides information on the spatial properties of clusters/patches in an image, such as the shape, size angle and distribution of particles within a given cluster/patch. This is typically run within the QCPA framework, but can be used in
RNL Chromaticity XYZ Saturation Images
The receptor noise limited (RNL) chromaticity colour space is convenient because the Euclidean distance between any two points in this space is equal to the Delta-S of the RNL model (in units of “just noticeable differences”, JNDs). This means that
Colour Maps
Colour measurements have historically been plotted and compared as single points in a colour space (such as a Maxwell triangle, or a tetrahedral colour space). The area or volumes occupied by these average colour points has also been used to
Pattern Energy (Granularity) Analysis
We provide tools for performing a pattern analysis based on Fast Fourier bandpass filtering, often called a granularity analysis. This form of analysis is increasingly widely used to measure animal markings (Godfrey et al., 1987; Stoddard and Stevens, 2010), and
GabRat
GabRat is a method developed for measuring the level of edge disruption around a given target. The method uses Gabor filtering, and measures the ratio (hence “Gabor -ratio” > GabRat) of the targets’ “true” outline edge intensity, compared to the
Region Of Interest (ROI) selection tips & tricks
One of the great benefits of the micaToolbox and its components is that it runs on ImageJ which comes with an extensive suite of tools for image manipulation. Particularly useful is the ability to do very easy and efficient selecting
Boundary Strength Analysis
The Boundary Strength Analysis (BSA) is essentially a combination and extention of both the Adjacency Analyis and the Visual Contrast Analysis, published by John Endler et al. in 2018 using Matlab. It uses the off-diagonal of the transition matrix to
Visual Contrast Analysis
The’Visual Contrast Analysis’ is an umbrella term for a variety of pattern parameters which were first conceptualised by John Endler in the early 90s (Endler 1990, 1991, 1992; Endler & Mielke 2005). These parameters seek to combine both chromatic and
Adjacency Analysis
The Adjacency Analysis (Endler 2012) is an analytical framework designed to capture colour pattern geometry. It is based on the concept of running horizontal and vertical sampling transects over a segmented image (Fig. 1) where the transitions from one pixel