README.md

In jiho/morphr: Analyse the Morphology of Objects on Images

morphr

R package to describe morphological variations and create "morphotypes" from greyscale images.

Installation

morphr is not on CRAN (yet), you need to install it from this github repository. It contains Fortran code which needs to be compiled. This requires the gfortran compiler which can be installed with your package manager on Linux, from R Tools for Mac or via Homebrew on macOS, and from RTools on Windows. Once gfortran is installed, issue the following command in R

remotes::install_github("jiho/morphr")

Usage

Use img_read() and img_show() to read and display images, as well as other functions starting with img_ to manipulate them or compute properties from them.

Use morphospace() to create a morphological space, i.e. a description of the morphological features of the images on a n-dimensional space, through a Principal Component Analysis. Optionally, but frequently, use mask_extreme() to remove extreme values and the yeo_johnson() transformation to make the distributions of each variable more Gaussian-looking before the PCA.

Use morph() to "morph" (i.e. fuse) several images into one, which is representative of the original batch of images.

Use ggimg_grid() to display several images and ggmorph_radial(), ggmorph_tile() to describe a morphological space by displaying such morphs at regular locations in that space. Each of those high level functions allow to perform arbitrary pre-processing on the input images to chop some parts, contrast them, rotate them, etc. on the fly.

Two first axes of a morphospace for planktonic organisms, with larger organisms on the right and darker organisms at the bottom.

jiho/morphr documentation built on May 11, 2024, 9:32 p.m.