SizeExtractR

<h4>Goal</h4><p>The goal of SizeExtractR is to facilitate scientific projects that have research questions relating to size, from pure biology to ecology on individual to landscape scales, by providing a protocol with a user-friendly set of interactive tools for image analysis (ImageJ-macros) and database formation and quality checking (R-package).</p><p>Uses include demographics, population dynamics, and size as a proxy of energy investment.</p><h4><a href="https://github.com/liamlachs/SizeExtractR#image-analysis"></a>Image Analysis</h4><p>The ImageJ tools and protocol serve to optimise the slow task of manually outlining objects from sets of images. A scale is required within each image. These tools can save considerable time, and are a most-suited to image analysis applications where machine-learning or other automated outlining classifiers are innefective or out of scope.</p><h4><a href="https://github.com/liamlachs/SizeExtractR#r-package"></a>R package</h4><p>The R tools are used to synthesis all data into one master dataset, with all variables of interest included. Quality control tools are integrated into the database formation. A ggplot2-based plotting function to visualise size-frequency distribution is also provided. R-package can be accessed through 10.5281/zenodo.5997934.</p><h4><a href="https://github.com/liamlachs/SizeExtractR#size-metrics"></a>Size Metrics</h4><p>Measures of size that are captured using SizeExtractR tools include:</p><ul><li>area</li><li>minimum and maximum diameter</li><li>estimated spherical volume</li><li>perimeter length</li></ul><h4><a href="https://github.com/liamlachs/SizeExtractR#other-metrics"></a>Other Metrics</h4><p>Users can also record additional categorical variables of interest using a simple labeling system. For instance, the tools were developed on a coral bleaching demography data set, so coral species, bleaching status, partial mortality, and parasitism were all recorded as categorical annotations relating to individual outlined objects (corals).<br></p><h4>Contents of Data Repository</h4><p>Relevant data and code for:</p><ul><li>SizeExtractR ImageJ macros<br>(on Github: SizeExtractR/inst/ImageJ_macro_code.zip)</li><li>SizeExtractR R package<br></li><li>Timed image analysis</li></ul>