SizeExtractR
Goal
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).
Uses include demographics, population dynamics, and size as a proxy of energy investment.
Image Analysis
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.
R package
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.
Size Metrics
Measures of size that are captured using SizeExtractR tools include:
- area
- minimum and maximum diameter
- estimated spherical volume
- perimeter length
Other Metrics
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).
Contents of Data Repository
Relevant data and code for:
- SizeExtractR ImageJ macros
(on Github: SizeExtractR/inst/ImageJ_macro_code.zip) - SizeExtractR R package
- Timed image analysis
