README.md

In liamlachs/SizeExtractR: Extracts object size metrics from scaled images analysed in SizeExtractR ImageJ protocols

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 like 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 great option for image analysis applications that are not suited to machine-learning or other automated outlining classifiers.

R package

The R tools are used to synthesis all data into one master dataset, with all variables of interest included. Additional problem-solving tools are also provided.

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).

Example

This is the output from a Lachs et al. (2021) that used an earlier version of SizeExtractR to assess coral demography and population dynamics before and after mass bleaching in 2016.

Coral Population Size Structure:

liamlachs/SizeExtractR documentation built on Feb. 13, 2022, 9:46 p.m.