SizeExtractR

SizeExtractR extracts size metrics from scaled images to enable quantitative analysis of biological and ecological size-related processes across cellular to landscape scales.

Key Features:

• Semi-automated workflow: Implements a semi-automated workflow to expedite extraction of size dimensions from scaled images.
• ImageJ macros: Uses ImageJ macros to perform rapid size extraction and image annotation.
• R package: Provides quality control, data collation, calibration, and visualization through an R package.
• Size dimensions extracted: Extracts seven common size dimensions, including planar area, minimum and maximum diameter, perimeter, and others.
• Alphanumeric annotations: Records custom categorical variables (e.g., species ID) via alphanumeric annotations.
• Automated archiving: Automatically archives results to enable re-analysis and verification of size extraction processes.
• Performance: Reduces image analysis time by up to 49% compared to fully manual methods.
• Dataset scalability: Integration of ImageJ macros and the R package enables processing of large datasets with reduced manual intervention.

Scientific Applications:

• Coral bleaching assessment: Quantifies changes in coral population dynamics following mass coral bleaching events.
• Population dynamics and demography: Applied in marine and terrestrial studies to measure population dynamics and demographic patterns.
• Energy investment in eggs: Used to assess energy investment in eggs via size measurements.
• Growth assessment of nursery-reared corals: Measures growth in nursery-reared corals.
• Size-based ecological and physiological analyses: Supports analyses linking size metrics to cellular energetics, species fitness, and ecological interactions.

Methodology:

SizeExtractR combines ImageJ macros for size extraction and annotation with an R package for quality control, calibration, data collation, visualization, and automatic archiving.