Resazurin Assay Development

This repository contains all code, data, and documentation for the development and application of the resazurin assay to measure oyster metabolic responses to environmental stress. The project integrates multiple experimental datasets, analysis scripts, and outputs, supporting research in oyster health, aquaculture, and genetics.

See our landing page for information on resazurin protocols, recent findings, experimental design tools, and data explor apps!

Manuscript

This repository contains data to accompany the manuscript:

Huffmyer et al. (2026) From Blue to Pink: Resazurin as a High-Throughput Proxy for Metabolic Rate in Oysters

Data that is included in this manuscript includes the directories listed in "respository structure" below.

Clam dashboard

This repository now includes an auto-updating clam dashboard page that is built from plate reader exports under data/clam.

• Dashboard source page: clam-dashboard.qmd
• Output data artifacts: output/clam/dashboard-data.csv and output/clam/dashboard-qc.csv
• GitHub Actions workflow: .github/workflows/update-clam-dashboard.yml

The dashboard QMD parses data/clam/**/plate-*-T*.txt during render, writes the output CSVs, and then renders the interactive page. When matching files are pushed to main, the workflow rebuilds the dashboard and redeploys the site.

Repository Structure

resazurin-assay-development/
│
├── _quarto.yml                # Quarto website configuration
├── index.qmd                  # Technical documentation landing page
├── public-summary.qmd         # Public summary for general audiences
├── README.md                  # Project overview
├── resazurin-assay-development.Rproj # RStudio project file
│
├── data/                      # Raw and processed data for all projects
│   ├── 10k-seed/              # Data for large seed thermal stress project
│   ├── oxygen-correlation/    # Data for oxygen-resazurin correlation
│   ├── spat-stress/           # Data for small seed thermal stress project
│   ├── testing/               # Data for method validation/testing
│   ├── thermal-curve/         # Data for resazurin thermal curve project
│   └── usda-families/         # Data for family metabolic responses project
│
├── scripts/                   # RMarkdown analysis scripts
│   ├── 10k-seed/              # Analyses for large seed thermal stress project
│   ├── oxygen-correlation/    # Oxygen-resazurin analyses
│   ├── spat-stress/           # Analyses for small seed thermal stress project
│   ├── testing/               # Method validation scripts
│   ├── thermal-curve/         # resazurin thermal curve project
│   └── usda-families/         # family metabolic responses project
│
├── figures/                   # Figures and diagrams
│   ├── resazurin-applications-diagram.md # Visual schematic
│   └── ...                    # Project-specific figures
│
├── output/                    # Analysis outputs for each project (tables, processed data)
│   ├── 10k-seed/
│   ├── oxygen-correlation/
│   ├── spat-stress/
│   ├── thermal-curve/
│   └── usda-families/
│
├── docs/                      # Quarto website output
│   ├── index.html
│   ├── public-summary.html
│   └── figures/
│
└── ...                        # Additional documentation and metadata

Project Connections

• Large seed thermal stress project: Examines oyster seed response to thermal stress, connecting acute temperature effects to resazurin measurements and mortality. Related repo
• Small seed thermal stress project: Explores thermal stress response in spat. Related repo
• Family metabolic responses project: Investigates genetic variation in stress response among oyster families, comparing absorbance and fluorescence modes.
• Oxygen correlation: Links resazurin assay results to direct oxygen consumption measurements for validation.
• Resazurin thermal curve: Analyzes metabolic responses across temperature gradients in USDA families.
• Testing: Contains method validation and protocol optimization scripts.

Purpose of Key Scripts

• scripts/10k-seed/resazurin-analysis-10k-seed.Rmd: Analyzes metabolic rate data for large seed thermal stress Project.
• scripts/10k-seed/survival-analysis-10k-seed.Rmd: Survival analysis based on resazurin data in large seed thermal stress project.
• scripts/oxygen-correlation/oxygen-rate-extraction.Rmd: Extracts respiration rates from oxygen data.
• scripts/oxygen-correlation/oxygen-resazurin-correlations.Rmd: Correlates oxygen and resazurin measurements.
• scripts/oxygen-correlation/resazurin-analysis.Rmd: Analyzes individual oyster resazurin data for oxygen comparison.
• scripts/spat-stress/resazurin-analysis-spat-stress.Rmd: Analyzes small seed thermal stress project data.
• scripts/testing/shell-vs-open.Rmd: Compares empty shell vs live animal metabolic rates.
• scripts/thermal-curve/thermal-curve-analysis.Rmd: Analyzes resazurin thermal curve data.
• scripts/usda-families/resazurin-analysis-usda-families.Rmd: Analysis of metabolic rates between different families.

Data Organization

• Each project folder in data/ contains raw data files (CSV, XLSX) and metadata.
• output/ contains processed data and results from analysis scripts.
• figures/ contains visualizations and diagrams for each project.

Documentation

• index.qmd: Technical documentation and protocol details.
• public-summary.qmd: Lay summary for non-specialists.
• _quarto.yml: Website configuration for navigation and theming.

Visual Schematic

Below is a simplified flow diagram from figures/resazurin-applications-diagram.md:

OYSTER SAMPLE
	│
	▼
RESAZURIN ASSAY
 • Add dye
 • Apply stress
 • Measure signal
	│
	▼
METABOLIC ACTIVITY (Fluorescence Signal)

Applications: Breeding programs, health assessment, stress tolerance screening.

---

Getting Started

1. Clone the repository and open in RStudio.
2. Explore index.qmd for technical documentation.
3. Run analysis scripts in scripts/ for each project.
4. View outputs in output/ and figures in figures/.

Contact

For questions, see the GitHub repo or contact the authors listed in index.qmd.