Generating Interactive 3D Spatial Visualizations of Microbial Abundance in Poultry Litter Using RStudio
M A Peckenschneider1, E G Olson1, J K Byrnes2
1Meat Science and Animal Biologics Discovery, Department of Animal and Dairy Sciences, University of Wisconsin-Madison.
Journal of Visualized Experiments : Jove
|May 4, 2026
Summary
Interactive 3D visualizations reveal spatial patterns in poultry litter microbiology. This method highlights microbial clustering near moisture sources, offering a new way to analyze pen environments.
Area of Science:
- Agricultural Science
- Microbiology
- Data Visualization
Background:
- Traditional poultry litter assessments lack spatial detail.
- Static data representations fail to capture environmental heterogeneity.
Purpose of the Study:
- To develop interactive 3D visualizations for poultry litter analysis.
- To integrate microbial data with environmental parameters.
- To explore spatial gradients in poultry pen environments.
Main Methods:
- A grid-based sampling approach was used for poultry pens.
- Simulated and experimental datasets were processed in RStudio.
- Interactive 3D plots were generated using plotly.
Main Results:
- Aerobic bacterial loads varied from 5.9 to 8.6 log₁₀ CFU/g.
- Higher bacterial abundance was observed near water lines (P = 0.023).
- 3D plots showed microbial clustering around moisture-rich areas.
Conclusions:
- Interactive 3D visualization is a powerful tool for analyzing poultry litter spatial heterogeneity.
- The protocol provides a reproducible method for visualizing microbial communities.
- Further validation in commercial settings is recommended.
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