This repository contains a workflow to study the distribution of tertiary lymphatic structures in the meninges of rodents. Currently, results are available for the following strains:

• APOE3
• APOE4
• APP
• C57
• Dp1Tyb
• Tau
• Tau sibling

Cross-strain comparisons were performed for the following combinations of strains:

• Dp1Tyb and C57
• Tau and C57

All reports and plots can be accessed from the reports subdirectory or clicking in one of the links above.

To obtain results from new data, the analysis should be executed locally based on the following steps:

1. Clone this repository on your local machine
2. Store the structures.csv, angles.csv and opac_meninges.png files in the data subdirectory
3. Modify or add new data to the structures.csv and angles.csv files
4. Run process.R to obtain a new version of the processed data saved as processed_data.csv
5. Run main.R. If new strains were added, include their names in the list found in this script

• main.R: this script runs meninges_report.qmd and returns one md report for every strain, from which the file name is deduced
• process.R: this script preprocesses the structures.csv and angles.csv that reside in the data subdirectory and returns processed_data.csv as output
• globals.R: this script imports necessary packages and defines custom constants and functions used by the other scripts
• meninges_report.qmd: this Quarto notebook hosts the code that performs the within-strain analysis and generates the corresponding plots
• comparison.qmd: this Quarto notebook hosts the code that performs the between-strain analysis and generates the corresponding plots