OFT Analysis Pipeline for DeepLabCut Data

An R-based pipeline for analyzing Open Field Test (OFT) behavioral data from DeepLabCut tracking output.

Required Files

• DLCAnalyzer_Functions_final.R - Core DLCAnalyzer functions (download from ETHZ-INS/DLCAnalyzer)
• OFT_Analysis_Pipeline.R - Main analysis functions
• OFT_Main.R - Configuration and execution script

1. Place `DLCAnalyzer_Functions_final.R` in your R code directory

2. Update file paths in `OFT_Main.R`:
```r
source("path/to/DLCAnalyzer_Functions_final.R")
source("path/to/OFT_Analysis_Pipeline.R")
setwd("path/to/your/data")

Data Structure

Input Directory Structure

Working Directory/
├── filtered_csv/           # DLC output files (*_filtered.csv)
└── Annotation/             # Arena corner annotations
    ├── Subject1/
    │   └── Subject1_annotation.csv
    └── Subject2/
        └── Subject2_annotation.csv

Output Directory Structure

Working Directory/
├── tracking_csv/           # Merged tracking files
│   └── *_tracking.csv
└── OFT_Results/
    ├── Results/           # Individual CSV results
    ├── Plots/             # Trajectory heatmaps
    ├── Temporal/          # Per-minute analysis
    └── Combined_Results.csv

Usage

Basic Analysis

source("OFT_Main.R")
results <- run_analysis()

Output Files

Combined_Results.csv

Main output file containing all behavioral metrics:

• Locomotion: Total distance, speed, movement time
• Zone metrics: Time, distance, and transitions for each zone

Trajectory Plots

Density heatmaps showing spatial occupancy with zone boundaries

Temporal Analysis

Per-minute breakdown of distance traveled and zone occupancy

Behavioral Metrics

The Combined_Results.csv file contains comprehensive behavioral metrics from the Open Field Test analysis. Each row represents one subject/video file.

Metric Descriptions

Basic Information

• ID: Subject/file identifier (extracted from filename)
• Duration_min: Total recording duration in minutes

General Locomotion Metrics

• Total_Distance_cm: Total distance traveled during the entire session (cm)
• Distance_Moving_cm: Distance traveled only during movement periods (cm)
• Average_Speed_cm_s: Mean speed across entire session including stationary periods (cm/s)
• Speed_Moving_cm_s: Mean speed calculated only during movement periods (cm/s)
• Time_Moving_s: Total time spent in motion (seconds)
• Time_Stationary_s: Total time spent stationary/immobile (seconds)
• Percent_Moving: Percentage of session time spent moving (%)

Center Zone Metrics

The center zone typically represents 36% of the arena area (60% × 60% of dimensions)

• Center_Time_s: Total time spent in the center zone (seconds)
• Center_Distance_cm: Distance traveled within the center zone (cm)
• Center_Transitions: Number of entries into the center zone (count)
• Center_Percent: Percentage of total time spent in center zone (%)

Periphery Zone Metrics

The periphery is the outer ring of the arena, excluding corners

• Periphery_Time_s: Total time spent in the periphery zone (seconds)
• Periphery_Distance_cm: Distance traveled within the periphery zone (cm)
• Periphery_Transitions: Number of entries into the periphery zone (count)
• Periphery_Percent: Percentage of total time spent in periphery zone (%)

Corner Zone Metrics

The four corner regions of the arena

• Corners_Time_s: Total time spent in all corner zones combined (seconds)
• Corners_Distance_cm: Distance traveled within corner zones (cm)
• Corners_Transitions: Number of entries into corner zones (count)
• Corners_Percent: Percentage of total time spent in corners (%)

Anxiety-Related Indices

• Center_Periphery_Ratio: Ratio of center time to periphery time (higher = less anxious behavior)
• Thigmotaxis_Index: Wall-hugging behavior index; periphery time/(center + periphery time) (0-1 scale; higher = more thigmotactic/anxious behavior)

Configuration Dependencies

These metrics are calculated based on your config settings:

• movement_cutoff: Threshold for determining movement vs. stationary (default: 3 cm/s)
• center_scale: Size of center zone (default: 0.6 = 60% of arena width/height)
• periphery_scale: Size of periphery boundary (default: 0.8)
• corner_scale: Size of corner zones (default: 0.25)

License

• OFT Analysis Pipeline (this repository): MIT License
• Required dependency (DLCAnalyzer): GPL-3.0 License

Citation

If you use this pipeline, please cite:

• DeepLabCut: Mathis et al. (2018)
• DLCAnalyzer