# Open Field Test Behavioral Analysis - ReadMe Document
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This document outlines the process for evaluation of open field test behaviors as listed in the recent Brockway et al. manuscript, "Somatostatin Peptide Signaling Dampens Cortical Circuits and Promotes Exploratory Behavior”. Three MATLAB functions are sequentially performed to quantify specific exploratory behaviors of mice following DeepLabCut video tracking analysis.

## Description of the Data and file structure

Open field test behavioral analysis using MATLAB is performed following successful DeepLabCut video tracking. The three-stage algorithm uses the following distinct body positions for different behavioral classifications: the head, caudal to the shoulder joint in the center of the body, and the trunk of the tail. Additional tracked positions bound the corners of the 50 cm x 50 cm arena, the 10 cm x 10 cm square in each corner, and the 30 cm x 30 cm center square.

**OFTAnalysis_Stage1**
This function loads the .csv video file outputs following DeepLabCut video tracking and saves the tracking data into .mat file format for continued MATLAB analysis. Data is saved as a MATLAB structure containing tracking data coordinates, body part names, mouse ID as denoted in the file and any additional data from the .csv file. The function will save separate .mat files for each .csv file in the containing folder and will create an OFTData structure array containing the above listed variables.
1. Open the folder containing the tracked .csv files
2. Run OFTAnalysis_Stage1

**OFTAnalysis_Stage2**
This function will load the individual .mat OFTData structure array and calculate parameters as outlined in the Brockway et al. manuscript, "Somatostatin Peptide Signaling Dampens Cortical Circuits and Promotes Exploratory Behavior”. The second stage of open field test analysis saves additional variables needed for analysis to the original OFTData structure array. Additionally, this function calculates parameters not outlined in the manuscript for further detailed analysis of mouse behavior.
1. Run OFTAnalysis_Stage2 following successful completion of OFTAnalysis_Stage1

**OFTAnalysis_Stage3**
The final stage of open field test analysis functions to perform a population analysis of a data set. This function will generate a table containing parameters of interest that can then be used for continued statistical analysis and figure generation. Successful completion of OFTAnalysis_Stage3 will save all parameters in a table titled OFTTable.mat in the original containing folder.
1. Run OFTAnalysis_Stage3 following successful completion of OFTAnalysis_Stage2

## Sharing and Access Information

These scripts were used in the behavioral analysis of open field test behaviors for the Brockway et al. manuscript, "Somatostatin Peptide Signaling Dampens Cortical Circuits and Promotes Exploratory Behavior”. Citation for the BioRxiv preprint provided below.

Brockway D, Moyer J, Aloimonos C, Clarity T, Griffith K, Smith G, Dao N, Hossain M, Drew P, Gordon J, Kupferschmidt D, Crowley N, Somatostatin peptide signaling dampens cortical circuits and promotes exploratory behavior, *BioRxiv*, doi: 10.1101/2022.07.18.499817