Zebrafish Data Analysis

This repository provides Python scripts for analyzing and visualizing zebrafish experimental data generated by the ViewPoint ZebraBox device as well as formating and analyzing clocklab data. The experimental dataset and format can be requested from the author. Note that this codebase is tailored for specific experiments and may have limited applicability for other use cases. Follow the steps below to set up the environment and run the analysis.

Prerequisites

1. Install Python (version 3.7 or higher).
2. Ensure pip is installed and available in your system's PATH.

Setup Instructions

1. Clone the Repository
   Clone this repository to your local machine.

   git clone https://github.com/your-repo/ZebraFishDataAnalysis.git
   cd ZebraFishDataAnalysis

2. Set Up a Virtual Environment
   Create and activate a virtual environment to manage dependencies.

   python -m venv venv
   # On Windows
   venv\Scripts\activate
   # On macOS/Linux
   source venv/bin/activate

3. Install Dependencies
   Install the required Python packages from requirements.txt.

   pip install -r requirements.txt

4. Update Configuration
   Open the configuration.json file and update the following fields to match your inputs:

   • Set the correct file directory and sheet name for your excel files
   • Add any wells to exclude in the wellsToExclude field.

   Example:

   {
       "inputFileDirectory": "InputFiles",
       "inputFileSheetName": "Data",
       "wellsToExclude": [1 ,2, 6]
   }

Running the Analysis

Run the ZebrafishDataAnalysis.py script to start the analysis.

python ZebrafishDataAnalysis.py

Notes

• Ensure the configuration file is correctly updated before running the script.
• For any issues, please open an issue in the repository.