SUBPREP is a python toolbox specifically designed for subcellular calcium imaging. It is a computationally efficient preprocessing pipeline for ROI selection (after using video preprocessing softwares like suite2p), movement artifact identification, and ROI grouping for axon imaging. For more detailed description, please go to bioRxiv link

• Prerequisites
• Installation
  • 1. Download the Repository
  • 2. Set Up a Virtual Environment Using env.yml
  • 3. Install the SUBPREP Package
• Demo
• Contact

Before you begin, ensure you have the following installed:

• Python 3.x: SUBPREP requires Python version 3.x to run.
• Git: Git is required to download the repository.
• Conda: Conda is recommended for managing the virtual environment.

You can either download SUBPREP directly as a ZIP file or use Git to clone the repository.

1. Go to the SUBPREP GitHub page.
2. Click the green Code button and select Download ZIP.
3. Extract the ZIP file to a location of your choice.

If you have Git installed, you can clone the repository directly:

1. Open a terminal (eg. Anaconda prompt).
2. Run the following command:

   git clone https://github.com/anqijiang/subprep.git
   

1. Open a terminal (eg. Anaconda prompt).
2. Navigate to the SUBPREP folder from last step
3. Create the virtual environment using the following command: (this step will take a while)

   conda env create -f env.yml

4. Activate the virtual environment:

   conda activate subprep
   

1. Under the package directory and subprep virtual environment activated, run:

   pip install -e .

   This step will allow the package to be editable. You can adjust the code based on your research needs.

Once the environment is set up and subprep installed, you can begin playing around using demo.ipynb under jupyter folder.

1. Ensure that the virtual environment is activated.
2. Open the jupyter notebook file.
3. Change the directory in the jupyter notebook file to your local directory to load example data.

If you have any questions or need additional assistance, feel free to contact: anqijiang@uchicago.edu Any feedbacks welcomed.