Calcium-analysis

Python implementation of calcium imaging analysis pipeline for cardiac myocytes for Automated image analysis of cardiac myocyte Ca2+ dynamics

How to use this package

To install and use this package, follow the steps below:

1. Clone this repository to your local machine.

git clone https://github.com/retroam/Calcium-analysis.git

2. Navigate to the cloned repository.

cd Calcium-analysis

3. Install the required dependencies.

pip install -r requirements.txt

4. Run the scripts in the calcium_analysis directory. For example, to run the data_extraction.py script, use the following command:

python calcium_analysis/run_analysis.py

This script extracts data from regions of interest in an image stack and saves the results. 32: 5. Similarly, you can run the other scripts in the calcium_analysis directory. Each script has a specific function in the calcium imaging analysis pipeline. For more information on what each script does, refer to the comments in the script files.

Command Line Interface

You can also run the package as a command line interface using the main function in the cli.py file. Here's the command to do this:

python -m calcium_analysis.cli --image_fld <path_to_image_folder> --save_fld <path_to_save_folder> --sd <standard_deviation_value>

Where:

• --image_fld is the path to the image folder.
• --save_fld is the path to the save folder.
• --sd is the standard deviation value.