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Evaluating attributes of Mitochondria

This script will help to evaluate volume, skeleton size and cable length of Mitochondria

Preparation

To enable your computer to run the script, first install these applications:

>>> conda install -c anaconda git

Create the conda environment

We need to create an environment for the script to run successfully, There is a environment.yml file in the parent directory in the repository, this file stores the infomation of package needed.

  • Create the conda environment and install dependency packages as listed in environment.yml
>>> conda env create -f environment.yml
  • Activate the environment which just been created.
>>> conda activate evaluate

Run the script

In main.py, evaluate method takes three parameters
  • dataset directory, which is the directory of the source data you want to evaluate
  • output directory, which is the directory where you want the output file to be generated, this directory should not be exist at the time you run the script
  • data resolution, which is the resolution of the source data

Open up main.py, modify the parameters dataset directory, output directory and the data resolution (optional) and save the modification.

Then run main.py. The output file out.csv will be generated in the output directory you defined. >>> python main.py

Note

The directory sould be passed in absolute path. So if you encounter error message like "directory does not exist", try to use getcwd from os libiary for correct directory.

Reference