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GPM phenotyping scripts

This project is composed of Python scripts and ImageJ macros for use with the high throughput Erysiphe necator fungicide and UV-C efficacy assays developed by Alexander Wong, Eliza Allen, and Jason Toney.

License

This project is licensed under the GNU General Public License v3.0. For more details, please see the LICENSE file.

Installation

  1. Install Python 3.9 or 3.10.
  2. Install the additional required dependencies:
    Windows: Run setup/InstallDependencies.bat
    Linux: Untested/Unsupported
    Mac: Untested/Unsupported

Updates (without using git)

  1. Run setup/update.py to automatically download and install the latest version of this repository in a non-git environment.

Usage

  1. Place image albums into the "ECHO Images" directory.
  2. Run batch_process.py to process the image albums. The results will be
    compiled into an Excel workbook named GPMPhenotypingAssay_Workbook.xlsx
    found in this directory. The results of the analysis will also be
    outputted to the screen.

TODO

  • improve code style and readability