/SeedGerm

SeedGerm: automated seed phenotyping

Primary LanguagePython

SeedGerm

Joshua Colmer1, Aaron Bostrom1, Joshua Ball 1, Daniel Reynolds1, Ji Zhou1,2,3*

1Earlham Institute, Norwich Research Park, Norwich UK
2University of East Anglia, Norwich Research Park, Norwich UK
3Plant Phenomics Research Center, UK-China Plant Phenomics Centre, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China

Install Python, Anaconda and Libraries

If you wish to run SeedGerm from the code, you will need to set up Python on your system.

  1. Install Python releases:

    • Read the beginner’s guide to Python if you are new to the language: https://wiki.python.org/moin/BeginnersGuide

    • For Windows users, Python 3 release can be downloaded via: https://www.python.org/downloads/windows/

    • For Mac OS users, Python 3 release can be downloaded via: https://www.python.org/downloads/mac-osx/

    • SeedGerm only supports Python 3

  2. Install Anaconda Python distribution:

    • Read the install instruction using the URL: https://docs.continuum.io/anaconda/install

    • For Windows users, a detailed step-by-step installation guide can be found via: https://docs.continuum.io/anaconda/install/windows

    • For Mac OS users, a detailed step-by-step installation guide can be found via: https://docs.continuum.io/anaconda/install/mac-os.html

    • An Anaconda Graphical installer can be found via: https://www.continuum.io/downloads

    • We recommend users install the latest Anaconda Python distribution

  3. Install packages:

    • SeedGerm uses a number of 3rd-party libraries that you may need to add to your conda environment. These include, but are not limited to:

     scikit-image
 scikit-learn
 Keras
 opencv
 pandas

    To install these in your environment, check out: https://conda.io/docs/user-guide/tasks/manage-pkgs.html

    • Please refer to the README.txt file for a more comprehensive list of packages and functional versions

Running SeedGerm

Please see the README.txt file that is included in this repository.

We have a Windows .exe file you can download.