Publication Release

SeedGerm

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

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

^*Correspondence: [email protected], [email protected]

Install Python, Anaconda and Libraries

If you wish to run SeedGerm from the source 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 Anaconda Python 3.7

3. Install packages:

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

    scikit-image
    scikit-learn
    Keras
   

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

Running SeedGerm

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

Alternatively to the source code, a stand-alone Windows .exe file for SeedGerm is available for download.