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
*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.
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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
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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
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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 KerasTo 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.