PhytoOracle

PhytoOracle is a scalable, distributed workflow manager for analyzing highthroughput phenotyping data.
It is designed to process data from the UA Gantry, but can be adapted to work on data coming from other platforms.
PhytoOracle uses a master-worker framework for distributed computing (HPC, Cloud, etc.) and can run jobs on nearly all unix-like environments.

Documentation

See detailed documentation here for instruction manuals.

Supported Sensors and Pipelines

• StereoTopRGB
• FlirIr
• PSII
• StereoTop3D
• Hyperspectral (VNIR/SWIR)

For more information on types and description of each camera used, access the documentation above.

Resources

• Code availability (GitHub)
• Containers repository (DockerHub)

License

PhytoOracle is licensed under the MIT License.

Issues and Questions

Need help? Found a bug? Raise an issue on our github page here.

For specific workflows and adapting a pipeline for your own work contact:

• Emmanuel Gonzalez: emmanuelgonzalez [at] email.arizona.edu

• Michele Cosi: cosi [at] email.arizona.edu

For plant detection and plant clustering:

• Travis Simmons: travis.simmons [at] ccga.edu

For the orthomosaicing algorithm:

• Ariyan Zarei: ariyanzarei [at] email.arizona.edu

Acknowledgements

This project partially built on code initially developed by the TERRA-REF project and AgPipeline team. We thank the University of Arizona Advanced Cyberinfrastrcture Concept class of 2019 for additional work.

This material based upon work supported by Cyverse & CCTools. Cyverse is based upon work supported by the National Science Foundation under Grant Numbers: DBI-0735191, DBI-1265383, DBI-1743442. CCTools is based upon work supported by the National Science Foundation under Grant Numbers: CCF-0621434 and CNS-0643229.