# TERRA-REF Documentation ## beta - [Introduction](https://docs.terraref.org/beta/undefined.md) - [Data Sources](https://docs.terraref.org/beta/data-sources.md) - [Software](https://docs.terraref.org/beta/software.md) - [Scientific Objectives and Experimental Design](https://docs.terraref.org/beta/scientific-objectives-and-experimental-design.md) - [Protocols](https://docs.terraref.org/beta/scientific-objectives-and-experimental-design/protocols.md) - [Controlled Environment Protocols](https://docs.terraref.org/beta/scientific-objectives-and-experimental-design/protocols/controlled-environment-protocols.md) - [Manual Field Data Protocols](https://docs.terraref.org/beta/scientific-objectives-and-experimental-design/protocols/manual-field-data-protocols.md) - [Phenotractor Protocols](https://docs.terraref.org/beta/scientific-objectives-and-experimental-design/protocols/phenotractor-protocols.md) - [Sensor Calibration](https://docs.terraref.org/beta/scientific-objectives-and-experimental-design/protocols/sensor-calibration.md) - [Template Protocol](https://docs.terraref.org/beta/scientific-objectives-and-experimental-design/protocols/template-protocol.md) - [UAV Protocols](https://docs.terraref.org/beta/scientific-objectives-and-experimental-design/protocols/uav-protocols.md) - [Experimental Design](https://docs.terraref.org/beta/scientific-objectives-and-experimental-design/experimental-design.md) - [Experimental Design Danforth](https://docs.terraref.org/beta/scientific-objectives-and-experimental-design/experimental-design/experimental-design-danforth.md) - [Sorghum Lines Danforth](https://docs.terraref.org/beta/scientific-objectives-and-experimental-design/experimental-design/experimental-design-danforth/sorghum-lines-danforth.md) - [Experimental Design Genomics](https://docs.terraref.org/beta/scientific-objectives-and-experimental-design/experimental-design/experimental-design-genomics.md) - [Sorghum Lines Genomics Year 1](https://docs.terraref.org/beta/scientific-objectives-and-experimental-design/experimental-design/experimental-design-genomics/sorghum-lines-genomics-year-1.md) - [Sorghum Lines Genomics Year 1 (continued)](https://docs.terraref.org/beta/scientific-objectives-and-experimental-design/experimental-design/experimental-design-genomics/sorghum-lines-genomics-year-1-continued.md) - [Sorghum Lines Genomics Year 2](https://docs.terraref.org/beta/scientific-objectives-and-experimental-design/experimental-design/experimental-design-genomics/sorghum-lines-genomics-year-2.md) - [Experimental Design MAC](https://docs.terraref.org/beta/scientific-objectives-and-experimental-design/experimental-design/experimental-design-mac.md) - [User Manual](https://docs.terraref.org/beta/user-manual.md) - [What Data is Available](https://docs.terraref.org/beta/user-manual/what-data-is-available.md) - [Data Products](https://docs.terraref.org/beta/user-manual/data-products.md) - [Environmental conditions](https://docs.terraref.org/beta/user-manual/data-products/environmental-conditions.md) - [Fluorescence intensity imaging](https://docs.terraref.org/beta/user-manual/data-products/fluorescence-intensity-imaging.md) - [Genomics data](https://docs.terraref.org/beta/user-manual/data-products/genomics-data.md) - [Geospatial information](https://docs.terraref.org/beta/user-manual/data-products/geospatial-information.md) - [Hyperspectral imaging data](https://docs.terraref.org/beta/user-manual/data-products/hyperspectral-imaging-data.md) - [Infrared heat imaging data](https://docs.terraref.org/beta/user-manual/data-products/infrared-heat-imaging-data.md) - [Multispectral imaging data](https://docs.terraref.org/beta/user-manual/data-products/multispectral-imaging-data.md) - [Meteorological data](https://docs.terraref.org/beta/user-manual/data-products/meteorological-data.md) - [Controlled Environment phenotype data](https://docs.terraref.org/beta/user-manual/data-products/plantcv-trait-data.md) - [Point Cloud Data](https://docs.terraref.org/beta/user-manual/data-products/point-cloud-data.md) - [How to Access Data](https://docs.terraref.org/beta/user-manual/how-to-access-data.md) - [Using Clowder (Sensor and Genoomics data)](https://docs.terraref.org/beta/user-manual/how-to-access-data/using-clowder-sensor-and-genoomics-data.md) - [Using Globus (Sensor and Genomics data)](https://docs.terraref.org/beta/user-manual/how-to-access-data/using-globus-sensor-and-genomics-data.md) - [Using BETYdb (trait data, experimental metadata)](https://docs.terraref.org/beta/user-manual/how-to-access-data/using-betydb-trait-data-experimental-metadata.md) - [Accessing BETYdb via ArcMap and other GIS software](https://docs.terraref.org/beta/user-manual/how-to-access-data/using-betydb-trait-data-experimental-metadata/accessing-betydb-via-arcmap-and-other-gis-software.md) - [Using CoGe (Genomics)](https://docs.terraref.org/beta/user-manual/how-to-access-data/using-coge-genomics.md) - [Using CyVerse (Genomics)](https://docs.terraref.org/beta/user-manual/how-to-access-data/using-cyverse-genomics.md) - [Using Analysis Workbench (all data)](https://docs.terraref.org/beta/user-manual/how-to-access-data/using-analysis-workbench-all-data.md) - [Data Use Policy](https://docs.terraref.org/beta/user-manual/data-use-policy.md) - [Manuscripts and Authorship Guidelines](https://docs.terraref.org/beta/user-manual/manuscripts-and-authorship-guidelines.md) - [Release / reprocessing schedule](https://docs.terraref.org/beta/user-manual/release-reprocessing-schedule.md) - [Technical Documentation](https://docs.terraref.org/beta/technical-documentation.md) - [Data Standards](https://docs.terraref.org/beta/technical-documentation/data-standards.md) - [Existing Data Standards](https://docs.terraref.org/beta/technical-documentation/data-standards/existing-data-standards.md) - [Agronomic and Phenotype Data Standards](https://docs.terraref.org/beta/technical-documentation/data-standards/agronomic-and-phenotype-data-standards.md) - [Genomic Data Standards](https://docs.terraref.org/beta/technical-documentation/data-standards/genomic-data-standards.md) - [Sensor Data Standards](https://docs.terraref.org/beta/technical-documentation/data-standards/sensor-data-standards.md) - [Data Standards Committee](https://docs.terraref.org/beta/technical-documentation/data-standards/data-standards-committee.md) - [Directory Structure](https://docs.terraref.org/beta/technical-documentation/directory-structure.md) - [Data Storage](https://docs.terraref.org/beta/technical-documentation/data-storage.md) - [Data Transfer](https://docs.terraref.org/beta/technical-documentation/data-transfer.md) - [Data Processing Pipeline](https://docs.terraref.org/beta/technical-documentation/data-processing-pipeline.md) - [Geospatial Time Series Structure](https://docs.terraref.org/beta/technical-documentation/data-processing-pipeline/geospatial-time-series-structure.md) - [Data Backup](https://docs.terraref.org/beta/technical-documentation/data-backup.md) - [Data Collection](https://docs.terraref.org/beta/technical-documentation/data-collection.md) - [Data Product Creation](https://docs.terraref.org/beta/technical-documentation/data-product-creation.md) - [Genomic Data](https://docs.terraref.org/beta/technical-documentation/data-product-creation/genomic-data.md) - [Hyperspectral Data](https://docs.terraref.org/beta/technical-documentation/data-product-creation/hyperspectral-data.md) - [Quality Assurance and Quality Control](https://docs.terraref.org/beta/technical-documentation/quality-assurance-and-quality-control.md) - [Developer Manual](https://docs.terraref.org/beta/developer-manual.md) - [Submitting data to Clowder](https://docs.terraref.org/beta/developer-manual/submitting-data-to-clowder.md) - [Submitting data to BETYdb](https://docs.terraref.org/beta/developer-manual/submitting-data-to-betydb.md) - [Submitting Data to CoGe](https://docs.terraref.org/beta/developer-manual/submitting-data-to-coge.md) - [Developing Clowder Extractors](https://docs.terraref.org/beta/developer-manual/developing-clowder-extractors.md) - [Tutorials](https://docs.terraref.org/beta/tutorials.md) - [Appendix](https://docs.terraref.org/beta/appendix.md) - [Code of Conduct](https://docs.terraref.org/beta/appendix/code-of-conduct.md) - [Collaboration Tools](https://docs.terraref.org/beta/appendix/collaboration-tools.md) - [Glossary](https://docs.terraref.org/beta/appendix/glossary.md) ## revisions - [Introduction](https://docs.terraref.org/revisions/master.md) - [Data Sources](https://docs.terraref.org/revisions/data-sources.md) - [Software](https://docs.terraref.org/revisions/software.md) - [Scientific Objectives and Experimental Design](https://docs.terraref.org/revisions/scientific-objectives-and-experimental-design.md) - [Protocols](https://docs.terraref.org/revisions/scientific-objectives-and-experimental-design/protocols.md) - [Controlled Environment Protocols](https://docs.terraref.org/revisions/scientific-objectives-and-experimental-design/protocols/controlled-environment-protocols.md) - [Manual Field Data Protocols](https://docs.terraref.org/revisions/scientific-objectives-and-experimental-design/protocols/manual-field-data-protocols.md) - [Phenotractor Protocols](https://docs.terraref.org/revisions/scientific-objectives-and-experimental-design/protocols/phenotractor-protocols.md) - [Sensor Calibration](https://docs.terraref.org/revisions/scientific-objectives-and-experimental-design/protocols/sensor-calibration.md) - [Template Protocol](https://docs.terraref.org/revisions/scientific-objectives-and-experimental-design/protocols/template-protocol.md) - [UAV Protocols](https://docs.terraref.org/revisions/scientific-objectives-and-experimental-design/protocols/uav-protocols.md) - [Experimental Design](https://docs.terraref.org/revisions/scientific-objectives-and-experimental-design/experimental-design.md) - [Experimental Design Danforth](https://docs.terraref.org/revisions/scientific-objectives-and-experimental-design/experimental-design/experimental-design-danforth.md) - [Sorghum Lines Danforth](https://docs.terraref.org/revisions/scientific-objectives-and-experimental-design/experimental-design/experimental-design-danforth/sorghum-lines-danforth.md) - [Experimental Design Genomics](https://docs.terraref.org/revisions/scientific-objectives-and-experimental-design/experimental-design/experimental-design-genomics.md) - [Sorghum Lines Genomics Year 1](https://docs.terraref.org/revisions/scientific-objectives-and-experimental-design/experimental-design/experimental-design-genomics/sorghum-lines-genomics-year-1.md) - [Sorghum Lines Genomics Year 1 (continued)](https://docs.terraref.org/revisions/scientific-objectives-and-experimental-design/experimental-design/experimental-design-genomics/sorghum-lines-genomics-year-1-continued.md) - [Sorghum Lines Genomics Year 2](https://docs.terraref.org/revisions/scientific-objectives-and-experimental-design/experimental-design/experimental-design-genomics/sorghum-lines-genomics-year-2.md) - [Experimental Design MAC](https://docs.terraref.org/revisions/scientific-objectives-and-experimental-design/experimental-design/experimental-design-mac.md) - [User Manual](https://docs.terraref.org/revisions/user-manual.md) - [What Data is Available](https://docs.terraref.org/revisions/user-manual/what-data-is-available.md) - [Data Products](https://docs.terraref.org/revisions/user-manual/data-products.md) - [Environmental conditions](https://docs.terraref.org/revisions/user-manual/data-products/environmental-conditions.md) - [Fluorescence intensity imaging](https://docs.terraref.org/revisions/user-manual/data-products/fluorescence-intensity-imaging.md) - [Genomics data](https://docs.terraref.org/revisions/user-manual/data-products/genomics-data.md) - [Geospatial information](https://docs.terraref.org/revisions/user-manual/data-products/geospatial-information.md) - [Hyperspectral imaging data](https://docs.terraref.org/revisions/user-manual/data-products/hyperspectral-imaging-data.md) - [Infrared heat imaging data](https://docs.terraref.org/revisions/user-manual/data-products/infrared-heat-imaging-data.md) - [Multispectral imaging data](https://docs.terraref.org/revisions/user-manual/data-products/multispectral-imaging-data.md) - [Meteorological data](https://docs.terraref.org/revisions/user-manual/data-products/meteorological-data.md) - [Phenotype data](https://docs.terraref.org/revisions/user-manual/data-products/phenotype-data.md) - [Point Cloud Data](https://docs.terraref.org/revisions/user-manual/data-products/point-cloud-data.md) - [How to Access Data](https://docs.terraref.org/revisions/user-manual/how-to-access-data.md) - [Using Clowder (Sensor and Genoomics data)](https://docs.terraref.org/revisions/user-manual/how-to-access-data/using-clowder-sensor-and-genoomics-data.md) - [Using Globus (Sensor and Genomics data)](https://docs.terraref.org/revisions/user-manual/how-to-access-data/using-globus-sensor-and-genomics-data.md) - [Using BETYdb (trait data, experimental metadata)](https://docs.terraref.org/revisions/user-manual/how-to-access-data/using-betydb-trait-data-experimental-metadata.md) - [Accessing BETYdb via ArcMap and other GIS software](https://docs.terraref.org/revisions/user-manual/how-to-access-data/using-betydb-trait-data-experimental-metadata/accessing-betydb-via-arcmap-and-other-gis-software.md) - [Using CoGe (Genomics)](https://docs.terraref.org/revisions/user-manual/how-to-access-data/using-coge-genomics.md) - [Using CyVerse (Genomics)](https://docs.terraref.org/revisions/user-manual/how-to-access-data/using-cyverse-genomics.md) - [Using Analysis Workbench (all data)](https://docs.terraref.org/revisions/user-manual/how-to-access-data/using-analysis-workbench-all-data.md) - [Data Use Policy](https://docs.terraref.org/revisions/user-manual/data-use-policy.md) - [Manuscripts and Authorship Guidelines](https://docs.terraref.org/revisions/user-manual/manuscripts-and-authorship-guidelines.md) - [Release / reprocessing schedule](https://docs.terraref.org/revisions/user-manual/release-reprocessing-schedule.md) - [Technical Documentation](https://docs.terraref.org/revisions/technical-documentation.md) - [Data Standards](https://docs.terraref.org/revisions/technical-documentation/data-standards.md) - [Existing Data Standards](https://docs.terraref.org/revisions/technical-documentation/data-standards/existing-data-standards.md) - [Agronomic and Phenotype Data Standards](https://docs.terraref.org/revisions/technical-documentation/data-standards/agronomic-and-phenotype-data-standards.md) - [Genomic Data Standards](https://docs.terraref.org/revisions/technical-documentation/data-standards/genomic-data-standards.md) - [Sensor Data Standards](https://docs.terraref.org/revisions/technical-documentation/data-standards/sensor-data-standards.md) - [Data Standards Committee](https://docs.terraref.org/revisions/technical-documentation/data-standards/data-standards-committee.md) - [Directory Structure](https://docs.terraref.org/revisions/technical-documentation/directory-structure.md) - [Data Storage](https://docs.terraref.org/revisions/technical-documentation/data-storage.md) - [Data Transfer](https://docs.terraref.org/revisions/technical-documentation/data-transfer.md) - [Data Processing Pipeline](https://docs.terraref.org/revisions/technical-documentation/data-processing-pipeline.md) - [Geospatial Time Series Structure](https://docs.terraref.org/revisions/technical-documentation/data-processing-pipeline/geospatial-time-series-structure.md) - [Data Backup](https://docs.terraref.org/revisions/technical-documentation/data-backup.md) - [Data Collection](https://docs.terraref.org/revisions/technical-documentation/data-collection.md) - [Data Product Creation](https://docs.terraref.org/revisions/technical-documentation/data-product-creation.md) - [Genomic Data](https://docs.terraref.org/revisions/technical-documentation/data-product-creation/genomic-data.md) - [Hyperspectral Data](https://docs.terraref.org/revisions/technical-documentation/data-product-creation/hyperspectral-data.md) - [Quality Assurance and Quality Control](https://docs.terraref.org/revisions/technical-documentation/quality-assurance-and-quality-control.md) - [Systems Configuration](https://docs.terraref.org/revisions/technical-documentation/systems-configuration.md) - [Developer Manual](https://docs.terraref.org/revisions/developer-manual.md) - [Submitting data to Clowder](https://docs.terraref.org/revisions/developer-manual/submitting-data-to-clowder.md) - [Submitting data to BETYdb](https://docs.terraref.org/revisions/developer-manual/submitting-data-to-betydb.md) - [Submitting Data to CoGe](https://docs.terraref.org/revisions/developer-manual/submitting-data-to-coge.md) - [Developing Clowder Extractors](https://docs.terraref.org/revisions/developer-manual/developing-clowder-extractors.md) - [Tutorials](https://docs.terraref.org/revisions/tutorials.md) - [Appendix](https://docs.terraref.org/revisions/appendix.md) - [Code of Conduct](https://docs.terraref.org/revisions/appendix/code-of-conduct.md) - [Collaboration Tools](https://docs.terraref.org/revisions/appendix/collaboration-tools.md) - [Glossary](https://docs.terraref.org/revisions/appendix/glossary.md) ## Primary version - [Introduction](https://docs.terraref.org/master.md) - [Scientific Objectives](https://docs.terraref.org/scientific-objectives-and-experimental-design.md) - [Experimental Design](https://docs.terraref.org/experimental-design.md) - [The Maricopa Agricultural Center (MAC)](https://docs.terraref.org/experimental-design/experimental-design-mac.md) - [Controlled Environment Phenotyping](https://docs.terraref.org/experimental-design/experimental-design-danforth.md) - [Genomics](https://docs.terraref.org/experimental-design/experimental-design-genomics.md) - [Data](https://docs.terraref.org/user-manual.md) - [How to Access Data](https://docs.terraref.org/user-manual/how-to-access-data.md) - [Data Products](https://docs.terraref.org/user-manual/data-products.md) - [Environmental conditions](https://docs.terraref.org/user-manual/data-products/environmental-conditions.md) - [Phenotype Data](https://docs.terraref.org/user-manual/data-products/phenotype-data.md): Under Construction - [Genomics data](https://docs.terraref.org/user-manual/data-products/genomics-data.md) - [Fluorescence intensity imaging](https://docs.terraref.org/user-manual/data-products/fluorescence-intensity-imaging.md) - [Geospatial information](https://docs.terraref.org/user-manual/data-products/geospatial-information.md) - [Hyperspectral imaging data](https://docs.terraref.org/user-manual/data-products/hyperspectral-imaging-data.md) - [Infrared heat imaging data](https://docs.terraref.org/user-manual/data-products/infrared-heat-imaging-data.md) - [Meteorological data](https://docs.terraref.org/user-manual/data-products/meteorological-data.md) - [Point Cloud Data](https://docs.terraref.org/user-manual/data-products/point-cloud-data.md) - [Controlled Environment phenotype data](https://docs.terraref.org/user-manual/data-products/plantcv-trait-data.md) - [Data Use Policy](https://docs.terraref.org/user-manual/data-use-policy.md) - [Manuscripts and Authorship Guidelines](https://docs.terraref.org/user-manual/manuscripts-and-authorship-guidelines.md) - [Protocols](https://docs.terraref.org/protocols.md) - [Field Scanner](https://docs.terraref.org/protocols/field-scanner.md) - [Sensor Calibration](https://docs.terraref.org/protocols/sensor-calibration.md) - [Hyperspectral Data](https://docs.terraref.org/protocols/hyperspectral-data.md) - [Controlled Environment Protocols](https://docs.terraref.org/protocols/controlled-environment-protocols.md) - [Manual Field Data Protocols](https://docs.terraref.org/protocols/manual-field-data-protocols.md): Data were collected manually using standard field methods. These measurements are used to calibrate and validate phenotypes derived from sensor-collected data. - [Phenotractor Protocols](https://docs.terraref.org/protocols/phenotractor-protocols.md) - [UAV Protocols](https://docs.terraref.org/protocols/uav-protocols.md) - [Genomic Protocols](https://docs.terraref.org/protocols/genomic-data.md) - [Technical Documentation](https://docs.terraref.org/technical-documentation.md) - [Software](https://docs.terraref.org/technical-documentation/software.md) - [Data Standards](https://docs.terraref.org/technical-documentation/data-standards.md) - [Existing Data Standards](https://docs.terraref.org/technical-documentation/data-standards/existing-data-standards.md) - [Agronomic and Phenotype Data Standards](https://docs.terraref.org/technical-documentation/data-standards/agronomic-and-phenotype-data-standards.md) - [Genomic Data Standards](https://docs.terraref.org/technical-documentation/data-standards/genomic-data-standards.md) - [Sensor Data Standards](https://docs.terraref.org/technical-documentation/data-standards/sensor-data-standards.md) - [Data Standards Committee](https://docs.terraref.org/technical-documentation/data-standards/data-standards-committee.md) - [Data Product Levels](https://docs.terraref.org/technical-documentation/data-product-creation.md) - [Directory Structure](https://docs.terraref.org/technical-documentation/directory-structure.md) - [Data Transfer](https://docs.terraref.org/technical-documentation/data-transfer.md) - [Data Processing Pipeline](https://docs.terraref.org/technical-documentation/data-processing-pipeline.md) - [Time Series Data in Geostreams](https://docs.terraref.org/technical-documentation/geospatial-time-series-structure.md) - [Data Backup](https://docs.terraref.org/technical-documentation/data-backup.md) - [Systems Configuration](https://docs.terraref.org/technical-documentation/systems-configuration.md) - [Code of Conduct](https://docs.terraref.org/code-of-conduct.md) - [Appendix](https://docs.terraref.org/appendix.md) - [Glossary](https://docs.terraref.org/appendix/glossary.md) - [Accessing BETYdb with GIS Software](https://docs.terraref.org/appendix/accessing-betydb-with-gis-software.md) - [References](https://docs.terraref.org/references.md) - [Developer Manual](https://docs.terraref.org/archived-documentation/developer-manual.md) - [Submitting data to Clowder](https://docs.terraref.org/archived-documentation/developer-manual/submitting-data-to-clowder.md) - [Submitting data to BETYdb](https://docs.terraref.org/archived-documentation/developer-manual/submitting-data-to-betydb.md) - [Submitting Data to CoGe](https://docs.terraref.org/archived-documentation/developer-manual/submitting-data-to-coge.md) - [Developing Clowder Extractors](https://docs.terraref.org/archived-documentation/developer-manual/developing-clowder-extractors.md)