Code from: Using cameras for precise measurement of two-dimensional plant features

Images are used frequently in plant phenotyping to capture measurements. This chapter offers a repeatable method for capturing two-dimensional measurements of plant parts in field or laboratory settings using a variety of camera styles (cellular phone, DSLR), with the addition of a printed calibration pattern. The method is based on calibrating the camera using information available from the EXIF tags from the image, as well as visual information from the pattern. Code is provided to implement the method, as well as a dataset for testing. We include steps to verify protocol correctness by imaging an artifact. The use of this protocol for two-dimensional plant phenotypoing will allow data capture from different cameras and environments, with comparison on the same physical scale.

• Resource Title: Code repository: camera-as-scanner.

  File Name: Web Page, url: https://github.com/amy-tabb/camera-as-scanner

  Code for calibrating a camera using a pattern, EXIF tags, and then warping to physical dimensions times a scaling factor. Originally for use in two-dimensional plant phenotyping.




• Resource Title: Code repository: aruco-pattern-write.

  File Name: Web Page, url: https://github.com/amy-tabb/aruco-pattern-write

  Basic code for generating a gird of aruco patterns.




• Resource Title: Code repository: camera-as-scanner-data.

  File Name: Web Page, url: https://github.com/amy-tabb/camera-as-scanner-data

  A minimal working example to verify that the installation of camera-as-scanner is working as expected.




• Resource Title: Data and Code from: Using cameras for precise measurement of two-dimensional plant features: CASS (Zenodo).

  File Name: Web Page, url: http://doi.org/10.5281/zenodo.3677473