PlantCV v2.0

The PlantCV release v2.0 marks the final commit used in our upcoming manuscript describing improvements to PlantCV since v1.0. If you are updating from v1, please see our instructions here.

A brief description of changes since the v1.0 release:

• Changed license from GPLv2 to MIT
• Reformatted code for PEP8 compliance
• General improvements for Python2.7 and 3 compatibility
• Updated documentation (installation methods, tutorials, contribution guide, function documentation)
• Added issue and pull request templates
• Added continuous integration (Travis CI)
• Added unit test coverage (Coveralls)
• Added continuous documentation (Read the Docs)
• Added Jupyter notebook integration
• Improved metadata parsing
• Rewrote the parallelization and data management tool in Python (plantcv-pipeline.py)
• New functions
  • White balance (white_balance)
  • Triangle auto-threshold (triangle_auto_threshold)
  • Otsu auto-threshold (otsu_auto_threshold)
  • Adaptive threshold (adaptive_threshold)
  • Gaussian blur (gaussian_blur)
  • Size marker normalization (report_size_marker_area)
  • Multi-plant detection (cluster_contours, cluster_contours_split_img, rotate_img, shift_img)
  • Combined image processing (get_nir, resize, crop_position_mask)
  • Watershed segmentation (watershed_segmentation)
  • Landmarking functions for morphometrics (acute, acute_vertex, x_axis_pseudolandmarks, y_axis_pseudolandmarks, scale_features)
• Added machine learning training (plantcv.learn submodule) and classifier tools
  • Training program (plantcv-train.py) with two methods:
    • Naive Bayes (naive_bayes)
    • Naive Bayes multiclass (naive_bayes_multiclass)
  • Classifier (naive_bayes_classifier)

Citation

Gehan MA., Fahlgren N., Abbasi A., Berry JC., Callen ST., Chavez L., Doust AN., Feldman MJ., Gilbert KB., Hodge JG., Steen Hoyer J., Lin A., Liu S., Lizárraga C., Lorence A., Miller M., Platon E., Tessman M., Sax T. 2017. PlantCV v2.0: Image analysis software for high-throughput plant phenotyping. PeerJ Preprints 5:e3225v1. DOI: 10.7287/peerj.preprints.3225v1.

PlantCV v1.1

This is a minor release that adds mkdocs build files to the v1.0 release so that documentation can be built automatically with readthedocs.

PlantCV v1.0

PlantCV release v1.0 marks the final commit used in our manuscript [1]. If you want to repeat an analysis from the paper, checkout tag v1.0 after cloning the repository.

1. Fahlgren N, Feldman M, Gehan MA, Wilson MS, Shyu C, Bryant DW, Hill ST, McEntee CJ, Warnasooriya SN, Kumar I, Ficor T, Turnipseed S, Gilbert KB, Brutnell TP, Carrington JC, Mockler TC, Baxter I (2015) A versatile phenotyping system and analytics platform reveals diverse temporal responses to water availability in Setaria. Molecular Plant, in press.