# Welcome to the Interactive Documentation for PlantCV

The [PlantCV project](http://plantcv.danforthcenter.org/) is an open-source imaging processing package for plant phenotyping. The Jupyter notebooks contained here are the interactive version of some of the [PlantCV documentation](http://plantcv.readthedocs.io/en/latest/). The Jupyter notebooks can be used directly in an executable environment provided by [Binder](https://mybinder.org/), or they can be cloned and run locally.

Please note, intermediate images output while running the tutorials below will not look identical to images found in the [PlantCV documentation](http://plantcv.readthedocs.io/en/latest/). Various changes have been made to suit the image size, but please refer to the [troubleshooting](https://plantcv.readthedocs.io/en/latest/analysis_approach/#troubleshooting) section of the PlantCV documentation if you run into any issues. Also, feel free to upload your own images and adjust parameters and Workflows to fit them. 

## Table of Contents

### Tutorials

- [VIS Workflow](notebooks/vis_tutorial.ipynb)
- [NIR Workflow](notebooks/nir_tutorial.ipynb)
- [PSII Workflow](notebooks/psII_tutorial.ipynb)
- [VIS/NIR Workflow](notebooks/vis_nir_tutorial.ipynb)
- [Multi-Plant Workflow](notebooks/multi_plant_tutorial.ipynb)
- [Machine Learning Workflow](notebooks/machine_learning.ipynb)
- [Color Correction Workflow](notebooks/color_correct_tutorial.ipynb) 
- [Watershed Segmentation Workflow](notebooks/segmentation.ipynb) 
- [Region of Interest Tools](notebooks/roi_package.ipynb)
- [Thresholding Tools](notebooks/threshold.ipynb)
- [Input/Output Tools](notebooks/input_output.ipynb) 
- [Morphology Workflow](notebooks/morphology_tutorial.ipynb) 
- [Thermal Workflow](notebooks/thermal.ipynb) 

### Example Use of Functions 
- **plantcv.acute_vertex** 
    - [VIS/NIR Workflow](notebooks/vis_nir_tutorial.ipynb)
- **plantcv.analyze_bound_horizontal**
    - [VIS Workflow](notebooks/vis_tutorial.ipynb)
    - [VIS/NIR Workflow](notebooks/vis_nir_tutorial.ipynb)
- **plantcv.analyze_bound_vertical**
    - [VIS/NIR Workflow](notebooks/vis_nir_tutorial.ipynb)
- **plantcv.analyze_color**
    - [VIS Workflow](notebooks/vis_tutorial.ipynb)
    - [VIS/NIR Workflow](notebooks/vis_nir_tutorial.ipynb)
- **plantcv.analyze_nir_intensity** 
    - [NIR Workflow](notebooks/nir_tutorial.ipynb)
    - [VIS/NIR Workflow](notebooks/vis_nir_tutorial.ipynb)
- **plantcv.analyze_objects**
    - [NIR Workflow](notebooks/nir_tutorial.ipynb)
    - [PSII Workflow](notebooks/psII_tutorial.ipynb)
    - [VIS Workflow](notebooks/vis_tutorial.ipynb)
    - [VIS/NIR Workflow](notebooks/vis_nir_tutorial.ipynb)
- **plantcv.analyze_thermal_values**
    - [Thermal Workflow](notebooks/thermal.ipynb) 
- **plantcv.apply_mask**
    - [Machine Learning Workflow](notebooks/machine_learning.ipynb)
    - [NIR Workflow](notebooks/nir_tutorial.ipynb)
    - [PSII Workflow](notebooks/psII_tutorial.ipynb)
    - [Watershed Segmentation Workflow](notebooks/segmentation.ipynb) 
    - [VIS Workflow](notebooks/vis_tutorial.ipynb)
    - [VIS/NIR Workflow](notebooks/vis_nir_tutorial.ipynb)
- **plantcv.auto_crop**
    - [VIS/NIR Workflow](notebooks/vis_nir_tutorial.ipynb)
- **plantcv.background_subtraction**
    - [NIR Workflow](notebooks/nir_tutorial.ipynb)
- **plantcv.canny_edge_detect**
    - [Region of Interest Tools](notebooks/roi_package.ipynb)
- **plantcv.closing**
    - [VIS Workflow](notebooks/vis_tutorial.ipynb)
- **plantcv.cluster_contour**
    - [Multi-Plant Workflow](notebooks/multi_plant_tutorial.ipynb)
- **plantcv.cluster_contour_splitimg**
    - [Multi-Plant Workflow](notebooks/multi_plant_tutorial.ipynb)
- **plantcv.crop_position_mask**
    - [VIS/NIR Workflow](notebooks/vis_nir_tutorial.ipynb)
- **plantcv.dilate**
    - [Multi-Plant Workflow](notebooks/multi_plant_tutorial.ipynb)
    - [NIR Workflow](notebooks/nir_tutorial.ipynb)
- **plantcv.distance_transform** 
    - [NIR Workflow](notebooks/nir_tutorial.ipynb)
- **plantcv.erode**
    - [NIR Workflow](notebooks/nir_tutorial.ipynb)
- **plantcv.fill**
    - [Multi-Plant Workflow](notebooks/multi_plant_tutorial.ipynb)
    - [NIR Workflow](notebooks/nir_tutorial.ipynb)
    - [PSII Workflow](notebooks/psII_tutorial.ipynb)
    - [VIS Workflow](notebooks/vis_tutorial.ipynb)
- **plantcv.fluor_fvfm**
    - [PSII Workflow](notebooks/psII_tutorial.ipynb)
- **plantcv.gaussian_blur**
    - [VIS Workflow](notebooks/vis_tutorial.ipynb)
- **plantcv.get_nir**
    - [VIS/NIR Workflow](notebooks/vis_nir_tutorial.ipynb)
- **plantcv.hist_equalization**
    - [NIR Workflow](notebooks/nir_tutorial.ipynb)
- **plantcv.image_add** 
    - [NIR Workflow](notebooks/nir_tutorial.ipynb)
- **plantcv.image_subtract**
    - [NIR Workflow](notebooks/nir_tutorial.ipynb)
- **plantcv.invert** 
    - [NIR Workflow](notebooks/nir_tutorial.ipynb)
    - [PSII Workflow](notebooks/psII_tutorial.ipynb)
- **plantcv.laplace_filter** 
    - [NIR Workflow](notebooks/nir_tutorial.ipynb)
- **plantcv.logical_and**
    - [NIR Workflow](notebooks/nir_tutorial.ipynb)
    - [VIS/NIR Workflow](notebooks/vis_nir_tutorial.ipynb)
- **plantcv.logical_or**
    - [NIR Workflow](notebooks/nir_tutorial.ipynb)
    - [VIS Workflow](notebooks/vis_tutorial.ipynb)
- **plantcv.logical_xor** 
    - [VIS Workflow](notebooks/vis_tutorial.ipynb)
- **plantcv.median_blur**
    - [NIR Workflow](notebooks/nir_tutorial.ipynb)
    - [PSII Workflow](notebooks/psII_tutorial.ipynb)
    - [VIS/NIR Workflow](notebooks/vis_nir_tutorial.ipynb)
    - [VIS Workflow](notebooks/vis_tutorial.ipynb)
- **plantcv.morphology.find_branch_pts**
    - [Morphology Workflow](notebooks/morphology_tutorial.ipynb)
- **plantcv.morphology.find_tips**
    - [Morphology Workflow](notebooks/morphology_tutorial.ipynb)
- **plantcv.morphology.prune**
    - [Morphology Workflow](notebooks/morphology_tutorial.ipynb)
- **plantcv.morphology.segment_angles**
    - [Morphology Workflow](notebooks/morphology_tutorial.ipynb)
- **plantcv.morphology.segment_curvature**
    - [Morphology Workflow](notebooks/morphology_tutorial.ipynb)
- **plantcv.morphology.segment_euclidean_length**
    - [Morphology Workflow](notebooks/morphology_tutorial.ipynb)
- **plantcv.morphology.segment_id**
    - [Morphology Workflow](notebooks/morphology_tutorial.ipynb)
- **plantcv.morphology.segment_insertion_angle**
    - [Morphology Workflow](notebooks/morphology_tutorial.ipynb)
- **plantcv.morphology.segment_path_length**
    - [Morphology Workflow](notebooks/morphology_tutorial.ipynb)
- **plantcv.morphology.segment_skeleton**
    - [Morphology Workflow](notebooks/morphology_tutorial.ipynb)
- **plantcv.morphology.segment_sort**
    - [Morphology Workflow](notebooks/morphology_tutorial.ipynb)
- **plantcv.morphology.segment_tangent_angle**
    - [Morphology Workflow](notebooks/morphology_tutorial.ipynb)
- **plantcv.morphology.skeletonize** 
    - [Morphology Workflow](notebooks/morphology_tutorial.ipynb)
- **plantcv.naive_bayes_classifier**
    - [Machine Learning Workflow](notebooks/machine_learning.ipynb)
- **plantcv.object_composition** 
    - [NIR Workflow](notebooks/nir_tutorial.ipynb)
    - [PSII Workflow](notebooks/psII_tutorial.ipynb)
    - [Watershed Segmentation Workflow](notebooks/segmentation.ipynb)
    - [VIS/NIR Workflow](notebooks/vis_nir_tutorial.ipynb)
    - [VIS Workflow](notebooks/vis_tutorial.ipynb)
- **plantcv.opening**
    - [VIS Workflow](notebooks/vis_tutorial.ipynb)
- **plantcv.outputs.add_observation**
    - [Machine Learning Workflow](notebooks/machine_learning.ipynb)
- **plantcv.output_mask**
    - [Machine Learning Workflow](notebooks/machine_learning.ipynb)
- **plantcv.plot_hist**
    - [Input/Output Tools](notebooks/input_output.ipynb) 
- **plantcv.plot_image**
    - [Input/Output Tools](notebooks/input_output.ipynb) 
    - [Machine Learning Workflow](notebooks/machine_learning.ipynb)
    - [NIR Workflow](notebooks/nir_tutorial.ipynb)
    - [PSII Workflow](notebooks/psII_tutorial.ipynb)
    - [Watershed Segmentation Workflow](notebooks/segmentation.ipynb) 
- **plantcv.print_image**
    - [Input/Output Tools](notebooks/input_output.ipynb) 
    - [NIR Workflow](notebooks/nir_tutorial.ipynb)
- **plantcv.readbayer**
    - [Input/Output Tools](notebooks/input_output.ipynb) 
- **plantcv.rectangle_mask** 
    - [NIR Workflow](notebooks/nir_tutorial.ipynb)
    - [Region of Interest Tools](notebooks/roi_package.ipynb)
- **plantcv.report_size_marker_area** 
    - [Multi-Plant Workflow](notebooks/multi_plant_tutorial.ipynb)
- **plantcv.resize**
    - [VIS/NIR Workflow](notebooks/vis_nir_tutorial.ipynb)
- **plantcv.rgb2gray**
    - [Thresholding Tools](notebooks/threshold.ipynb)
- **plantcv.rgb2gray_hsv**
    - [PSII Workflow](notebooks/psII_tutorial.ipynb)
    - [Thresholding Tools](notebooks/threshold.ipynb)
    - [VIS/NIR Workflow](notebooks/vis_nir_tutorial.ipynb)
    - [VIS Workflow](notebooks/vis_tutorial.ipynb)
- **plantcv.rgb2gray_lab**
    - [Multi-Plant Workflow](notebooks/multi_plant_tutorial.ipynb)
    - [Watershed Segmentation Workflow](notebooks/segmentation.ipynb) 
    - [Thresholding Tools](notebooks/threshold.ipynb)
    - [VIS/NIR Workflow](notebooks/vis_nir_tutorial.ipynb)
    - [VIS Workflow](notebooks/vis_tutorial.ipynb)
- **plantcv.roi.circle**
    - [Region of Interest Tools](notebooks/roi_package.ipynb)
- **plantcv.roi.ellipse**
    - [Region of Interest Tools](notebooks/roi_package.ipynb)
- **plantcv.roi.from_binary_image**
    - [Region of Interest Tools](notebooks/roi_package.ipynb)
- **plantcv.roi.rectangle** 
    - [Multi-Plant Workflow](notebooks/multi_plant_tutorial.ipynb)
    - [NIR Workflow](notebooks/nir_tutorial.ipynb)
    - [PSII Workflow](notebooks/psII_tutorial.ipynb)
    - [Region of Interest Tools](notebooks/roi_package.ipynb)
    - [VIS/NIR Workflow](notebooks/vis_nir_tutorial.ipynb)
    - [VIS Workflow](notebooks/vis_tutorial.ipynb)
    - [Thermal Workflow](notebooks/thermal.ipynb)
- **plantcv.roi_objects**
    - [Multi-Plant Workflow](notebooks/multi_plant_tutorial.ipynb)
    - [NIR Workflow](notebooks/nir_tutorial.ipynb)
    - [PSII Workflow](notebooks/psII_tutorial.ipynb)
    - [Region of Interest Tools](notebooks/roi_package.ipynb)
    - [VIS/NIR Workflow](notebooks/vis_nir_tutorial.ipynb)
    - [VIS Workflow](notebooks/vis_tutorial.ipynb)
    - [Thermal Workflow](notebooks/thermal.ipynb)
- **plantcv.rotate**
    - [Multi-Plant Workflow](notebooks/multi_plant_tutorial.ipynb)
- **plantcv.scharr_filter**
    - [NIR Workflow](notebooks/nir_tutorial.ipynb)
- **plantcv.shift_img** 
    - [Color Correction Workflow](notebooks/color_correct_tutorial.ipynb) 
    - [Multi-Plant Workflow](notebooks/multi_plant_tutorial.ipynb)
- **plantcv.sobel_filter**
    - [NIR Workflow](notebooks/nir_tutorial.ipynb)
- **plantcv.threshold.binary**
    - [Multi-Plant Workflow](notebooks/multi_plant_tutorial.ipynb)
    - [NIR Workflow](notebooks/nir_tutorial.ipynb)
    - [PSII Workflow](notebooks/psII_tutorial.ipynb)
    - [Watershed Segmentation Workflow](notebooks/segmentation.ipynb) 
    - [Thresholding Tools](notebooks/threshold.ipynb)
    - [VIS/NIR Workflow](notebooks/vis_nir_tutorial.ipynb)
    - [VIS Workflow](notebooks/vis_tutorial.ipynb)
    - [Thermal Workflow](notebooks/thermal.ipynb)
- **plantcv.threshold.gaussian** 
    - [Thresholding Tools](notebooks/threshold.ipynb)
- **plantcv.threshold.mean**
    - [Thresholding Tools](notebooks/threshold.ipynb)
- **plantcv.threshold.otsu**
    - [Thresholding Tools](notebooks/threshold.ipynb)
- **plantcv.threshold.texture**
    - [Thresholding Tools](notebooks/threshold.ipynb)
- **plantcv.threshold.triangle**
    - [Thresholding Tools](notebooks/threshold.ipynb)
- **plantcv.transform.correct_color**
    - [Color Correction Workflow](notebooks/color_correct_tutorial.ipynb) 
- **plantcv.transform.create_color_card_mask**
    - [Color Correction Workflow](notebooks/color_correct_tutorial.ipynb) 
- **plantcv.transform.find_color_card**
    - [Color Correction Workflow](notebooks/color_correct_tutorial.ipynb) 
- **plantcv.transform.quick_color_check**
    - [Color Correction Workflow](notebooks/color_correct_tutorial.ipynb) 
- **plantcv.transform.rescale**
    - [Thermal Workflow](notebooks/thermal.ipynb)
- **plantcv.transform.save_matrix**
    - [Color Correction Workflow](notebooks/color_correct_tutorial.ipynb) 
- **plantcv.visualzie.clustered_contours**
    - [Multi-Plant Workflow](notebooks/multi_plant_tutorial.ipynb)
- **plantcv.visualize.colorize_masks**
    - [Machine Learning Workflow](notebooks/machine_learning.ipynb)
- **plantcv.visualize.pseudocolor**
    - [NIR Workflow](notebooks/nir_tutorial.ipynb)
    - [PSII Workflow](notebooks/psII_tutorial.ipynb)
    - [Thermal Workflow](notebooks/thermal.ipynb)
- **plantcv.watershed_segmentation**
    - [Watershed Segmentation Workflow](notebooks/segmentation.ipynb) 
- **plantcv.white_balance**
    - [Multi-Plant Workflow](notebooks/multi_plant_tutorial.ipynb)
- **plantcv.within_frame**
    - [Multi-Plant Workflow](notebooks/multi_plant_tutorial.ipynb)
- **plantcv.x_axis_pseudolandmarks**
    - [VIS Workflow](notebooks/vis_tutorial.ipynb)
- **plantcv.y_axis_pseudolandmarks**
    - [VIS Workflow](notebooks/vis_tutorial.ipynb)