#!/usr/bin/env python # coding: utf-8 # In[ ]: # In[ ]: # 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) # In[ ]: