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mkdocs.yml
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site_name: PlantCV
site_url: http://plantcv.readthedocs.io/
site_description: Plant phenotyping using computer vision
site_author: PlantCV Development Team
repo_url: https://github.com/danforthcenter/plantcv
copyright: Copyright 2020, Donald Danforth Plant Science Center
theme: readthedocs
nav:
- Home: index.md
- Documentation:
- 'Installation': installation.md
- 'Updating PlantCV': updating.md
- 'Frequently Asked Questions': faq.md
- 'Analysis Approaches': analysis_approach.md
- 'Using Jupyter Notebooks': jupyter.md
- 'Summary of Output Measurements': output_measurements.md
- 'Contributing':
- 'Contributing to PlantCV': CONTRIBUTING.md
- 'Code of Conduct': CODE_OF_CONDUCT.md
- 'Adding/Editing Documentation': documentation.md
- Tutorials:
- 'VIS Workflow': vis_tutorial.md
- 'NIR Workflow': nir_tutorial.md
- 'PSII Workflow': psII_tutorial.md
- 'VIS/NIR Dual Workflow': vis_nir_tutorial.md
- 'Multi Plant Workflow': multi-plant_tutorial.md
- 'Machine Learning': machine_learning_tutorial.md
- 'Workflow Parallelization': pipeline_parallel.md
- 'Exporting Data': db-exporter.md
- 'Color Correction Workflow': transform_color_correction_tutorial.md
- 'Morphology Workflow': morphology_tutorial.md
- 'Thermal Workflow': thermal_tutorial.md
- 'Hyperspectral Workflow': hyperspectral_tutorial.md
- 'PlantCV Namespace':
- 'PlantCV':
- 'Analyze color': analyze_color.md
- 'Analyze NIR': analyze_NIR_intensity.md
- 'Analyze PSII': fluor_fvfm.md
- 'Analyze Shape': analyze_shape.md
- 'Analyze Thermal': analyze_thermal_values.md
- 'Apply Mask': apply_mask.md
- 'Auto Crop': auto_crop.md
- 'Background Subtraction': background_subtraction.md
- 'Boundary Line Tools':
- 'Horizontal Boundary Tool': analyze_bound_horizontal.md
- 'Vertical Boundary Tool': analyze_bound_vertical.md
- 'Canny Edge Detection': canny_edge_detect.md
- 'Closing': closing.md
- 'Cluster Contours': cluster_contours.md
- 'Cluster Contours and Split Images': cluster_contours_splitimg.md
- 'Color Palette': color_palette.md
- 'Colorspace Conversion':
- 'RGB to Gray': rgb2gray.md
- 'RGB to LAB': rgb2lab.md
- 'RGB to HSV': rgb2hsv.md
- 'Crop': crop.md
- 'Crop and Position Mask': crop_position_mask.md
- 'Dilation': dilate.md
- 'Distance Transform': distance_transform.md
- 'Erosion': erode.md
- 'Fill Objects': fill.md
- 'Fill Holes': fill_holes.md
- 'Find Objects': find_objects.md
- 'Flip Image': flip.md
- 'Filters':
- 'Laplace Filter': laplace_filter.md
- 'Sobel Filter': sobel_filter.md
- 'Scharr Filter': scharr_filter.md
- 'Gaussian Blur': gaussian_blur.md
- 'Get Kernel': get_kernel.md
- 'Get NIR Images': get_nir.md
- 'Histogram Normalization': HistEqualization.md
- 'Hyperspectral Data':
- 'Analyze index': analyze_index.md
- 'Analyze spectral': analyze_spectral.md
- 'Calibrate': calibrate.md
- 'Spectral Index': spectral_index.md
- 'Extract wavelength': extract_wavelength.md
- 'Spectral data objects': Spectral_data.md
- 'Image Add': image_add.md
- 'Image Subtract': image_subtract.md
- 'Invert': invert.md
- 'Landmark Analysis':
- 'Acute Vertex': acute_vertex.md
- 'x-Axis Pseudolandmarks': x_axis_pseudolandmarks.md
- 'y-Axis Pseudolandmarks': y_axis_pseudolandmarks.md
- 'Scale Features': scale_features.md
- 'Landmark Reference Point Distribution': landmark_reference_pt_dist.md
- 'Logical Operations':
- 'Logical Operations-And': logical_and.md
- 'Logical Operations-Or': logical_or.md
- 'Logical Operations-XOr': logical_xor.md
- 'Median Blur': median_blur.md
- 'Morphology Functions':
- 'Analyze_stem': analyze_stem.md
- 'Check Cycles': check_cycles.md
- 'Find Branches': find_branch_pts.md
- 'Find Tips': find_tips.md
- 'Prune': prune.md
- 'Segment Angles': segment_angle.md
- 'Combine Segments': segment_combine.md
- 'Segment Curvature': segment_curvature.md
- 'Segment Euclidean Length': segment_euclidean_length.md
- 'Segment ID': segment_id.md
- 'Segment Insertion Angle': segment_insertion_angle.md
- 'Segment Path Length': segment_pathlength.md
- 'Segment Skeleton': segment_skeleton.md
- 'Segment Sort': segment_sort.md
- 'Segment Tangent Angle': segment_tangent_angle.md
- 'Skeletonize': skeletonize.md
- 'Naive Bayes Classifier': naive_bayes_classifier.md
- 'Object Composition': object_composition.md
- 'Opening': opening.md
- 'Output Mask': output_mask.md
- 'Outputs Class': outputs.md
- 'Params (Debugging)': params.md
- 'Print Image': print_image.md
- 'Print Results': print_results.md
- 'Plot Image': plot_image.md
- 'Read Image': read_image.md
- 'Read Bayer Raw Image': read_bayer.md
- 'Rectangle Mask': rectangle_mask.md
- 'Report Size Marker': report_size_marker.md
- 'Resize': resize.md
- 'Region of Interest Tools':
- 'Create a Circular ROI': roi_circle.md
- 'Create an Elliptical ROI': roi_ellipse.md
- 'Create a Rectangular ROI': roi_rectangle.md
- 'Create a Custom ROI': roi_custom.md
- 'Create ROI from Binary Image': roi_from_binary_image.md
- 'Create Multi ROIs': 'roi_multi.md'
- 'Filter Objects by ROI': roi_objects.md
- 'Convert ROI to Mask': roi2mask.md
- 'Rotate': rotate2.md
- 'Shift Image': shift.md
- 'Spatial Clustering': spatial_clustering.md
- 'Spectral Index': spectral_index.md
- 'Standard Deviation Filter': stdev_filter.md
- 'Thresholding Methods':
- 'Binary Threshold': binary_threshold.md
- 'Custom Range Threshold': custom_range_threshold.md
- 'Gaussian Adaptive Threshold': gaussian_threshold.md
- 'Mean Adaptive Threshold': mean_threshold.md
- 'Otsu Auto Threshold': otsu_threshold.md
- 'Saturation Threshold': saturation_threshold.md
- 'Triangle Auto Threshold': triangle_threshold.md
- 'Texture Threshold': texture_threshold.md
- 'Transformation Methods':
- 'Auto-Detect Color Card': find_color_card.md
- 'Create Color Card Mask': create_color_card_mask.md
- 'Convert Color Card to Matrix': get_color_matrix.md
- 'Calculate Moore-Penrose Inverse Matrix': mp_inverse.md
- 'Create Color Correction Matrix': transformation_matrix.md
- 'Apply Color Correction Matrix': apply_transformation_matrix.md
- 'Color Correction Workflow': transform_correct_color.md
- 'Quick Color Check': quick_color_check.md
- 'Load Matrix': load_matrix.md
- 'Save Matrix': save_matrix.md
- 'Nonuniform Illumination Correction': nonuniform_illumination.md
- 'Rescale Image Values': transform_rescale.md
- 'Visualization Methods':
- 'Auto Threshold Methods': visualize_auto_threshold_methods.md
- 'Clustered Contours': visualize_clustered_contours.md
- 'Colorize Masks': visualize_colorize_masks.md
- 'Colorspaces': visualize_colorspace.md
- 'Histogram': visualize_histogram.md
- 'Pseudocolor': visualize_pseudocolor.md
- 'Watershed Segmentation': watershed.md
- 'White balance': white_balance.md
- 'Within Frame': within_frame.md
- 'Machine Learning Training':
- 'Naive Bayes': naive_bayes.md
- 'Naive Bayes Multiclass': naive_bayes_multiclass.md
- 'Parallelization':
- 'Job Builder': job_builder.md
- 'Metadata Parser': metadata_parser.md
- 'Multiprocess': multiprocess.md
- 'Process Results': process_results.md
- 'Workflow Parallelization': pipeline_parallel.md
- 'Accessory tools': tools.md
markdown_extensions:
- toc:
permalink: True
- admonition