sleap-roots - HackMD

# sleap-roots ---- - Trait calculations involving the primary root filter for the max primary root length in case more than one primary root is detected - Dicots vs monocots - Dicots have very obvious primary root with lateral roots emanating from it - Monocots (rice) have a primary root, crown roots and lateral/hair roots (not tracked) - Sometimes, it is desirable to compute traits on the primary root - Crown roots come from the seed - Multiple plant vs single plant per image - Multiple plants per image with multiple roots per plant requires that we match roots ---- - `Series` class: """Data and predictions for a single image series. Attributes: `series_name`: Unique identifier for the series. `h5_path`: Optional path to the HDF5-formatted image series. `primary_path`: Optional path to the primary root predictions file. At least one of the primary, lateral, or crown paths must be provided. `lateral_path`: Optional path to the lateral root predictions file. At least one of the primary, lateral, or crown paths must be provided. `crown_path`: Optional path to the crown predictions file. At least one of the primary, lateral, or crown paths must be provided. `primary_labels`: Optional `sio.Labels` corresponding to the primary root predictions. `lateral_labels`: Optional `sio.Labels` corresponding to the lateral root predictions. `crown_labels`: Optional `sio.Labels` corresponding to the crown predictions. `video`: Optional `sio.Video` corresponding to the image series. `csv_path`: Optional path to the CSV file containing the expected plant count. Methods: `load`: Load a set of predictions for this series. `__len__`: Length of the series (number of images). `__getitem__`: Return labeled frames for predictions. `__iter__`: Iterator for looping through predictions. `get_frame`: Return labeled frames for predictions. `plot`: Plot predictions on top of the image. `get_primary_points`: Get primary root points. `get_lateral_points`: Get lateral root points. `get_crown_points`: Get crown root points. Properties: `expected_count`: Fetch the expected plant count for this series from the CSV. `group`: Group name for the series from the CSV. `qc_fail`: Flag to indicate if the series failed QC from the CSV. """ - `Series.load` classmethod: """Load a set of predictions for this series. Args: `series_name`: Unique identifier for the series. `h5_path`: Optional path to the HDF5-formatted image series, which will be used to load the video. `primary_path`: Optional path to the primary root '.slp' predictions file. `lateral_path`: Optional path to the lateral root '.slp' predictions file. `crown_path`: Optional path to the crown '.slp' predictions file. `csv_path`: Optional path to the CSV file containing the expected plant count. Returns: An instance of Series loaded with the specified predictions. """ ---- - Needs multiple roots: - convex hull - area - perimeter - distances between hull vertices - angles of hull simplices - root counts - root width(left index, right index) - scanlines - ellipse features - semi-major axis - semi-minor axis - aspect ratio - angle - index of root from top - Single root: - base point - x-coordinates - y-coordinates - tip point - x-coordinates - y-coordinates - total length - base-to-tip line length - base-to-tip angle - base to first node angle - Problems for monocots: - root widths - bases - index of root from top ---- # DicotPipeline Metadata - plant_name: series name - frame: frame index, 72 frames in total, 0 to 71 Scalar traits (25) - primary_angle_proximal: primary root angle with base node and proximal node - primary_angle_distal: primary root angle with base node and distal node - primary_distal_pt: the very distal point, if the last one is invisible, use the last second point - primary_length: length of primary root - primary_base_tip_dist: primary root base to tip distance - lateral_count: number of lateral roots - curve_index: primary root curvature index - primary_tip_pt: the tip of the primary root, if invisible, curve_index should be nan - base_length: top and deepest bases distance y-axis - base_length_ratio: ratio of top-deep length to primary root length - primary_tip_pt_y: tip of primary root in y axis - base_median_ratio: ratio of median value in all lateral base points to tip of primary root in y axis - base_ct_density: number of base points to maximum primary root length - chull_perimeter: perimeter of convex hull - chull_area: area of convex hull - chull_max_width: maximum width of convex hull - chull_max_height: maxinum height of convex hull - ellipse_a: semi-major axis length of the fitted ellipse - ellipse_b: semi-minor axis length of the fitted ellipse - ellipse_ratio: ratio of the major to minor lengths - network_length: total root length (primary + lateral) - network_width_depth_ratio: width-to-depth ratio of bounding box for root network - network_solidity: total root length divided by the convex hull area - network_length_lower: total root length in the lower fraction (2/3) - network_distribution_ratio: ratio of the root length in the lower fraction (2/3) over total root length - scanline_first_ind: index of the first scanline that intersects with roots - scanline_last_ind: index of the last scanline that intersects with roots Non-scalar traits (10) - lateral_angles_proximal: lateral root angle with proximal node among all lateral roots within one frame - lateral_angles_distal: lateral root angle with distal node among all lateral roots within one frame - lateral_lengths: lengths of lateral roots - root_widths: array of root widths based on paired lateral root bases - root_widths_inds: array of indices of matched base pairs for root width calculation (not included in csv) - root_widths_left_bases: array of coordinates of left bases used for root widths calculation (not included in csv) - root_widths_right_bases: array of coordinates of right bases used for root widths calculation (not included in csv) - lateral_base_xs: x-coordinate of each lateral root base point - lateral_base_ys: y-coordinate of each lateral root base point - lateral_tip_xs: x-coordinate of each lateral root tip point - lateral_tip_ys: y-coordinate of each lateral root tip point - chull_line_lengths: lengths of lines connecting any two vertices on the convex hull - scanline_intersection_counts: number of intersection with the roots at each scanline Summary functions (9) - min - max - mean - median - std - p5 - p25 - p75 - p95 25 + 10 * 9 = 115 traits (per frame) 115 * 9 = 1035 traits (per plant) ```mermaid graph LR primary_pts --> primary_max_length_pts lateral_pts --> root_widths lateral_pts --> lateral_count lateral_pts --> lateral_proximal_node_inds lateral_pts --> lateral_distal_node_inds lateral_pts --> lateral_lengths lateral_pts --> lateral_base_pts lateral_pts --> lateral_tip_pts lateral_pts --> pts_list lateral_pts --> pts_all_array lateral_pts --> lateral_angles_distal lateral_pts --> lateral_angles_proximal lateral_pts --> network_length_lower pts_all_array --> ellipse pts_all_array --> bounding_box pts_all_array --> convex_hull primary_max_length_pts --> pts_all_array primary_max_length_pts --> primary_proximal_node_ind primary_max_length_pts --> primary_angle_proximal primary_max_length_pts --> primary_distal_node_ind primary_max_length_pts --> primary_angle_distal primary_max_length_pts --> primary_length lateral_distal_node_inds --> lateral_angles_distal lateral_proximal_node_inds --> lateral_angles_proximal primary_max_length_pts --> primary_base_pt primary_max_length_pts --> primary_tip_pt primary_max_length_pts --> root_widths primary_max_length_pts --> pts_list primary_max_length_pts --> network_length_lower lateral_base_pts --> lateral_base_xs lateral_base_pts --> lateral_base_ys lateral_base_pts --> base_ct_density lateral_tip_pts --> lateral_tip_xs lateral_tip_pts --> lateral_tip_ys lateral_lengths --> network_distribution_ratio lateral_lengths --> network_length primary_proximal_node_ind --> primary_angle_proximal primary_distal_node_ind --> primary_angle_distal primary_base_pt --> primary_base_pt_y primary_tip_pt --> primary_tip_pt_y primary_base_pt --> primary_base_tip_dist primary_tip_pt --> primary_base_tip_dist ellipse --> ellipse_a ellipse --> ellipse_b bounding_box --> network_width_depth_ratio bounding_box --> network_length_lower convex_hull --> chull_perimeter convex_hull --> chull_area convex_hull --> chull_max_width convex_hull --> chull_max_height convex_hull --> chull_line_lengths lateral_base_ys --> base_length lateral_base_ys --> base_median_ratio primary_length --> curve_index primary_length --> base_length_ratio primary_length --> base_ct_density primary_length --> network_distribution_ratio primary_length --> network_length pts_list --> scanline_intersection_counts primary_tip_pt_y --> base_median_ratio primary_base_tip_dist --> curve_index ellipse --> ellipse_ratio scanline_intersection_counts --> scanline_last_ind scanline_intersection_counts --> scanline_first_ind chull_area --> network_solidity network_length --> network_solidity network_length_lower --> network_distribution_ratio base_length --> base_length_ratio ``` ---- # YoungerMonocotPipeline - At 3 DAG the primary and crown roots are distinct. We train one model on primary roots and another for primary + crown roots--we will refer to this class as the `crown` roots for brevity. Metadata - plant_name: series name - frame: frame index, 72 frames in total, 0 to 71 Scalar traits (21) - primary_angle_proximal: primary root angle with base node and proximal node - primary_angle_distal: primary root angle with base node and distal node - primary_distal_pt: the very distal point, if the last one is invisible, use the last second point - primary_length: length of primary root - primary_base_tip_dist: primary root base to tip distances - crown_count: number of crown roots - curve_index: primary root curvature index - primary_tip_pt: the tip of the primary root, if invisible, curve_index should be nan - primary_tip_pt_y: tip of primary root in y axis - chull_perimeter: perimeter of convex hull - chull_area: area of convex hull - chull_max_width: maximum width of convex hull - chull_max_height: maxinum height of convex hull - ellipse_a: semi-major axis length of the fitted ellipse - ellipse_b: semi-minor axis length of the fitted ellipse - ellipse_ratio: ratio of the major to minor lengths - network_length: total root length (crown) - network_width_depth_ratio: width-to-depth ratio of bounding box for root network - network_solidity: total root length divided by the convex hull area - network_length_lower: total root length in the lower fraction (2/3) - network_distribution_ratio: ratio of the root length in the lower fraction (2/3) over total root length - scanline_first_ind: index of the first scanline that intersects with roots - scanline_last_ind: index of the last scanline that intersects with roots Non-scalar traits (8) - crown_angles_proximal: crown root angle with proximal node among all crown roots within one frame - crown_angles_distal: crown root angle with distal node among all crown roots within one frame - crown_lengths: lengths of crown roots - crown_base_tip_dists: crown root base to tip distances - crown_curve_indices: curvature index for each crown roots in a frame - crown_tip_pt_xs: x-coordinate of each crown root tip point - crown_tip_pt_ys: y-coordinate of each crown root tip point - chull_line_lengths: lengths of lines connecting any two vertices on the convex hull - scanline_intersection_counts: number of intersection with the roots at each scanline Summary functions (9) - min - max - mean - median - std - p5 - p25 - p75 - p95 21 + 9 * 9 = 102 traits (per frame) 102 * 9 = 918 traits (per plant) ```mermaid graph LR primary_pts --> primary_max_length_pts crown_pts --> crown_count crown_pts --> crown_proximal_node_inds crown_pts --> crown_distal_node_inds crown_pts --> crown_lengths crown_pts --> crown_base_pts crown_pts --> crown_tip_pts crown_pts --> scanline_intersection_counts crown_pts --> pts_all_array crown_pts --> crown_angles_distal crown_pts --> crown_angles_proximal crown_pts --> network_length_lower pts_all_array --> ellipse pts_all_array --> bounding_box pts_all_array --> convex_hull primary_max_length_pts --> primary_proximal_node_ind primary_max_length_pts --> primary_angle_proximal primary_max_length_pts --> primary_distal_node_ind primary_max_length_pts --> primary_angle_distal primary_max_length_pts --> primary_length crown_distal_node_inds --> crown_angles_distal crown_proximal_node_inds --> crown_angles_proximal primary_max_length_pts --> primary_base_pt primary_max_length_pts --> primary_tip_pt primary_max_length_pts --> network_length_lower crown_tip_pts --> crown_tip_xs crown_tip_pts --> crown_tip_ys crown_lengths --> network_distribution_ratio crown_lengths --> network_length crown_tip_pts --> crown_base_tip_dists crown_base_pts --> crown_base_tip_dists crown_lengths --> crown_curve_indices crown_base_tip_dists --> crown_curve_indices primary_proximal_node_ind --> primary_angle_proximal primary_distal_node_ind --> primary_angle_distal primary_tip_pt --> primary_tip_pt_y primary_base_pt --> primary_base_tip_dist primary_tip_pt --> primary_base_tip_dist ellipse --> ellipse_a ellipse --> ellipse_b bounding_box --> network_width_depth_ratio bounding_box --> network_length_lower convex_hull --> chull_perimeter convex_hull --> chull_area convex_hull --> chull_max_width convex_hull --> chull_max_height convex_hull --> chull_line_lengths primary_length --> curve_index primary_base_tip_dist --> curve_index ellipse --> ellipse_ratio scanline_intersection_counts --> scanline_last_ind scanline_intersection_counts --> scanline_first_ind chull_area --> network_solidity network_length --> network_solidity network_length_lower --> network_distribution_ratio ``` ---- # OlderMonocotPipeline - At 10 DAG the primary and crown roots are very similar. We only use one root class to detect primary and crown roots at this age. We will refer to this class as the `crown` roots for brevity. Metadata - plant_name: series name - frame: frame index, 72 frames in total, 0 to 71 Scalar traits (15) - crown_count: number of crown roots - chull_perimeter: perimeter of convex hull - chull_area: area of convex hull - chull_max_width: maximum width of convex hull - chull_max_height: maximum height of convex hull - ellipse_a: semi-major axis length of the fitted ellipse - ellipse_b: semi-minor axis length of the fitted ellipse - ellipse_ratio: ratio of the major to minor lengths - network_length: sum of crown root lengths per frame - network_width_depth_ratio: width-to-depth ratio of bounding box for root network - network_solidity: total root length divided by the convex hull area - network_length_lower: total root length in the lower fraction (2/3) - network_distribution_ratio: ratio of the root length in the lower fraction (2/3) over total root length - scanline_first_ind: index of the first scanline that intersects with roots - scanline_last_ind: index of the last scanline that intersects with roots - angle_chull_r1_left_intersection_vector: angle from gravity vector to vector made by r0 to r1 on the left side of a crown root system - angle_chull_r1_right_intersection_vector: angle from gravity vector to vector made by r0 to r1 on the right side of a crown root system - chull_area_above_r1_intersection - chull_area_below_r1_intersection Non-scalar traits (8) - curve_indices: crown root curvature index for all crown roots in one frame - crown_tip_pt: the tip of the crown root, if invisible, curve_index should be nan - crown_angles_proximal: crown root angle with proximal node for all crown roots in one frame - crown_angles_distal: crown root angle with distal node for all crown roots in one frame - crown_lengths: lengths of crown roots - crown_tip_xs: x-coordinate of each crown root tip point - crown_tip_ys: y-coordinate of each crown root tip point - chull_lengths: lengths of lines connecting any two vertices on the convex hull - scanline_intersection_counts: number of intersection with the roots at each scanline Summary functions (9) - min - max - mean - median - std - p5 - p25 - p75 - p95 15 + 10 * 9 = 225 traits (per frame) 216 * 9 = 2025 traits (per plant) ```mermaid graph LR crown_pts --> crown_count crown_pts --> crown_proximal_node_inds crown_pts --> crown_distal_node_inds crown_pts --> crown_lengths crown_pts --> crown_base_pts crown_pts --> crown_tip_pts crown_pts --> crown_angles_distal crown_pts --> crown_angles_proximal crown_pts --> network_length_lower crown_pts --> crown_r1_pts crown_pts --> chull_areas_r1_intersection crown_pts --> scanline_intersection_counts crown_pts --> ellipse crown_pts --> bounding_box crown_pts --> convex_hull crown_pts --> chull_r1_intersection_vectors crown_distal_node_inds --> crown_angles_distal crown_proximal_node_inds --> crown_angles_proximal crown_tip_pts --> crown_tip_xs crown_tip_pts --> crown_tip_ys crown_tip_pts --> crown_base_tip_dists crown_lengths --> network_length crown_base_pts --> crown_base_tip_dists crown_lengths --> crown_curve_indices crown_r1_pts --> chull_areas_r1_intersection ellipse --> ellipse_a ellipse --> ellipse_b bounding_box --> network_width_depth_ratio bounding_box --> network_length_lower convex_hull --> chull_perimeter convex_hull --> chull_area convex_hull --> chull_max_width convex_hull --> chull_max_height convex_hull --> chull_line_lengths convex_hull --> chull_areas_r1_intersection ellipse --> ellipse_ratio scanline_intersection_counts --> scanline_last_ind scanline_intersection_counts --> scanline_first_ind crown_r1_pts --> chull_r1_intersection_vectors crown_base_pts --> chull_r1_intersection_vectors network_length --> network_solidity network_length --> network_distribution_ratio crown_base_tip_dists --> crown_curve_indices chull_area --> network_solidity network_length_lower --> network_distribution_ratio chull_areas_r1_intersection --> chull_area_above_r1_intersection chull_areas_r1_intersection --> chull_area_below_r1_intersection chull_r1_intersection_vectors --> chull_r1_left_intersection_vector chull_r1_intersection_vectors --> chull_r1_right_intersection_vector chull_r1_left_intersection_vector --> angle_chull_r1_left_intersection_vector chull_r1_right_intersection_vector --> angle_chull_r1_right_intersection_vector ``` ---- # MultipleDicotPipeline This pipeline is meant to be used when the number of primary roots per image is known. This information is used to select the frames that have the correct number of primary roots only. Metadata - plant_name: series name - frame: frame index, 72 frames in total, 0 to 71 Scalar traits (2) - scanline_first_ind: index of the first scanline that intersects with roots for multiple plants - scanline_last_ind: index of the last scanline that intersects with roots for multiple plants Non-scalar traits (33) - primary_angles_proximal: primary root angle with base node and proximal node - primary_angles_distal: primary root angle with base node and distal node - primary_distal_pts: the very distal point, if the last one is invisible, use the last second point - primary_lengths: length of primary root - primary_base_tip_dists: primary root base to tip distance - lateral_counts: number of lateral roots - curve_indices: primary root curvature index - primary_tip_pts: the tip of the primary root, if invisible, curve_index should be nan - base_lengths: top and deepest bases distance y-axis - base_length_ratios: ratio of top-deep length to primary root length - primary_tip_pt_ys: tip of primary root in y axis - base_median_ratios: ratio of median value in all lateral base points to tip of primary root in y axis - base_ct_densitys: number of base points to maximum primary root length - chull_perimeters: perimeter of convex hull of individual plant - chull_areas: area of convex hull of individual plant - chull_max_widths: maximum width of convex hull of individual plant - chull_max_heights: maximum height of convex hull of individual plant - ellipse_as: semi-major axis length of the fitted ellipse of individual plant - ellipse_bs: semi-minor axis length of the fitted ellipse of individual plant - ellipse_ratios: ratio of the major to minor lengths of individual plant - network_lengths: total root length (primary + lateral) of individual plant - network_width_depth_ratios: width-to-depth ratio of bounding box for root network of individual plant - network_solidities: total root length divided by the convex hull area of individual plant - network_length_lowers: total root length in the lower fraction (2/3) of individual plant - network_distribution_ratios: ratio of the root length in the lower fraction (2/3) over total root length of individual plant - lateral_angles_proximal: lateral root angle with proximal node among all lateral roots within one frame - lateral_angles_distal: lateral root angle with distal node among all lateral roots within one frame - lateral_lengths: lengths of lateral roots - lateral_base_xs: x-coordinate of each lateral root base point - lateral_base_ys: y-coordinate of each lateral root base point - lateral_tip_xs: x-coordinate of each lateral root tip point - lateral_tip_ys: y-coordinate of each lateral root tip point - chull_line_lengths: lengths of lines connecting any two vertices on the convex hull - scanline_intersection_counts: number of intersection with the roots at each scanline for multiple plants Summary functions (9) - min - max - mean - median - std - p5 - p25 - p75 - p95 25 + 10 * 2 = 45 traits (per frame) 45 * 9 = 405 traits (per plant) ```mermaid graph LR primary_pts --> primary_pts_no_nans lateral_pts --> lateral_pts_no_nans primary_pts_no_nans --> filtered_pts_expected_plant_ct lateral_pts_no_nans --> filtered_pts_expected_plant_ct expected_plant_ct --> filtered_pts_expected_plant_ct filtered_pts_expected_plant_ct --> primary_pts_expected_plant_ct filtered_pts_expected_plant_ct --> lateral_pts_expected_plant_ct primary_pts_expected_plant_ct --> plant_associations_dict lateral_pts_expected_plant_ct --> plant_associations_dict plant_associations_dict --> associated_primary_pts plant_associations_dict --> associated_lateral_pts plant_associations_dict --> plantwise_pts_arrays associated_lateral_pts --> lateral_counts associated_lateral_pts --> lateral_proximal_node_inds associated_lateral_pts --> lateral_distal_node_inds associated_lateral_pts --> lateral_lengths associated_lateral_pts --> lateral_base_pts associated_lateral_pts --> lateral_tip_pts associated_lateral_pts --> scanline_intersection_counts associated_lateral_pts --> lateral_angles_distal associated_lateral_pts --> lateral_angles_proximal associated_lateral_pts --> network_length_lower associated_primary_pts --> primary_proximal_node_inds associated_primary_pts --> primary_angles_proximal associated_primary_pts --> primary_distal_node_inds associated_primary_pts --> primary_angles_distal associated_primary_pts --> primary_lengths associated_primary_pts --> primary_base_pts associated_primary_pts --> primary_tip_pts associated_primary_pts --> scanline_intersection_counts associated_primary_pts --> network_lengths_lower plantwise_pts_arrays --> ellipses plantwise_pts_arrays --> bounding_boxes plantwise_pts_arrays --> convex_hulls lateral_distal_node_inds --> lateral_angles_distal lateral_proximal_node_inds --> lateral_angles_proximal lateral_base_pts --> lateral_base_xs lateral_base_pts --> lateral_base_ys lateral_base_pts --> base_ct_densities lateral_tip_pts --> lateral_tip_xs lateral_tip_pts --> lateral_tip_ys lateral_lengths --> network_distributions_ratio lateral_lengths --> network_lengths primary_proximal_node_inds --> primary_angles_proximal primary_distal_node_inds --> primary_angles_distal primary_base_pts --> primary_base_pt_ys primary_tip_pts --> primary_tip_pt_ys primary_base_pts --> primary_base_tip_dists primary_tip_pts --> primary_base_tip_dists ellipses --> ellipse_as ellipses --> ellipse_bs bounding_boxes --> network_width_depth_ratios bounding_boxes --> network_lengths_lower convex_hulls --> chull_perimeters convex_hulls --> chull_areas convex_hulls --> chull_max_widths convex_hulls --> chull_max_heights convex_hulls --> chull_line_lengths lateral_base_ys --> base_lengths lateral_base_ys --> base_median_ratios primary_lengths --> curve_indices primary_lengths --> base_length_ratios primary_lengths --> base_ct_densities primary_lengths --> network_distribution_ratios primary_lengths --> network_lengths primary_tip_pt_ys --> base_median_ratios primary_base_tip_dists --> curve_indices ellipses --> ellipse_ratios scanline_intersection_counts --> scanline_last_inds scanline_intersection_counts --> scanline_first_inds chull_areas --> network_solidities network_lengths --> network_solidities network_length_lowers --> network_distribution_ratios base_lengths --> base_length_ratios ``` ---- # PrimaryRootPipeline This pipeline is meant to be used to compute traits of a single primary root per image. Metadata - plant_name: series name - frame: frame index, 72 frames in total, 0 to 71 Scalar traits (11) - primary_length: length of primary root - primary_base_tip_dist: primary root base to tip distance - curve_index: primary root curvature index primary_tip_pt: the tip of the primary root, if invisible, curve_index should be nan - primary_base_pt_x: base of primary root in x axis - primary_base_pt_y: base of primary root in y axis - primary_tip_pt_x: tip of primary root in x axis - primary_tip_pt_y: tip of primary root in y axis - primary_base_tip_dists: primary root base to tip distance - primary_lengths: length of primary root - primary_angle_proximal: primary root angle with base node and proximal node - primary_angle_distal: primary root angle with base node and distal node ```mermaid graph LR primary_pts --> primary_max_length_pts primary_max_length_pts --> primary_proximal_node_ind primary_max_length_pts --> primary_distal_node_ind primary_max_length_pts --> primary_angle_proximal primary_proximal_node_ind --> primary_angle_proximal primary_max_length_pts --> primary_angle_distal primary_distal_node_ind --> primary_angle_distal primary_max_length_pts --> primary_length primary_max_length_pts --> primary_base_pt primary_max_length_pts --> primary_tip_pt primary_base_pt --> primary_base_pt_x primary_base_pt --> primary_base_pt_y primary_tip_pt --> primary_tip_pt_x primary_tip_pt --> primary_tip_pt_y primary_base_pt --> primary_base_tip_dist primary_tip_pt --> primary_base_tip_dist primary_length --> curve_index primary_base_tip_dist --> curve_index primary_max_length_pts --> bounding_box ``` ---- # MultiplePrimaryRootPipeline ```mermaid graph LR primary_pts --> filtered_primary_pts_with_expected_ct expected_plant_ct --> filtered_primary_pts_with_expected_ct filtered_primary_pts_with_expected_ct --> primary_proximal_node_ind filtered_primary_pts_with_expected_ct --> primary_distal_node_ind filtered_primary_pts_with_expected_ct --> primary_angle_proximal primary_proximal_node_ind --> primary_angle_proximal filtered_primary_pts_with_expected_ct --> primary_angle_distal primary_distal_node_ind --> primary_angle_distal filtered_primary_pts_with_expected_ct --> primary_length filtered_primary_pts_with_expected_ct --> primary_base_pt filtered_primary_pts_with_expected_ct --> primary_tip_pt primary_base_pt --> primary_base_pt_x primary_base_pt --> primary_base_pt_y primary_tip_pt --> primary_tip_pt_x primary_tip_pt --> primary_tip_pt_y primary_base_pt --> primary_base_tip_dist primary_tip_pt --> primary_base_tip_dist primary_length --> curve_index primary_base_tip_dist --> curve_index filtered_primary_pts_with_expected_ct --> bounding_box ``` ---- # LateralRootPipeline Metadata - plant_name: series name - frame: frame index, 72 frames in total, 0 to 71 Scalar traits (2) - lateral_count: number of lateral roots - total_lateral_length: total lateral root length Non-scalar traits (7) - lateral_angles_proximal: lateral root angle with proximal node among all lateral roots within one frame - lateral_angles_distal: lateral root angle with distal node among all lateral roots within one frame - lateral_lengths: lengths of lateral roots - lateral_base_xs: x-coordinate of each lateral root base point - lateral_base_ys: y-coordinate of each lateral root base point - lateral_tip_xs: x-coordinate of each lateral root tip point - lateral_tip_ys: y-coordinate of each lateral root tip point Summary functions (9) - min - max - mean - median - std - p5 - p25 - p75 - p95 2 + 7 * 9 = 65 traits (per frame) 65 * 9 = 585 traits (per plant) ```mermaid graph LR lateral_pts --> lateral_count lateral_pts --> lateral_proximal_node_inds lateral_pts --> lateral_distal_node_inds lateral_pts --> lateral_lengths lateral_pts --> lateral_base_pts lateral_pts --> lateral_tip_pts lateral_pts --> lateral_angles_distal lateral_pts --> lateral_angles_proximal lateral_lengths --> total_lateral_length lateral_distal_node_inds --> lateral_angles_distal lateral_proximal_node_inds --> lateral_angles_proximal lateral_base_pts --> lateral_base_xs lateral_base_pts --> lateral_base_ys lateral_tip_pts --> lateral_tip_xs lateral_tip_pts --> lateral_tip_ys ``` ---- # Tip

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{%youtube youtube_id %}	Externals
$L^aT_eX$	L^aT_eX
:::info This is a alert area. :::	This is a alert area.