Operations¶

This page documents all available pipeline operations and their parameters.

Image/Contour Operations¶

contour¶

Generate binary contour from 3D image using morphological active contours.

Parameters:

iterations (int, default: 25): Number of morphological Chan-Vese iterations
smoothing (int, default: 1): Smoothing iterations per cycle
masking_factor (float, default: 0.75): Initial mask threshold factor
target_resolution (list[float], default: [0.5, 0.5, 0.5]): Target resolution for resampling
gaussian_sigma (list[float], default: [1.0, 1.0, 1.0]): Gaussian filter sigma
gaussian_iterations (int, default: 5): Number of Gaussian smoothing iterations
register_stack (bool, default: True): Apply stack registration
chan_vese_lambda1 (float, default: 1.0): Chan-Vese lambda1 parameter
chan_vese_lambda2 (float, default: 1.0): Chan-Vese lambda2 parameter
fill_slices (bool, default: True): Fill holes in XY slices
crop (bool, default: True): Automatically crop image

create_mesh¶

Create mesh from contour using marching cubes.

Parameters:

step_size (int, default: 1): Step size for marching cubes

create_cellular_mesh¶

Create mesh from segmented image (one mesh per cell).

Parameters:

verbose (bool, default: True): Print progress information

Mesh Processing Operations¶

smooth¶

Laplacian smoothing.

Parameters:

iterations (int, default: 100): Number of smoothing iterations
relaxation_factor (float, default: 0.01): Relaxation factor (0-1)
feature_smoothing (bool, default: False): Smooth along features
boundary_smoothing (bool, default: True): Smooth boundary edges

smooth_taubin¶

Taubin smoothing (less shrinkage than Laplacian).

Parameters:

iterations (int, default: 100): Number of smoothing iterations
pass_band (float, default: 0.1): Pass band for filter (0-2)
feature_smoothing (bool, default: False): Smooth along features
boundary_smoothing (bool, default: True): Smooth boundary edges

smooth_boundary¶

Smooth only boundary edges.

Parameters:

iterations (int, default: 20): Number of smoothing iterations
sigma (float, default: 0.1): Smoothing sigma

remesh¶

Regularize faces using ACVD algorithm.

Parameters:

n_clusters (int, default: 10000): Target number of faces
subdivisions (int, default: 3): Number of subdivisions for clustering

decimate¶

Reduce mesh complexity by removing faces.

Parameters:

target_reduction (float, default: 0.5): Fraction of faces to remove (0-1)
volume_preservation (bool, default: True): Preserve mesh volume

subdivide¶

Increase mesh resolution by subdividing faces.

Parameters:

n_subdivisions (int, default: 1): Number of subdivision iterations
subfilter (str, default: “linear”): Subdivision filter (‘linear’, ‘butterfly’, ‘loop’)

repair_holes¶

Fill small holes in the mesh.

Parameters:

max_hole_edges (int, default: 100): Maximum hole size to fill (in edges)
refine (bool, default: True): Refine the filled region

repair¶

Full mesh repair using MeshFix.

Parameters: None

make_manifold¶

Remove non-manifold edges.

Parameters:

hole_edges (int, default: 300): Size of holes to fill after removal

filter_curvature¶

Remove vertices outside curvature threshold range.

Parameters:

threshold (float or list[float], default: 0.4): Single value for symmetric range [-t, t] or [min, max] list

remove_normals¶

Remove vertices based on normal angle.

Parameters:

threshold_angle (float, default: 60.0): Angle threshold in degrees
flip (bool, default: False): Flip normal orientation before filtering
angle_type (str, default: “polar”): Type of angle (‘polar’ or ‘azimuth’)

remove_bridges¶

Remove triangles where all vertices are on the boundary.

Parameters: None

remove_tongues¶

Remove tongue-like artifacts.

Parameters:

radius (float, default: 50.0): Radius for boundary point neighborhood
threshold (float, default: 6.0): Threshold for boundary/euclidean distance ratio
hole_edges (int, default: 100): Size of holes to fill after removal

extract_largest¶

Keep only the largest connected component.

Parameters: None

clean¶

Remove degenerate cells.

Parameters:

tolerance (float, default: None): Tolerance for point merging

triangulate¶

Convert all faces to triangles.

Parameters: None

compute_normals¶

Compute surface normals.

Parameters:

flip (bool, default: False): Flip all normals
consistent (bool, default: True): Make normals consistent
auto_orient (bool, default: False): Orient normals outward

flip_normals¶

Flip all surface normals.

Parameters: None

correct_normal_orientation¶

Correct normal orientation relative to an axis.

Parameters:

relative (str, default: “x”): Axis to use for orientation (‘x’, ‘y’, ‘z’)

rotate¶

Rotate mesh around an axis.

Parameters:

axis (str, default: “x”): Axis to rotate around (‘x’, ‘y’, ‘z’)
angle (float, default: 0.0): Rotation angle in degrees

clip¶

Clip mesh with a plane.

Parameters:

normal (str or list[float], default: “x”): Plane normal (‘x’, ‘y’, ‘z’, ‘-x’, ‘-y’, ‘-z’) or [nx, ny, nz]
origin (list[float], default: None): Point on clipping plane
invert (bool, default: True): Invert clipping direction

erode¶

Erode mesh by removing boundary points.

Parameters:

iterations (int, default: 1): Number of erosion iterations

ecft¶

ExtractLargest, Clean, FillHoles, Triangulate (combined operation).

Parameters:

hole_edges (int, default: 300): Size of holes to fill

Domain Operations¶

compute_curvature¶

Compute mesh curvature.

Parameters:

curvature_type (str, default: “mean”): Type of curvature (‘mean’, ‘gaussian’, ‘minimum’, ‘maximum’)

filter_scalars¶

Apply filter to curvature field.

Parameters:

function (str, default: “median”): Filter function (‘median’, ‘mean’, ‘minmax’, ‘maxmin’)
iterations (int, default: 1): Number of filter iterations

segment_domains¶

Create domains via steepest ascent on curvature field.

Parameters:

curvature_type (str, default: None): Curvature type to compute if not already in context

merge_angles¶

Merge domains within angular threshold from meristem.

Parameters:

threshold (float, default: 20.0): Angular threshold in degrees
meristem_method (str, default: “center_of_mass”): Method for calculating meristem center

merge_distance¶

Merge domains within spatial distance threshold.

Parameters:

threshold (float, default: 50.0): Distance threshold
metric (str, default: “euclidean”): Distance metric (‘euclidean’ or ‘geodesic’)
method (str, default: “center_of_mass”): Method for calculating domain center

merge_small¶

Merge small domains to their largest neighbor.

Parameters:

threshold (int, default: 100): Size threshold for merging
metric (str, default: “points”): Size metric (‘points’ or ‘area’)
mode (str, default: “border”): Merge strategy (‘border’ or ‘area’)

merge_engulfing¶

Merge domains mostly encircled by a neighbor.

Parameters:

threshold (float, default: 0.9): Fraction of boundary that must be shared (0-1)

merge_disconnected¶

Connect domains isolated from meristem.

Parameters:

meristem_method (str, default: “center_of_mass”): Method for identifying meristem

merge_depth¶

Merge domains with similar depth values.

Parameters:

threshold (float, default: 0.0): Maximum depth difference for merging
mode (str, default: “max”): Aggregation mode (‘min’, ‘max’, ‘median’, ‘mean’)
exclude_boundary (bool, default: False): Exclude boundary vertices from calculation
min_points (int, default: 0): Minimum border points required for merging

define_meristem¶

Identify the meristem domain.

Parameters:

method (str, default: “center_of_mass”): Method for meristem identification

extract_domaindata¶

Extract geometric measurements for each domain.

Parameters: None

Output:

Creates a DataFrame with domain measurements including:

Domain index
Area
Centroid coordinates
Distance from apex
Angular position