config.yml

# UNIVERSAL
data_dir: "./example_data/"
work_dir: "./morphometrics/"
exp_name: "test" # Subdirectory of work folder for this experiment
segmentation_values: # The value used to represent each feature, and the name of the feature.
  OMM: 1
  IMM: 2
  ER: 3
cores: 6 # Number of cores to use for parallel processing.

#SEGMENTATION TO MESH 
surface_generation:
  angstroms: false # Default scaling adjusts so surfaces are nm-scaled, if set to true surfaces are not rescaled and remain angstrom-scaled.
  ultrafine: false # Not necessary under normal conditions but may help with unusually challenging membranes. Uses additional subdivision and resampling before cropping.
  extrapolation_distance: 1.5 # Distance in nm (or angstroms, if angstrom setting is True) to extrapolate the surface
  isotropic_remesh: false # If true, applies isotropic remeshing to create near-equilateral triangles with target average area.
  target_area: 1.0 # Target average triangle area in square units (nm^2 by default). Used when isotropic_remesh is true. Values between 1.0 and 3.0 generally yield good results, but smaller triangles significantly increase computation time.
  simplify: true # If true, decimates the mesh to max_triangles. Note: simplified surfaces will not be isotropic.
  max_triangles: 100000 # Only used if simplify is true. When using isotropic_remesh, target_area controls triangle count instead.
  octree_depth: 9 # Increase if the surface is too smooth, decrease if surface is too jagged - but has a HUGE effect.
  point_weight: 0.7 # Larger numbers have stronger weight towards fitting segmented points, smaller numbers have stronger weight towards generating a smooth surface
  neighbor_count: 400 # Number of neighbors used for normal estimation. Should not need to adjust this, but I am exposing it as a tuning variable. Values over 50 seem to all be equivalently good...
  smoothing_iterations: 1 # Number of smoothing iterations to perform for estimating normals. You should usually leave this at 1.

# PYCURV
curvature_measurements:
  radius_hit: 9 # This corresponds to the radius of the smallest feature of interest, roughly, for neighborhood determination. 8-15 seems to be a good range for mitochondria
  min_component: 30 # The minimum number of triangles for a component to be considered for curvature measurement.
  exclude_borders: 1 # Values greater than zero exclude the border from the curvature calculation by n nm/angstroms.
distance_and_orientation_measurements:
  mindist: 3 # Minimum distance between two points for them to be considered for distance measurement.
  maxdist: 400 # Maximum distance between two points for them to be considered for distance measurement.
  tolerance: 0.1 # Tolerance for determining if a triangle is contacted by a line.
  verticality: true # Measure verticality (angle relative to growth plane). 
  intra: # Intra-surface distance/orientation (verticality) measurements
    - OMM
    - IMM
    - ER
  relative_orientation: true # Measure relative orientation (angle relative to nearest neighbor surface).
  inter: # Intersurface distance/orientation measurements. Writes out symmetrically so you do not need to give symmetric options.
    OMM:
      - IMM
      - ER
 
# thickness_measurements:
#   sampling: 1.0
#   fit_curve: True 
#   flip_y: false
#   leaflets: true
#   components:
#     - Spherule
#     - ER
#     - NE
#     - OMM
#     - IMM