# Config file used for running the code/pipeline at: https://github.com/GrotjahnLab/surface_morphometrics
data_dir:"/data/instances_substacks"
work_dir:"/data/morphometrics_substacks"
segmentation_values:# The value used to represent each feature, and the name of the feature.
IM:1
OM:2
VM:3
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# If true, the surface is generated with a new high quality protocol. This makes calculation much slower but the surface is much better for sampling density.
mesh_sampling:1# Approximate mesh sampling rate, for ultrafine mode
simplify:true# Non-simplified surfaces can be VERY slow, but are better for sampling the coulomb potential.
max_triangles:300000# If simplifying and more than this number of triangles are generated, the surface is decimated to this number
extrapolation_distance:1.5# default 1.5 Distance in nm (or angstroms, if angstrom setting is True) to extrapolate the surface
octree_depth:9# Increase if the surface is too smooth, decrease if surface is too jagged - but has a HUGE effect.
point_weight:0.2# Smaller numbers have stronger weight towards fitting segmented points, larger 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.
curvature_measurements:
radius_hit:15# (default 15) 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# (default 30) The minimum number of triangles for a component to be considered for curvature measurement.
exclude_borders:10# 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).
