diff --git a/notebooks/surface_morphometrics_config.yml b/notebooks/surface_morphometrics_config.yml
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-# 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).
-  intra: # Intra-surface distance/orientation (verticality) measurements
-  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.
-    VM:
-      - OM
-cores: 16 # Number of cores to use for parallel processing.