data_config.yaml

# set the working directory that contains all input
# and will contain all output files
wdir: './membrane_curvature/'

# file name for the mesh of the segmented cell
mesh_fname: 'cell_0.8dec.stl'

# a reference mesh that can be used to confine measurements
# to the actual membrane of the cell, this is important when
# some of the cell membrane is cutoff at the boundary of
# the image volume. Generally this reference mesh will
# be created from a simple thresholding of the image volume
# to annotate the empty resin of a uniform intensity value.
# if none of the cell is cutoff at the 
# boundary of the image volume then this can be set to null
ref_mesh_fname: 'resin_0.8dec.stl' #null

# if the reference mesh for finding the surface to measure
# curvature is of resin or not; generally this should remain True
reference_is_resin: True

# a slicer .fcsv markups file where each point
# corresponds to a virus particle that was annotated
# with a fiducial marker
markups_fname: 'viruses.fcsv'

# whether to deduplicate points in the markups
dedupe: True
# minimum distance between fiducials for them to be
# considered as representing separate virus particles
min_separation: 50

# Slicer saves fiducial coordinates in the LPS
# coordinate system while meshes generated in Slicer
# use the RAS coordinate system; if mesh or fiducials
# are generated in other software this may need to be False
lps_to_ras: True

# set parameters for calculating the mean curvature
# at points on the surface.
# curvature radius is in physical space of nanometers
curvature_radius: 100

# finally, the desired output filenames for the KDE plot
# and the summary statistics csv
kde_fname: 'Fig3C_cell1_0.2_curvature_kde.png'
csv_fname: 'Fig3C_cell1_0.2_curvature_summary.csv'