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Constructed Tessellated Neuronal Geometries (CTNG) (McDougal et al. 2013)
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CTNG (Constructive Tessellated Neuronal Geometry) is a tool for constructing a 3d tesselation of a neuron's surface from point-diameter data. Before use: compile the C and Cython routines: cd geometry3d python setup.py build_ext --inplace To use (for now displays the neuron, but could easily write data to a file): python ctng.py FILENAME_IN [FILENAME_OUT] [dx] where neuron_file is the name of the source morphology. e.g. python ctng.py Vn03082006-0-D.ASC out.tri 0.25 The first line of an output file lists the number of triangles and the area. Each triangle is listed on its own line in the following format: x1, y1, z1, x2, y2, z2, x3, y3, z3 Requires: g++ cython python numpy mayavi NEURON Most of the figures for the CTNG paper were made using the morphology from http://neuromorpho.org/neuroMorpho/neuron_info.jsp?neuron_name=Vn03082006-0-D Changelog: 2012-12-10 sphere tests for contains_surface is primary bugfix for case where no output file specified lowered minimum chunk width from 100 to 20 voxels 2013-01-21 refactoring, bugfixes surfaces now provably watertight (last change introduced holes) 2013-10-05 fix to extreme points of soma (was using axis, not the soma data) 2016-05-31 commented out some printfs and changed a tuple to a list to make it compile with current cython and python code now checking filenames and using the SWC loader if a .swc file is loaded
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