AnaMorph

Framework for creating 3d neuronal morphologies from point/diameter descriptions.

Build Status

Tested builds:

• Linux: GCC 5.4, Clang 7.
• OSX: Apple LLVM version 9.1.0.

Installing

1. Clone this repository using git:

   git clone https://github.com/NeuroBox3D/AnaMorph.git

2. Compile using cmake and make: In the following, we suppose the AnaMorph project has been cloned to $AnaMorphHome.

   cd $AnaMorphHome
   mkdir build && cd build
   cmake ..
   make

   AnaMorph makes heavy use of the C++11 standard. Up-to-date compilers are recommended. Once built successfully, the binary am_cellgen is present in \$AnaMorphHome/bin. You may want to add this to your \$PATH.

Basic Usage

The most basic way to use AnaMorph is this: Suppose we have a valid SWC file someCell.swc in the current directory.

am_cellgen -i someCell.swc

If all is well, then AnaMorph will output the final surface mesh as someCell_post-processed.obj. Often, however, AnaMorph's consistency analysis will find some intersections in the morphology. To force creation of the (potentially self-intersecting) surface, one can use

am_cellgen -i someCell.swc -force-meshing

Advanced usage

AnaMorph has several parameters adjustable on the command line. Some of them are used fairly frequently, e.g. -meshing-cansurf-angularsegments for the surface resolution:

am_cellgen -i someCell.swc -force-meshing -meshing-cansurf-angularsegments 6

will produce neurites with a resolution of 6 nodes per cross-section (the default setting). Smaller values for this parameter will result in coarser grids. For values lower than 5, the additional option -preserve-crease-edges is recommended to avoid unnatural twisting with loss of volume.

Preconditioning can be fine-tuned using the -cellnet-pc directive:

am_cellgen -i someCell.swc -force-meshing -cellnet-pc 3.52 1.76 9999999

The first two parameters will cause short edges to be collapsed. Smaller parameters allow for shorter edges, bigger parameters increase the smoothing effect of preconditioning.

The parametrization strategy chosen for the spline interpolation is set using the -cellnet-parametrization-strategy argument:

am_cellgen -i someCell.swc -force-meshing -cellnet-parametrization-strategy "centripetal"

The post-processing step of smoothing can be deactivated using:

am_cellgen -i someCell.swc -force-meshing -no-mesh-pp-hc

A comprehensive list of adjustable parameters is contained in the file $AnaMorphHome/doc/ReadMe. It is also displayed if you simply call

am_cellgen

without any arguments.