swc2vtk 1.1.0

SWC to VTK converter for visualize multi-compartment neurons and neural circuit simulations

SWC to VTK converter for visualizing neurons and neural circuit simulations in ParaView. This software helps making beautiful visualization of large scale multi-compartmental neuron simulations with a parallelized environment. If you need any further information, please check http://daisukemiyamoto.github.io/swc2vtk/ .

Dependency

• tqdm

• numpy

• [STRIKEOUT:PyVTK]

Install

• $ pip install swc2vtk

Usage

Basic way to generate VTK file from one SWC file

import swc2vtk
vtkgen = swc2vtk.VtkGenerator()
vtkgen.add_swc('simple.swc')
vtkgen.write_vtk('simple.vtk')

generate a VTK file from multiple SWC files

import swc2vtk
vtkgen = swc2vtk.VtkGenerator()
vtkgen.add_swc('simple.swc')
vtkgen.add_swc('simple1.swc')
vtkgen.add_swc('simple2.swc')
vtkgen.write_vtk('combined.vtk')

generate a VTK file from SWC file with simulation data

import swc2vtk
vtkgen = swc2vtk.VtkGenerator()
vtkgen.add_swc('simple.swc')
vtkgen.add_datafile('result.dat')
vtkgen.write_vtk('simple.vtk')

• data example

  each rows correspondence to SWC compartments

  -65.0
  -65.0
  -65.0
  -65.0

generate VTK files from SWC file with sequential simulation data

import swc2vtk
vtkgen = swc2vtk.VtkGenerator()
vtkgen.add_swc('simple.swc')

vtkgen.add_datafile('result1.dat')
vtkgen.write_vtk('simple1.vtk')

vtkgen.clear_datafile()
vtkgen.add_datafile('result2.dat')
vtkgen.write_vtk('simple2.vtk')

vtkgen.clear_datafile()
vtkgen.add_datafile('result3.dat')
vtkgen.write_vtk('simple3.vtk')

Output Examples

Single Neuron Morphology

single

• high resolution version

Coloring Multiple SWC Files

Coloring

Single Neuron Simulation

Neural Circuit Simulation

Volume Rendering

References

• SWC format: http://research.mssm.edu/cnic/swc.html

• http://neuromorpho.org/

• http://www.paraview.org/

• http://www.vtk.org/