swc2vtk

SWC to VTK converter for visualizing neurons and neural circuit simulations in ParaView.
This software helps making easy and beautiful visualization of large scale multi-compartmental neuron simulation with highly parallelized environments.

Dependency

• tqdm
• numpy
• 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')

generate VTK file for volume rendering

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

Settings

Visualization Quality

• Draw Mode change SWC compartment drawing method. Largeer number is better.
  • 0: simple cylinder
  • 1: one cylinder with variable top surface
  • 2: one cylinder with three cell mode
  • 3: one cylinder with a hemisphere

import swc2vtk
vtkgen = swc2vtk.VtkGenerator()
vtkgen.add_swc('simple.swc')
vtkgen.set_draw_mode(4)
vtkgen.write_vtk('simple.vtk')

• Division Number

import swc2vtk
vtkgen = swc2vtk.VtkGenerator()
vtkgen.add_swc('simple.swc')
vtkgen.set_division_number(20)
vtkgen.write_vtk('simple.vtk')

adjust compartment diameter

• normalize_diam

Output Examples

Single Neuron Morphology

• high resolution version

Coloring Multiple SWC Files

Single Neuron Simulation

Neural Circuit Simulation

Volume Rendering

References

• SWC format: http://research.mssm.edu/cnic/swc.html
• http://www.paraview.org/
• http://www.vtk.org/