swc2vtk 1.0.2

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 easy and beautiful visualization of large scale multi-compartmental neuron simulation with highly parallelized environments.

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')

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

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://www.paraview.org/

• http://www.vtk.org/