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

Project description

travisci Coverage Status python-2.7,3.3,3.4-blue license paraview NEURON

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

single

Coloring Multiple SWC Files

Coloring

Coloring

Single Neuron Simulation

Neural Circuit Simulation

Volume Rendering

Project details


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Source Distribution

swc2vtk-1.1.0.tar.gz (12.3 kB view hashes)

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