daisukemiyamoto/swc2vtk

swc to vtk converter for visualization of neuron and neural circuit simulation in ParaView

swc2vtk

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
• 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')

set fixed value for coloring VTK file

import swc2vtk
vtkgen = swc2vtk.VtkGenerator()
vtkgen.add_swc('simple1.swc')
vtkgen.write_vtk('simple1.vtk', fixedval=0.5)

vtkgen2 = swc2vtk.VtkGenerator()
vtkgen2.add_swc('simple2.swc')
vtkgen2.write_vtk('simple2.vtk', fixedval=1.0)

set fixed value for coloring neuron in a VTK file

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', coloring=True)

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

• data output example for NEURON

proc saveData() { local i localobj outfile strdef filename
    filename = $s1
    
    printf("filename: %s\n", filename)
    outfile = new File()
    outfile.wopen(filename)
    for(i=0; i<SectionNum; i=i+1){
    	  access Dend[i]
        outfile.printf("%f\n", v)
    }
    outfile.printf("\n")
    outfile.close()
}

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

Coloring Multiple SWC Files

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/

swc2vtk's Issues

complete test

documents

add line mode for data saving

use multi thread for swc conversion

draw synapse

Is it possible to genetate vtk files with conical frustum?

Firstly, thanks for your great tool. I was hoping to visualize the rendered vtk with conical frustum (as opposed to hexagonal). Is this possible to generate the vtk files with as smoother representation of the node radius?

output diam for cell data

Make package

• write setup.py
• register PyPI

Volume Rendering

• check volume rendering mode
• implement summation method for multi neuron simulation
• (consider point spread functions)