SWC to VTK converter for visualize multi-compartment neurons and neural circuit simulations
Project description
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
Install
[STRIKEOUT:$ pip install swc2vtk]
Usage
Basic way to generate VTK file from one SWC file
from swc2vtk.vtkgenerator import VtkGenerator
vtkgen = VtkGenerator()
vtkgen.add_swc('simple.swc')
vtkgen.write_vtk('simple.vtk')
generate a VTK file from multiple SWC files
from swc2vtk.vtkgenerator import VtkGenerator
vtkgen = 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
from swc2vtk.vtkgenerator import VtkGenerator
vtkgen = VtkGenerator()
vtkgen.add_swc('simple.swc')
vtkgen.add_datafile('result.dat')
vtkgen.write_vtk('simple.vtk')
- data exampleeach rows correspondence to SWC compartments
-65.0 -65.0 -65.0 -65.0
generate VTK files from SWC file with sequential simulation data
from swc2vtk.vtkgenerator import VtkGenerator
vtkgen = 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
from swc2vtk.vtkgenerator import VtkGenerator
vtkgen = 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
from swc2vtk.vtkgenerator import VtkGenerator
vtkgen = VtkGenerator()
vtkgen.add_swc('simple.swc')
vtkgen.set_draw_mode(4)
vtkgen.write_vtk('simple.vtk')
Division Number
from swc2vtk.vtkgenerator import VtkGenerator vtkgen = 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
Coloring Multiple SWC Files
Single Neuron Simulation
Neural Circuit Simulation
Volume Rendering
References
Project details
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Source Distribution
swc2vtk-1.0.0.tar.gz
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