swc2vtk

travisci 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

high resolution version

Coloring Multiple SWC Files

Single Neuron Simulation

Neural Circuit Simulation

Volume Rendering

References

Release files for swc2vtk 1.1.0

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for swc2vtk 1.1.0
File	Size	Uploaded
swc2vtk-1.1.0.tar.gz	12.3 kB	Jan 30, 2017	Details

Release files / swc2vtk-1.1.0.tar.gz

Download URL	swc2vtk-1.1.0.tar.gz
Size	12.3 kB
Tags	Source
SHA-256 checksum How to use checksums	`4dd9110e5b37b3d083b860ccb0c354f48aa8de2e9c7fdf485fcd8e6ba6c47ad3`
BLAKE2b-256 checksum How to use checksums	`2a40300a4a4d8584da423f325c84769a5bfefa935fa88966edb460ed22218d02`
Upload date	Jan 30, 2017
Uploaded using Trusted Publishing? What is trusted publishing?	No