shamrock-zhao/neuriteorientation

Multiscale analysis of neurite orientation

code in this repository is based on our paper Multiscale analysis of neurite orientation and spatial organization inneuronal images

Installation for ubuntu 14.04 TLS

Code depends on standard python based scientifc packages like scipy. numpy matplotlib and scikit-image

some extra dependency are

1. pycircstat https://github.com/circstat/pycircstat/

2. pyemd https://github.com/wmayner/pyemd

3. opencv

which can be installed using

pip install pycircstat

pip install pyemd

sudo apt-get install libopencv-dev python-opencv

Using code

please check the demo file dirAnalyzerDemo.py for setting the parameter There is a associated jupyter notebook dirAnalyzerDemo.ipynb

As code depends on presegmentation of images there is an another notebook localOstuBasedSegmentationUtility.ipynb for elementary segmentation based on OSTU