GitHub - fethallah/neurons: Automatically exported from code.google.com/p/neurons

1 Branch 0 Tags

Name	Name	Last commit message	Last commit date
Latest commit fethallah@gmail.com final file to dataset Dec 11, 2013 a7de081 · Dec 11, 2013 History 80 Commits
CellsDetection	CellsDetection	Basel Final 2013...repo mesed up, some cleaning required	Mar 5, 2013
Common	Common	add smoothing function	Mar 5, 2013
Evaluation	Evaluation	final file to dataset	Dec 11, 2013
FeaturesExtraction	FeaturesExtraction	minor issue fixed: tracked neurites are effectivelly labeled as tracked	Mar 7, 2013
Geodesics	Geodesics	Basel Final 2013...repo mesed up, some cleaning required	Mar 5, 2013
GreedyTracking	GreedyTracking	fix the rare case where there's no connection between neurites at all	Dec 11, 2013
IO	IO	improve readme	Aug 6, 2013
NeuritesDetection	NeuritesDetection	pruning functionality added at neurite detection level	Nov 17, 2013
NeuritesTracking	NeuritesTracking	fixing a bug on Kevin's Neurite tracking code	Mar 8, 2013
frangi_filter_version2a	frangi_filter_version2a	Basel Final 2013...repo mesed up, some cleaning required	Mar 5, 2013
gaimc	gaimc	Basel Final 2013...repo mesed up, some cleaning required	Mar 5, 2013
PathsToDatasets-10X-Final1.txt	PathsToDatasets-10X-Final1.txt	path to datasets of the whole screen split in 2 files	Nov 21, 2013
PathsToDatasets-10X-Final2.txt	PathsToDatasets-10X-Final2.txt	path to datasets of the whole screen split in 2 files	Nov 21, 2013
Readme.txt	Readme.txt	adding a Readme	Mar 6, 2013
processListOfPlates.m	processListOfPlates.m	vl_feat should not be in the svn	Mar 5, 2013
processPlate.m	processPlate.m	Basel Final 2013...repo mesed up, some cleaning required	Mar 5, 2013
setpaths.m	setpaths.m	ffc	Aug 9, 2013
trkTracking.m	trkTracking.m	added the neurite prunning at the sequence level	Nov 17, 2013

Repository files navigation

======================================================
Synergia Computer Vision pipeline
F. Benmansour and K. Smith
======================================================

1- Prerequisites:
    	a- vlfeat 0.9.16 available at http://www.vlfeat.org/download/vlfeat-0.9.16-bin.tar.gz
	b- Enter the Geodesics directory and run from matlab "compile_mex"

2- The code have been organised into many subdirectories:
  	Common
	IO
	CellsDetection
	GreedyTracking
	Geodesics
	NeuritesDetection
	NeuritesTracking
	FeaturesExtraction
	frangi_filter_version2a
	gaimc

3- The most important functions and scripts are:
 	a- trkTracking : to be run for one single sequence
	b- processPlate.m
	c- processListOfPlates.m