nCorrect

A toolkit for the correction and normalization of SWC files from neuron morphology experiments.

Usage

Parameters

allAddress: user-specified text file containing the location of all .swc files (one file path per line)

imgAddress: user-specified file location of .tif input image of interest

outAddress: user-specified output folder

a : Strength of the intensity background term weight (suggested value is 1.00)

b : Strength of the color angle background term weight (suggested value is 0.85)

c : Strength of radius expansion term weight (suggested value is 3.75)

Tcol : Threshold of cosine similarity between two colors (suggested value is 0.90)

Tbkg : Threshold for node intensity background (suggested value is 0.47)

Tmin : Minimum threshold for lower intensity condition (suggested value is 0.05)

Tmax : Maximum threshold for lower intensity condition (suggested value is 0.30)

smin : Minimum color sum for lower intensity condition (example value is 10000)

smax : Maximum color sum for lower intensity condition (example value is 85000)

rmax : Maximum node radius (example value is 12)

Running

Compile by

javac Optimize4D.java

Run by

java Optimize4D allAddress imgAddress outAddress a b c Tcol Tbkg Tmin Tmax smin smax rmax