A toolkit for the correction and normalization of SWC files from neuron morphology experiments.
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)
Compile by
javac Optimize4D.java
Run by
java Optimize4D allAddress imgAddress outAddress a b c Tcol Tbkg Tmin Tmax smin smax rmax