Re: NeuronJ + Straighten Plugin
Posted by
S.I. Rusu on
Jan 10, 2007; 9:38am
URL: http://imagej.273.s1.nabble.com/NeuronJ-Straighten-Plugin-tp3700634p3700635.html
here is a macro that creates a polyline selection from a excel file
containing the coordinates of a trace from Neuronj:
macro "NjTraces"{
dir=getDirectory("image");
ntraces=getFileList(dir+"\\traces");
j=ntraces.length;
for (k=1;k<j;k++){
r=File.openAsString(dir+"traces\\trace.N"+k+".xls");
s=split(r, "\n");
l=lengthOf(s);
startx=newArray(l);
starty=newArray(l);
for (i=0; i<l;i++){
coord=split(s[i], "\t");
startx[i]=coord[0];
}
for (i=0; i<l;i++){
coord=split(s[i], "\t");
starty[i]=coord[1];
}
makeSelection("polyline", startx, starty);
roiManager("Add");
}
}
you'll have to export the traces as "tab-delimited text files: separate
file for each tracing" and save it as an excel file. also the traces
must be saved (rename to "trace") in a new folder (called "traces") in
the directory containing the image. it can still be improved....
hope it helps.
silviu
>
> My idea is to first create a segmented/curved linear ROI from the file,
> and then laungh the Straighten Plugin. Do anybody know how I can get a
> ROI to be build from a text file containing coordinates ?
>
--
Silviu Rusu,
Erasmus MC Rotterdam
Ee 1230
Tel: +31 10 46 38094
Fax: +31 10 40 89459
Dr. Molewaterplein 50
NL-3015 GE Rotterdam
email:
[hidden email]
web:
http://www2.eur.nl/fgg/neuro/