NeuronJ + Straighten Plugin

[lechristophe]

Dear all,

In the release notes of the last version of NeuronJ (1.1, see
http://imagescience.bigr.nl/meijering/software/neuronj/releases.html),
is stated :

"It is now possible to export the tracing vertex coordinates as tab- or
comma-delimited text files. This facilitates using the tracings in other
programs or plugins, such as for example the Straighten plugin."

That's precisely what I'm trying to do. I get delimited text files
corresponding to NeuronJ tracings, but how to get from those files to
draw a tracing in the Straighten Plugin ?

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 ?

Secondly, do you think it's doable to control either NeuronJ or
Straighten via a macro ? What arguments can I pass to Straighten to
automate the Straighten procedure ? Do I have to learn Java and write a
proper plugin for that ?

The possibility of controling/automating complex plugins like NeuronJ
and Straighten is what motivates me to switch from Macro writing to
Plugin writing. Is it possible anyway ? The source of the NeuronJ plugin
is not avalaible, even if I could find a copy of the 1.0 source
somewhere (previous version was open).

  --
Christophe Leterrier

Postdoc
INSERM UMR641 Neurobiology of ionic channels
IFR Jean Roche - Mediterranee University
Marseille, France

[S.I. Rusu]

  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: [phone]
Fax: [phone]
Dr. Molewaterplein 50
NL-3015 GE Rotterdam
email: [hidden email]
web: http://www2.eur.nl/fgg/neuro/

[lechristophe]

Thank you very much ! I'll try your code and modify it to my needs.

Christophe Leterrier

S.I. Rusu wrote

  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: [phone]
Fax: [phone]
Dr. Molewaterplein 50
NL-3015 GE Rotterdam
email: [e-mail]
web: http://www2.eur.nl/fgg/neuro/