(In reply to comment #0)
> Hi, 
> I have created swc format from the tree. 
> However it seems to have only one branch instead of several which I have
> traced. 
> It gives the error that I can select only one connect set of paths for swc. 
> All the trees are connected it seems to me.. 
> but maybe around the soma, the points which I thought was a single point might
> have been points that were nearby. 
> How could I solve this problem? 

In the Path Window, each set of connected paths have a single parent in the first column.  If you have more than one such tree, then they're not all connected.

Just to be clear, paths are only joined if you start (or end) them with the modifier key held down. Just starting a path at the same point in the stack does not cause them to be joined.

If you want to join up two disconnected paths, create a new path which is joined at the beginning and end to bridge the gap.  (You may then want to set the primary path if that's changed.)

If you're still having problems, please attach your traces file to this bug report (using the "Create a New Attachment" link) and I'll take a look.

regards,
mark

Created attachment 22
the screen capture of the path window 

Hi 
Thanks for your comment.
However, it doesn't work the way you explained.
I have tried to press (1) command + shift (2) command (3) alt (4) alt+ shift 
(I tried with alt also since in the document below it was mentioned that if one is using mac, should be using alt :  http://www.longair.net/edinburgh/imagej/tracer/instructions.html )
None of those seem to give me a hierarchical structure. 
The new path that is created is not created as a substructure of the initial path. 
(Image attached)

(In reply to comment #2)
> Created an attachment (id=22) [details]
> the screen capture of the path window 
> 
> Hi 
> Thanks for your comment.
> However, it doesn't work the way you explained.
> I have tried to press (1) command + shift (2) command (3) alt (4) alt+ shift 
> (I tried with alt also since in the document below it was mentioned that if one
> is using mac, should be using alt : 
> http://www.longair.net/edinburgh/imagej/tracer/instructions.html )
> None of those seem to give me a hierarchical structure. 
> The new path that is created is not created as a substructure of the initial
> path. 
> (Image attached)

I've tried this on a Mac and it works as I expect with Shift+Alt.  One thing I didn't emphasize above is that you must have an existing path selected (so appearing green in the display) in order to create a branch off that path - otherwise it wouldn't know which path to join to.  Is it possible that you didn't have a path selected when trying to create the branch?

regards,
mark

Yes! 
I hadn't selected a path previously. 
Now it works after selecting the path!!! 
Thanks a lot! 

However it is still not clear to me 
what each of the key 'shift', 'alt' or 'command' does.. 

Best wishes

Yihwa  

Created attachment 24
the error window

There was an error which I couldn't identify. 
Attached is the error. 
I couldn't find from the all paths window the 'Temporary Path'.
I guess all the traces should be 'completed' to be displayed in the path window. 

The only document I found regarding temporary path was below. 
Click yes to confirm temporary path.
http://pacific.mpi-cbg.de/wiki/index.php/Testing_Procedure_for_Simple_Neurite_Tracer

(In reply to comment #4)
> Yes! 
> I hadn't selected a path previously. 
> Now it works after selecting the path!!! 
> Thanks a lot! 
> 
> However it is still not clear to me 
> what each of the key 'shift', 'alt' or 'command' does.. 
> 
> Best wishes
> 
> Yihwa  

Great, I'm glad that's worked out.  I'll close this bug report.  (I will create a new bug for the extra one that you mention in your later comment - it's important for tracking what's fixed and what's broken that these are separate bugs.)

On any platform "Shift" makes sure that all of the three panes are centred on
the red crosshairs.  On Mac OS the "Alt" modifier says that you want to create
a join from (or to) another path, and restricts the motion of the crosshairs to
points on the selected paths.

The "Command" button (?) doesn't do anything special in Simple Neurite
Tracer.

I will be going over all the documentation and tutorials soon, and I will try
to make this all more clear.

regards,
mark