Dear Rommel,
On May 20, 2015, at 20:32, Rommel Santos wrote:
> I am user of neuromantic and trying to open my tracings on FIJI to perform a sholl analysis. Unfortunately the .swc tracings (from neuromantic) do not open up on FIJI. I do not know what I am doing wrong. Would you know a way to open neuromantic tracings on FIJI?
Please forgive me for the delay.
Believe or not, I only saw your email now while cleaning my inbox.
Sorry about that.
(to avoid this, it is always best to cc the ImageJ mailing list)
I can only guess that the tracing is being displayed "outside" the image canvas.
The SWC specification[1] does not store any metadata. So, if the tracing was obtained from multiple fields of view (or if the image used for tracing has been resized), there will be an inevitable offset between the traces and the origin of the field of view used used in Neuromantic (this also applies to z).
(That's why Mark implemented the SWC offset/scale options int the "SWC import dialog" in Simple Neurite Tracer, SNT).
I'm guessing you could try two things:
1) Specify and appropriate X,Y,Z offset in the "SWC import options" of Simple Neurite Tracer (By trial and error).
2) Use a placeholder image of exaggerated dimensions that emcompasses any existing offsets.
For 1) I found useful to have at hand a screenshot of the Neuromantic window before exporting the tracing, so that I can have a rough idea of the tracing displacement relatively to the upper left corner of the field of view.
For 2) You could use the File>New>Image command to generate an empty 8-bit image as large as your memory can handle, and then try to load the .swc file on it. This would fool SNT into thinking the tracing belonged to that particular canvas.
Let us know how it goes,
If it works, and I could link this answer to the FAQ of the Sholl Analysis page[2].
[1]
http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html[2]
http://imagej.net/Sholl#FAQBest,
-tiago
--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html
Locked
