Created attachment 26
the soma problem

(In reply to comment #0)
> Hi I am using simple neurite tracer and it seems the points don't seem to lie
> quite at the center. 
> This problem is severe close to the soma and also at the points where I give
> the end points. 
> Currently I have tried using both Hessian-based analysis (didn't quite optimize
> the sigma or multiplier yet), and Fit volume. 
> Neither of them quite seem to do the job. 
> I will attach an image in the following report. 
> 
> Best wishes
> Yihwa

Yihwa,

The effect you see in the soma is because the Hessian-based analysis particularly picks out tube-like structures, and the centre of the soma isn't tubelike.  (If you use the "Tubeness" plugin on your image you will probably see that the centre of the soma is completely dark, and only the surface is bright - the surface is more "tube-like" with this algorithm.)

The simplest solution for the soma is to turn off the "Hessian-based analysis" option for going from the centre of the soma to the start of the branch, and turn it on again for the genuinely tube-like parts of the structure.  (In general I turn this option on and off quite a bit when using the plugin, depending on whether the naive algorithm is actually producing better results. If you don't change the value of sigma then turning this option on and off won't take any time.)

I'm not sure what you mean by the problem at the end points - is that just that the path has kinks in it in the fainter regions?  Does switching off the option help in those situations?

Thanks for your bug report.

regards,
mark

Created attachment 27
example reconstruction from the simple neurite tracer 

Hi Mark, 

Thanks for the comment. 
I have attached an image from the simple neurite tracer. 
You can see some discontinuities, which I think are the points where I have put an end point. The algorithm seems to do pretty well between two points. However, the problem seems to arise at the location where I define at the end point. 
(I have turned on the hessian-based analysis for the tubular structures and didn't from the soma to the first tubular structure.)
I wonder if there is anyway to remove such discontinuities that arise due to the manual selection of intermediate(or end) points. 

Thank you in advance!

Best wishes

Yihwa

(In reply to comment #3)
>
> Hi Mark, 
> 
> Thanks for the comment. 
> I have attached an image from the simple neurite tracer. 
> You can see some discontinuities, which I think are the points where I have put
> an end point. The algorithm seems to do pretty well between two points.
> However, the problem seems to arise at the location where I define at the end
> point. 
> (I have turned on the hessian-based analysis for the tubular structures and
> didn't from the soma to the first tubular structure.)
> I wonder if there is anyway to remove such discontinuities that arise due to
> the manual selection of intermediate(or end) points. 
> 
> Thank you in advance!
> 
> Best wishes
> 
> Yihwa 

Yihwa,

At the moment the points you manually specify are considered fixed, so won't be adjusted by the "Fit Volume" option, for example.  This is a limitation that I intend to fix, but it needs a bit of careful work.  There are two plans I have for this:

- Allow manual adjustment of where the points are at any stage
- Allowing the fitting to adjust the manually placed points as well as the intermediate points

In the mean time, my suggestion would be to select the intermediate points in a zoomed-in view, using the three-pane view to find the midline of the neuron.  I've just released a version which has some improvements to make this easier, so make sure that you run "Help > Update Fiji" and check that VIB-lib.jar and Simple_Neurite_Tracer.jar are up-to-date.  Then there's a short tutorial here explaining what I mean:

   http://pacific.mpi-cbg.de/wiki/index.php/Simple_Neurite_Tracer:_Accurate_point_placement

Mark, am I correct in my assumption that you won't be able to fix this?

(In reply to comment #5)
> Mark, am I correct in my assumption that you won't be able to fix this?

I'm not likely to have any time to deal with this for a little while.  However, I had been talking with Fethallah about using the OOF preprocessed data to automatically refine point placement, and it's definitely something we'd both like to do.

If you don't mind, I'd like to leave this bug open - I've changed the title to more accurately reflect what the problem is.

Mark, I hope you don't mind that I am migrating this bug to the GitHub Issue tracker:

https://github.com/fiji/Simple_Neurite_Tracer/issues/1