Hi, 
I am trying to use APP2 to do neuron reconstruction, and encounter 2 questions:

1. How to tune APP2 parameters automatically?
Since I want to apply this method to around 100 neurons, I tried default parameters first.
However, in most of the cases, the number of branches are less than expected when compared with image data.
In a few cases, the reconstruction results are quite different from their original images.
I think this problem should be able to solved by adjusting the parameters, but so far I can't find a suitable set of parameters.
Any suggestion about how to solve this problem?

Here are the examples I tested (.lsm) and their corresponding results (.swc): download here
(because the image data is really huge, forgive me for only uploading some of them)
Except for bkg_thresh was changed to -1 (auto-thresholding), the rest of the parameters were set by default.
These neurons could be found here: BRC
(For example, the neuron name of the file "Cha-F-100065.lsm_x95_y103_z56_app2_-1.swc" is Cha-F-100065.)

2. If I already have neuron skeleton data, is that possible to use APP2 to re-estimate neurite radius? 
(I guess it can be done by inserting neuron skeleton from the parameter "inmarker_file" but failed.)
 
Thanks!