This is a part of my Capstone Research.
The software system will be distributed in both source code and installable system. The website is available at: http://www.farsight-toolkit.org/wiki/Open_Snake_Tracing_System. The DIADEM datasets used in the experiments are available at: http://diademchallenge.org/data_sets.html
quoted from "A Broadly Applicable 3-D Neuron Tracing Method Based on Open-Curve Snake" by Yu Wang & Arunachalam Narayanaswamy & Chia-Ling Tsai & Badrinath Roysam
I used open snake tracing system to extract vessel from original picture and acquired node links with radius from this system.
step 1, load the image/image set
use tif combine tool to create tif stack for 3D image
step 2. preprocessing
Preprocess and detect seeds in the image. Adjust parameters to control seed detecting result if you need.
step 3. tracing
use open snake tracing algorithm(4D region) to find routes(blue) and radius(red) linked by seeds. The 4th D is for radius of each node.
step 4. Edit tree (root, branch) and save output
output file is a swc format, each line recording a node.
1 2 5.54597 3.39991 0 0 -1 2 2 7.43347 5.8073 0 2.03415 1 3 2 8.73714 8.57442 0 2.39801 2
ID node_type X-position Y-position Z-position Radius link_to_ID