Open curve snake


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

blob.png

step 2. preprocessing

Preprocess and detect seeds in the image. Adjust parameters to control seed detecting result if you need.

blob.png

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.

blob.png

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

colums are 

ID    node_type    X-position    Y-position    Z-position    Radius    link_to_ID



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test123: aasdas Details Apr 13 16:39
admin: Thanks! Details Apr 09 11:46
admin: Google map api Details Apr 09 11:46
lqj12: cooooooooool Details Apr 08 21:34
Yunhan Huang: 这个功能是如何实现的? Details Apr 08 13:23