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principalskeleton_detection.wiki
Xiaoxiao Liu edited this page Mar 30, 2015
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svn co https://svn.janelia.org/penglab/projects/vaa3d_tools/released_plugins/v3d_plugins/principalskeleton_detection
- detect prinipcal skeleton...
- warp subject image to target by aligning their skeletons...
- open test data and demo web page
- about this plugin
- detect
- warp
- help
Usage : v3d -x principal_skeleton -f detect -i <inimg_file> <iniskele_file> <domain_file>
-o <deformskele_file> <cubicswc_file> -p <channel> <stop_thresh>
inimg_file name of input image file
iniskele_file name of input initial skeleton file (.marker)
domain_file name of input domain definition file (.domain)
deformskele_file name of output deformed skeleton control points in a marker file (.marker)
cubicswc_file name of output cubic-spline smoothed skeleton swc file (.swc)
channel the input channel value, default 2 and start from 0
stop_thresh stop threshold, default 0.01
e.g. v3d -x principal_skeleton -f detect -i input.raw iniskele_file.marker domain_file.domain
-o deformskele.marker cubicswc.swc -p 2 0.01
Usage : v3d -x principal_skeleton -f warp -i <subimg_file> <submak_file> <tarimg_file> <tarmak_file>
<domain_file> -o <outimg_file>
subimg_file file name of subject image
submak_file file name of subject skeleton (.marker)
tarimg_file file name of target image
tarmak_file file name of target skeleton (.marker)
domain_file file name of domain definition (.domain)
e.g. v3d -x principal_skeleton -f warp -i subimg.raw submak.marker tarimg.raw
tarmak.marker domain_file.domain -o outimg.raw
For more information of this plugin, please visit http://penglab.janelia.org/proj/principal_skeleton/supp/supp_index.htm
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