help > info on MOST-tracing plugin
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Sep 28, 2015  07:09 AM | Marco Peviani - San Raffaele Scientific Institute
info on MOST-tracing plugin
Hi,
I tried using MOSTvesseltracer plugin to trace vessel networks with quite good results.
However I would like to know a little more on the meaning of the parameters in the dialog box (seed-size, slip-size etc...) to understand how to change them to re-fine the results.


Can anyone help?

Thanks,
Marco
Sep 28, 2015  09:09 AM | Zhi Zhou
RE: info on MOST-tracing plugin
Threshold: Background threshold
Seed size: window size of the seed
Slip_size: window size to slip from seed
Sep 29, 2015  08:09 AM | Marco Peviani - San Raffaele Scientific Institute
RE: info on MOST-tracing plugin
Thanks!
M
Sep 30, 2015  03:09 AM | Marco Peviani - San Raffaele Scientific Institute
RE: info on MOST-tracing plugin
Bye the way...is there any publication we may refer to in order to understand how the plugin works and, eventually, to cite the authors in publications?
In detail....I would like to trace the length of individual branches and extract the tortuosity of vessels by comparing this result with the euclidean distance between different nodes. However, if I run the global_neuron_feature plugin I obtain a general quantitative description of the whole tracing. Should I use a different plugin to obtain these data?

Thanks M
Sep 30, 2015  11:09 AM | Zhi Zhou
RE: info on MOST-tracing plugin
MOST publication:
Wu, J., He, Y., Yang, Z., Guo, C., Luo, Q., Zhou, W., Chen, S., Li, A., Xiong, B. and Jiang, T. (2014) 3D BrainCV: Simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution, NeuroImage, 87, 199-208

You can also check the source code at https://svn.janelia.org/penglab/projects...

For your purpose, you can try to write a Vaa3D plugin to extract the information you need. Here is the instruction of how to write a plugin: https://github.com/Vaa3D/Vaa3D_Wiki/wiki...
Jul 15, 2019  09:07 PM | Zhang Zhou
RE: info on MOST-tracing plugin
Hi,

I found that in the dialog box(GUI) of MOST-tracing plugin, there is a check box about segmentPruning. However, using command line to invoke MOST plugin, it offers the other 4 parameters(ch, th, seed, slip) except segmrntPruning. Is there any interface/parameter of segmentPruning I can have access to in the command line MOST plugin.

Could you please help me?

Thanks Z
Jul 30, 2019  02:07 AM | Meng Ya Chen
RE: info on MOST-tracing plugin
Hi,
I have viewed the source code of this plug-in. If you call this plug-in in command line, segmenPruning will not function by default.
To enable segmenpruning in command line, you can find function AutoTrace in neurontracing_MOST->mostVesselTracer.cpp, add a parameter e.g. segmentflag (0 or 1), and find function trace_seed_list in the function AutoTrace and change the last parameter 0 to segmentflag, so that you can control whether to prune or not. You can also directly change the last parameter 0 of the function to 1, after you compile it, it will process segmenPruning by default.


Best Regards,
Mengya Chen