Source code forked from Zhi Zhou's work.
A Vaa3D neuron tracing plugin that does a 2D tracing and remapping to the 3D image block.
Made a few changes:
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Specifiy a marker file to find the soma in the last step. the algorithm automatically find soma for each connected components and generates a lot of broken segments. sorting enables choosing a root node. Here you can find a node closest to the given soma.
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Option to do swc resampling. Before: APP2 resamples its result to step 10 and back to 2, now you either resample to 10 or do nothing. Finally, it does a resampling to 10 again. After: you can choose to do no resampling at all.
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Auto bkg_thr:whole image block's mean + 0.5std, used for both region grow thr and APP2. For APP2 it's decreased by 5, but greater or equal than 0(In the past when it was lower than 0, it could cause a bug). for 0, it means APP2 would do an auto thresholding(which should be mean + 0.5std, depending on your APP2 version).
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sort swc: the algorithm identifies many connected components and assemble the segments by sorting the neuron. the threshold for linking broken parts is exposed. The larger the thr, the more likely 2 segments are joined.
Help is also updated.
Also, since the trace_raw command is usually not used or shown in the help, no modification has been done.