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fiji / SNT

Legacy project superseded by https://github.com/morphonets/SNT
GNU General Public License v3.0
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split (or measure) path between branching points and between branching and termini #67

Open bunbunet opened 4 years ago

bunbunet commented 4 years ago

Dear SNT developers, I posted this question on the forum.image.sc but I didn't receive any answer yet, I'm thus posting it here, I hope it can be the right place. I'm still not sure how and where to posts questions about imageJ plugins and I apologize if this is not the place for my kind of question.

I am importing in SNT v3.1.101 some Swc files that were traced in Neutube to perform some measurements. Yet I’ve two problems,

1) Minor issue: We tagged processes with different type determinants but this information is apparently lost in SNT (both in path manager and exported CSV file).

2) Major issue: Our cells have a number of small lateral processes (here a simple example with only two of them) that stem from a primary dendrites and we would like measure their numbers, lenght etc. We would also like to measure the inter-process distance. Yet impored swc are subdivided into paths that always continue past the branch point along one bifurcation, without caring about post-branch path lenght ( I guess they simply follow the order of nodes in the swc file). Rather we would like to split each path between branching points to divide them in segments (branch to branch and branch to termini),

A manual method would be useful (I could not yet figure it out!) However, as we have many cells and many processes a hint on how to do that programmatically would be much appreciated! If SNT is not the right software to perform such analyses, can anywone suggest and alternative?

Thank you very much

Federico

ctrueden commented 4 years ago

@bunbunet Posting on the Image.sc Forum was great. I expect @tferr is just very busy. Sorry I can't help with your SNT questions—I'm not knowledgeable enough about this plugin, unfortunately.

tferr commented 4 years ago

Really sorry @bunbunet for the late reply. Do you still need help with this?

bunbunet commented 4 years ago

Dear Tiago, Don't worry everybody is late! Thank you for answering, Indeed we did not progressed on that issue. The distance from branch to termini would be particularly important for us, toghter with the branch types that we annotated in Neutube but it is not imported in SNT

Ciao

Federico

Il mer 19 feb 2020, 05:18 Tiago Ferreira notifications@github.com ha scritto:

Really sorry @bunbunet https://github.com/bunbunet for the late reply. Do you still need help with this?

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