Hi there,

I'm trying to develop a 4D analysis for cell motility. To do this, I am generating reconstructions of cell morphology at different timepoints using the Neuron2(APP2) tracing plugin, which is working nicely. I then want to track changes in morphology as displacements of end points/tips in the reconstructions.

My question is: how can I extract the coordinate info of these dendrite tips from the SWC file Neuron2 plugin generates? I know if has the info available to it as the neuron_utilities->global_neuron_features plugin lists the number of tips. However, no column in the SWC file seems to identify point type (branch, tip, soma etc). 

Any help much appreciated!
James

We do not have this plugin in the released versions. But the source code of the plugin is under https://github.com/Vaa3D/vaa3d_tools/tree/master/hackathon/MK/Tip_marker_finder folder. You can build it by yourself.

Or you can provide the operating system (windows, mac or linux) you are using, we can build one for you to test.

Thanks for the fast reply. 

I am running Windows 10 64x. If you could build one to test that would be great, happy to give feedback.

BW,
James

Please check the attachment, unzip the attached file, and put the unzipped folder under C:\Program Files\Vaa3D-3.20\bin\plugins\ folder.

The tip finding plugin is under "Plug-In" --> "Tip_maker_finder". Please use "find_all" menu to generate all tips's location in a marker file.

Cheers,

Zhi

Holy moly you're fast. Thanks a lot - I'm added the plugin and it seems to be working great! I'll give some more detailed feedback when I've spent some time with it.

BW,
James