Standard method for creating dendrograms from neuron morphology data?

Show & Tell
, , ,
1

I have been working to create some dendrograms from existing neuron morphology data we have in a TrakEM2 project (FIJI plugin). I have converted the .xml project data into the SWC format which seems to be a good starting point.

My question is what do researchers generally use to create dendrogram plots of neuron morphology? I have investigated several options (SNT in FIJI, closed source programs like Neurolucida etc.). However, these won’t work; SNT dendrogram maker does not appear to scale the tree lengths in the plot to the real length and Neurolucida does not support SWC data. I am considering CATMAID since the API indicates it can import SWC, but is there a “standard” or widely used method/program for creating dendrograms from existing data? Or is this something where each lab uses their own method?

Also, if anyone has worked with TrakEM2 .xml projects and figure generation I would be very interested in any scripts or advice.

2

Hello

For our work using reconstructions from electron microscopy we have written in Python our own code to generate dendrograms with synapse distributions. We will post back here when the code is made publicly available.

Best

Nuno

3

The IVSCC and FMOST features notebooks in our neuron_morphology repo may also have some examples that will be helpful. The link is: https://github.com/AllenInstitute/neuron_morphology/tree/dev/doc_template/notebooks

4

Ah yea that does look like a great starting point. Thank you!

5

Awesome, I will keep an eye out. Thanks!