Adding support to read three-dimensional somata and build them accurately.

[marwan-abdellah]

Received some SWC morphology file from @orena1. The file contains multiple soma contours at different depths-of-field. These contours are being handled for the moment as basal dendrites. We therefore must integrate a utility to identify the presence of 3d somata contours and reconstruct them accurately with metaball algorithm only. I think that the SoftBody simulation might not be that accurate.

[marwan-abdellah]

@orena1 I am working on implementing the multi-layer soma. Can you provide a sample SWC file with reconstructed soma?

[orena1]

Thanks @marwan-abdellah : tracingSAC1_aftLunch_16.swc.zip

[marwan-abdellah]

@orena1 The profile is projected on a single plane. Don't you have another one with real 3d profile.

[orena1]

Maybe this: Downloads.zip

The original reconstruction is asc, I transformed it to swc using this website: https://neuroinformatics.nl/HBP/morphology-viewer/

Thanks!

[orena1]

Also this 2017-13-02-slice-2-cell-3-rotated.swc.zip Thanks

[marwan-abdellah]

@orena1 I was able to load and render the neuron, but I don't even find any contours to the soma. Are you sure they exist?

Projections with closeup on the soma

[orena1]

Hi @marwan-abdellah , maybe it's unrelated, this is where I got the morphology from: http://neuromorpho.org/neuron_info.jsp?neuron_name=2017-16-05-slice-1-cell-6-rotated thanks