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BlueBrain / NeuroMorphoVis

A lightweight, interactive, extensible and cross-platform framework for building, visualizing and analyzing digital reconstructions of neuronal morphology skeletons extracted from microscopy stacks.
https://portal.bluebrain.epfl.ch/
GNU General Public License v3.0
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Adding support to read three-dimensional somata and build them accurately. #120

Open marwan-abdellah opened 4 years ago

marwan-abdellah commented 4 years ago

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 commented 3 years ago

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

orena1 commented 3 years ago

Thanks @marwan-abdellah : tracingSAC1_aftLunch_16.swc.zip

marwan-abdellah commented 3 years ago

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

orena1 commented 3 years ago

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 commented 2 years ago

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

marwan-abdellah commented 2 years ago

@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? 2017-13-02-slice-2-cell-3-rotated_morphology_front-1 2017-13-02-slice-2-cell-3-rotated_morphology_front-2

Projections with closeup on 2017-13-02-slice-2-cell-3-rotated_morphology_front 2017-13-02-slice-2-cell-3-rotated_morphology_side 2017-13-02-slice-2-cell-3-rotated_morphology_top the soma

orena1 commented 2 years ago

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