editing neuron skeletons generated in rgl.plot3d

[Arthur Zhao]

Hi all,

i plotted (rgl.plot3d) a neuron in R and exported it (rgl.postscript) as a pdf file. But when i opened it in Adobe illustrator, it appeared as a large number of small segments (not all connected). This makes further editing rather difficult. 

What's the common or preferred method for making nice neuron figures ? 

Best,

arthur

[Gregory Jefferis]

I always generate pngs with plot3d / snapshot3d. You have to watch out for antialias settings for your graphics system or you can get staircase artefacts. Note that you can set a large and defined plot size with par3d. See also nview3d for some examples of setting viewpoints.

Unfortunately the vector output has limitations. I have used it in the past with neurons alone but rendering surfaces as well was not that reliable. Furthermore you are then at the mercy of the pdf viewer (these are not always consistent in my experience for this kind of scene) and if you have a complex scene they can blow up trying to render all your neuron segments. So my conclusion is to render the scene to a raster image.

When I want to make prettier visualisations, I send the neurons to Amira and then render them in volumetric mode (ie cylinders rather than lines). There is a package nat.amira which helps. Alternatives include paraview (which can open Vtk and obj files for neurons and surfaces) and blender. 

Best,

Greg. 

Sent from my iPhone

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