Customizing NEURON's appearance

The appearance of NEURON's graphical windows is controlled by definitions in the file $(NEURONHOME)/lib/nrn.defaults (under MSWindows it's c:\nrnxx\lib\nrn.def where xx is the version number). This is a plain ASCII file that you can edit with a text editor.

What's $(NEURONHOME)?
Start NEURON, and at the oc> prompt type
    neuronhome()
On my Linux box, this tells me that $(NEURONHOME) is
    /usr/local/nrn/share/nrn
and sure enough, nrn.defaults is in
    /usr/local/nrn/share/nrn/lib

How to change the background color used in shape plots and other graphs

Change the lines
   *Scene_background: #ffffff
   *Scene_foreground: #000000
to whatever you like. For example,
   *Scene_background: #000000
   *Scene_foreground: #ffffff
makes the background black and the axes and black traces white.

How create a custom colormap

The lines
//the color map for pseudocolor plotting for 3-D cells
*shape_scale_file: $(NEURONHOME)/lib/shape.cm2
tell you which file contains the colormap that will be used (under MSWin it's c:\nrnxx\lib\shape.cm2 ). The colormap file is read when NEURON is initially launched. If the file doesn't exist, NEURON uses a default scale.

The colormap file is plain ASCII, with one set of RGB values per line. NEURON comes with a couple of different scales in files shape.cm1 and shape.cm2.

Here's another one you might try:

95      0       95      
111     0       111
127     0       143
143     0       127
159     0       111
175     0       95
191     0       79
207     0       63
207     31      47
223     47      47
239     63      31
255     79      15
255     95      7
255     111     0
255     127     0
255     143     0
255     159     0
255     175     0
255     191     0
255     207     0
255     223     0
255     239     0
255     247     0
255     255     0
255     255     255

and yet another:

111     0       111
143     0       127
175     0       95
207     0       63
223     47      47
255     79      15
255     111     0
255     143     0
255     175     0
255     207     0
255     239     0
255     255     0
255     255     200

but you can make up anything you like.

Before you start cooking up your own schemes, you might want to look at the following:
"How NOT to Lie with Visualization" by Rogowitz & Treinish
"A Rule-based Tool for Assisting Colormap Selection" by Bergman et al.