NEURON's colormap

How create a custom colormap

$(NEURONHOME)/lib/nrn.def contains lots of definitions, including the name of the file to be used for the color map, e.g. on my PC, nrn.def currently contains the lines

  //the color map for pseudocolor plotting for 3-D cells
  *shape_scale_file: $(NEURONHOME)/lib/shape.cm2

which means that shape.cm2 will be used.

This 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. The UNIX/Linux distribution comes with a couple of different scales. Here's 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 here's 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.

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