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.