Brain colours

code underlying the colormaps in the paper Data visualization for inference in tomographic brain imaging EJN 2019

Background

Colour maps used in scientific litterature must reflect the underlying data. The problem with many maps is that while underlying values are represented by different colours (as red-green-blue values) they are not perceived as such. This is explained by the fact that human do not perceive colours in a uniform fashion, and that most colour maps have colour and luminance confounded. One solution is the make map in CIELAB (Luminance A:red-green B:blue-yellow) space. I share here usual maps but with luminance fixed (linearized as much as possible) based on Peter Kovesi paper and code: 'Good Colour Maps: How to Design Them' arXiv:1509.03700

Data and Code

This repository contains the Malab code used to generate colour maps as well as the maps as .csv, .mat (Matlab/SPM), .cmap (FSLeyes) and .lut (MRIcron, ImageJ) files. Brain colours data are made available under the Open Data Commons Attribution License.

Dependencies

• Initial colour maps are taken from MRIcron
• The luminance is fixed using equalisecolourmap.m and related files provided by Peter Kovesi. Note this also depends on deltaE2000.m.
• The vizualization is done using are RGB to LAB space converion using the colorspace.m and colormapline.m functions from Matteo Niccoli