Analyze colors of histological image in OD space

analyze_pixel_colors_OD.m

% (c) Jakob Nikolas Kather 2015
% contact: http://www.kather.me

% this code uses a histological image and performs the following steps
% - convert to optical density (OD) space (ref: Ruifrok et al. http://www.ncbi.nlm.nih.gov/pubmed/11531144)
% - plot image pixels in OD space
% - color pixels according to their original color
% this script can be used to visualize the color distribution of a given histological image

% get source image
imageURL = 'myImage.png';     % tested with images up to 400 x 400 px
imageRGB = imread(imageURL);

% show source image
figure();
imshow(imageRGB,[]);
set(gcf,'color','w');
title('original image (RGB)');
    
% convert to optical density (OD) space
imageOD = -log(double(imageRGB)+2);  % add 2 to avoid artifacts of log transform
imagePixelsRGB = reshape(double(imageRGB),[],3)/255;
imagePixelsOD = reshape(imageOD,[],3);
    
% plot pixels in OD space
figure();
scatter3(imagePixelsOD(:,1),imagePixelsOD(:,2),imagePixelsOD(:,3),10,imagePixelsRGB(:,:));
title('Pixels in OD space shown in their RGB color');
set(gcf,'color','w');