How can I create a .mat file in which I store the colour images and the corresponding histograms?

Make a 2D array of 1024 column by 50 rows

output = zeros(totalNumberOfImages, 1024); % Initialize
for imageNumber = 1 : totalNumberOfImages
  % Compute the 4 histograms...
  % Now save them
  output(imageNumber, :) = [count1, count2, count3, count4];
endM

do for all images, then save output (or whatever you want to call it) to a mat file

save(matFullFileName, 'output');