Use the FAQ to create a 3-D image, if there are not too many of them. Let's say you have 50 images, each with a different wavelength, then you'd do
image3d = zeros(rows, columns, numImages);
for k = 1 : numImages
thisImage = imread(...
image3d(:,:,k) = thisImage;
Then scan the image, writing out each spectrum. You should have an array that says what the wavelength is for each image.
[rows, columns, numImages] = size(image3d);
count = 1;
for row = 1 : rows
for col = 1 : columns
thisSpectrum = image3d(row, col, :);
filename = sprintf('Spectrum %d.txt', count);
fileID = fopen(filename, 'wt');
fprintf(fileID, '%f, %f\n', wavelengths, thisSpectrum);