Helper script that generates a library of png from a collection of multi tiffs

script.m

patterns = { 'nuc', 'endo', 'mit', 'lyso' };

for i=1:length(patterns)
    pattern = patterns{i};
    disp( pattern );
    mkdir(pattern);
    files = dir( '*.tif' );
    for j=1:1:length(files)
        file = files(j).name;
        disp( [ 'Opening ' file ] );
        filename = strcat(pattern, sprintf('%05d',j), '.png' );
        img = tif2img( file );
        img2 = cat( 3, cat( 3, img(:,:,1), img(:,:,2) ), img(:,:,2+i) );
        position = [5 5];
        footnote = [ pattern num2str(j) '.tif'];
        try
            img2 = insertText(img2,position,footnote);
        catch
            disp( 'Unable to insert text' );
        end
        img2 = uint8( img2 );
        filename = [ pwd filesep pattern filesep ...
            filename ];
        disp( [ 'Saving ' filename ] );
        imwrite( img2, filename );
    end
end