--- a
+++ b/matlab/gen_dataset2.m
@@ -0,0 +1,52 @@
+clear
+close all
+tic
+% path to folder containing training data
+old_trainset_folder = '/home/andrew/mitosis/MITOS/training/';
+map_folder = '/home/andrew/mitosis/maps/';
+
+% make training set directories
+new_trainset_folder = '/home/andrew/mitosis/mitosis-train-large/false/';
+if exist(new_trainset_folder, 'dir')
+    rmdir(new_trainset_folder, 's')
+end
+mkdir(new_trainset_folder)
+
+% count the total number of images for the waitbar
+N = 0;
+for j=1:5
+   % find the number of images in the folder
+    folder = [old_trainset_folder 'A' num2str(j-1, '%02u') '_v2/'];
+    n = length(dir([folder '*.csv']));
+    N = N + n;
+end
+
+% iterate over the twelve patients
+M = 0;
+P = 0;
+k = 0;
+h = waitbar(0,'Creating training set ... 0 %');
+for j=1:5
+    % find the number of images in the folder
+    folder = [old_trainset_folder 'A' num2str(j-1, '%02u') '_v2/'];
+    image_files = dir([folder '*.bmp']);
+    csv_files = dir([folder '*.csv']);
+    n = length(image_files);
+
+    % create new data set
+    for i=1:n
+        image_file = [folder image_files(i).name];
+        csv_file = [folder csv_files(i).name];
+        [pathstr,name,ext] = fileparts(image_file);
+        map_file = [map_folder name '.png'];
+        [m, p] = add_dataset2(image_file, csv_file, new_trainset_folder, map_file);
+        M = M + m;
+        P = P + p;
+        k = k + 1;
+        waitbar(k/N,h,['Creating training set ... ' num2str(100*k/N) ' %']);
+    end
+end
+
+close(h)
+toc
+disp(['Created ' num2str(P) ' window training images from ' num2str(N) ' large training images containing ' num2str(M) ' mitotic figures.'])
\ No newline at end of file