--- a
+++ b/HighResolutionSegmentationGeneration.py
@@ -0,0 +1,81 @@
+# %% Importing packages
+import numpy as np
+import cv2 as cv
+import matplotlib.pyplot as plt
+from matplotlib import patches
+plt.rcParams['figure.figsize'] = [5, 10]
+import os
+import tensorflow as tf
+from scipy.spatial import distance
+import time
+from glob import glob
+from joblib import Parallel, delayed
+from natsort import natsorted
+plt.rcParams['figure.figsize'] = [50, 150]
+
+# %% Citations
+#############################################################
+#############################################################
+
+
+
+# %% Defining Functions
+#############################################################
+#############################################################
+
+def process_file(file,
+                 original_seg_directory,
+                 high_res_seg_directory,
+                 save_directory):
+
+    try:
+        file_id = file.split('-')[0] + '_'
+        high_res_file = glob(high_res_seg_directory + file_id + '*.png')
+        assert len(high_res_file) > 0, \
+            f'could not find the pair to {file}, skipping file!'
+
+        original_image = cv.imread(file,cv.IMREAD_UNCHANGED)
+        original_seg = original_image[:,:,3]
+        high_res_seg = cv.imread(high_res_file[0],cv.IMREAD_UNCHANGED)
+        # 1: background, 2: muscle nuclei, 3: connective nuclei
+        # 4: muscle, 5: connective, 6: blood
+
+        original_seg[high_res_seg==1] = 0
+        original_seg[high_res_seg==6] = 7
+
+        original_image[:,:,3] = original_seg
+
+        new_name = file_id + 'ML5.png'
+
+        os.chdir(save_directory)
+        cv.imwrite(new_name,original_image)
+        os.chdir(original_seg_directory)
+
+
+    except AssertionError as e:
+        print(e)
+
+
+#############################################################
+#############################################################
+
+original_seg_directory = '/media/briancottle/Samsung_T5/ML_Dataset_3'
+high_res_seg_directory = '/home/briancottle/Research/Semantic_Segmentation/'\
+                        'High_Res_Ilastik_Segmentation_V10/'\
+                        'Ilastik_Segmentation_V10/'
+
+save_directory = '/media/briancottle/Samsung_T5/ML_Dataset_5'
+
+if not os.path.isdir(save_directory):
+    os.mkdir(save_directory)
+
+os.chdir(original_seg_directory)
+original_files = glob('*.png')
+
+contains_names_vascular = Parallel(
+    n_jobs=22, verbose=5)(delayed(process_file)
+    (file = name,
+    original_seg_directory = original_seg_directory,
+    high_res_seg_directory = high_res_seg_directory,
+    save_directory = save_directory) for name in original_files
+    )