--- a
+++ b/scripts/Overlay.py
@@ -0,0 +1,83 @@
+from PyQt5.QtCore import QThread, pyqtSignal
+from skimage import color
+import numpy as np
+from natsort import natsorted
+import os
+from PIL import Image
+
+
+
+class Overlay(QThread):
+    info = pyqtSignal(str)
+    countChanged = pyqtSignal(int)
+    figures = pyqtSignal()
+    maxcuts = pyqtSignal(int)
+
+    def __init__(self, path, save=False):
+        super().__init__()
+        self.inputpath = path
+        self.save = save
+        self.threshold = None
+
+    def run(self, debug=False):
+        files = [f for f in natsorted(os.listdir(self.inputpath)) if not f.endswith("Overlay.png")]
+        self.maxcuts.emit(len([f for f in files if f.endswith('.png')]))
+        i = 0
+        for file in files:
+            if file.endswith('.png'):
+                self.info.emit("Preparing "+file)
+                print(file)
+
+                image = np.array(Image.open(self.inputpath+os.sep+file))[:, :, :3]
+
+                # image = mpimg.imread(self.inputpath+os.sep+file)[:,:,:3]
+                self.info.emit("Reading " + file)
+                self.current_image = image[::10, ::10]
+                self.figures.emit()
+                self.overlay(image,filename=file, debug=debug, save=self.save)
+                self.countChanged.emit(int(i))  # EMIT the loading bar
+            self.info.emit(file + " Overlay Done")
+            i += 1
+        self.info.emit("All Overlays Saved - ready")
+
+    def overlay(self, image, filename, debug=False, save=False):
+
+        img_hsv = color.rgb2hsv(image)
+        img_hue = img_hsv[:, :, 0]
+        image_sat = img_hsv[:, :, 1]
+        hue = np.logical_and(img_hue > 0.02, img_hue < 0.10)  # BROWN PIXELS BETWEEN 0.02 and 0.10
+        self.info.emit("Preparing thresholds for " + filename)
+        if self.threshold:
+            mask = np.logical_and(hue, image_sat > self.threshold)
+        else:
+            print("normal threshold")
+            mask = np.logical_and(hue, image_sat > 0.79)
+        mask = mask.astype(int)
+        self.current_image = mask[::10, ::10]
+        self.figures.emit()
+        self.info.emit("Creating overlay for " + filename)
+        alpha = 0.9
+        imbw = color.rgb2gray(image)
+        rows, cols = imbw.shape
+        # Construct a colour image to superimpose
+        color_mask = np.zeros((rows, cols, 3))
+        color_mask[:, :, 1] = mask  # Change to 0,1,2, for rgb
+        # Construct RGB version of grey-level image
+        img_color = np.dstack((imbw, imbw, imbw))
+        img_hsv = color.rgb2hsv(img_color)
+        color_mask_hsv = color.rgb2hsv(color_mask)
+        img_hsv[..., 0] = color_mask_hsv[..., 0]
+        img_hsv[..., 1] = color_mask_hsv[..., 1] * alpha
+        self.info.emit("Converting to RGB " + filename)
+        img_masked = color.hsv2rgb(img_hsv)
+        # TODO : emit this fig nicely
+        # self.current_image = img_masked[img_masked.shape[0]-200:img_masked.shape[0]+200,
+        #                      img_masked.shape[0]-200:img_masked.shape[0]+200]
+        # self.figures.emit()
+        print("displaying output")
+        self.info.emit("Saving " + filename)
+
+        imagesave = Image.fromarray((img_masked * 255).astype(np.uint8))
+        imagesave.save(self.inputpath+os.sep+filename+'_Overlay.png')
+
+        # mpimg.imsave(self.inputpath+os.sep+filename+'_Overlay.png', img_masked)
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