Add support for cell counting of grayscale and 12-bit images

image_utils.py

@@ -106,6 +106,14 @@ def convert_12bit_to_16bit(image):
     return (new_image * 16)
 
 
+def convert_16bit_to_8bit(image):
+    if image.dtype == 'uint8':
+        return image
+
+    new_image = image.copy()
+    return (new_image/256).astype('uint8')
+
+
 def generate_ome_tiff_support_data(data, metadata: dict):
     use_color = image_utils.is_color_image(data)
 

image_utils_kivy.py

@@ -11,6 +11,9 @@ def image_to_texture(image) -> Texture:
     # Vertical flip
     image = cv2.flip(image, 0)
 
+    if not image_utils.is_color_image(image=image):
+        image = cv2.cvtColor(image, cv2.COLOR_GRAY2BGR)
+
     buf = image.tostring()
 
     image_texture = Texture.create(

modules/cell_count.py

@@ -150,6 +150,12 @@ def _within_bounds(subject, subject_key, criteria, criteria_key):
 
     def process_image(self, image, settings, include_images=['filtered_contours']):
 
+        if image.dtype != np.uint8:
+            if image.dtype == np.uint16:
+                image = image_utils.convert_16bit_to_8bit(image=image)
+            else:
+                raise NotImplementedError(f"Unable to process image of type {image.dtype}")
+
         if include_images=='all':
             include_images = [
                 'gray',