Updated

Author: JBeckwith

src/AnalysisFunctions.py

@@ -1836,9 +1836,9 @@ def number_of_puncta_per_segmented_cell_with_threshold(
             protein_string (string): will use this to find corresponding files
             imtype (string): image type previously analysed
             aboveT (int): do the calculation above or below threshold
-            z_project_first (boolean, boolean): if both True (default), does a z 
+            z_project_first (boolean, boolean): if both True (default), does a z
                                     projection before
-                                    thresholding cell size. 
+                                    thresholding cell size.
                                     If both false, does not z project and
                                     then does the analysis per z plane.
             q1 (float): if float, adds in IQR filter
@@ -1891,7 +1891,11 @@ def number_of_puncta_per_segmented_cell_with_threshold(
                         upper_cell_size_threshold=upper_cell_size_threshold,
                         z_project=z_project_first,
                     )
-                    image_size = cell_mask.shape if len(cell_mask.shape) < 2 else cell_mask.shape[:-1]
+                    image_size = (
+                        cell_mask.shape
+                        if len(cell_mask.shape) < 2
+                        else cell_mask.shape[:-1]
+                    )
 
                     x_m = centroids[:, 0]
                     y_m = centroids[:, 1]