Fixed a small bug in the viewer and added the viewer notebook

angelolab · Jan 9, 2025 · f7170b4 · f7170b4
1 parent 31b821d
commit f7170b4
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Showing 2 changed files with 244 additions and 3 deletions.
diff --git a/src/nimbus_inference/viewer_widget.py b/src/nimbus_inference/viewer_widget.py
@@ -100,8 +100,6 @@ def overlay(self, composite_image, add_boundaries=False, add_overlay=False):
             val = (np.max(composite_image, axis=(0,1))*0.5).astype(composite_image.dtype)
             val = np.min(val[val>0])
             composite_image[seg_boundaries] = [val]*3
-        else:
-            seg_boundaries = None
         return composite_image, seg_boundaries
 
     def create_composite_from_dataset(self, path_dict):
@@ -390,6 +388,12 @@ def __init__(
             disabled=False
         )
         self.dataset_select.observe(self.select_dataset, names='value')
+        self.overlay_checkbox = widgets.Checkbox(
+            value=False,
+            description='Overlay segmentations',
+            disabled=False
+        )
+
 
     def layout(self):
         """Creates layout for viewer."""
@@ -403,7 +407,6 @@ def layout(self):
                 self.dataset_select,
                 self.fov_select,
                 channel_selectors,
-                self.overlay_checkbox,
                 self.update_button
             # ]),
         ])