Upload app.py

app.py

@@ -1354,8 +1354,10 @@ def build_tab(tab_index, masks_state, image_state, result_state):
 
                 use_min_filter = gr.Checkbox(
                     label="Enable minimum size filter",
-                    value=False,
-                    info="Remove objects smaller than the threshold below"
+                    value=True,
+                    info="Remove objects smaller than the threshold below. "
+                         "At 0 the app uses its own recommendation "
+                         "(25th percentile of detected object sizes)."
                 )
                 min_size_slider = gr.Slider(
                     minimum=0,
@@ -1363,7 +1365,7 @@ def build_tab(tab_index, masks_state, image_state, result_state):
                     value=0,
                     step=10,
                     label="Minimum Cell Size (pixels)",
-                    interactive=False,
+                    interactive=True,
                 )
                 min_size_recommendation = gr.Markdown(
                     value="*Run segmentation to see recommended minimum*",
@@ -1396,11 +1398,11 @@ def build_tab(tab_index, masks_state, image_state, result_state):
                 gr.Markdown("### Stereological Counting")
                 use_stereo = gr.Checkbox(
                     label="Enable Stereological Counting",
-                    value=False,
+                    value=True,
                     info="Applied to the segmentation above — no re-segmenting needed"
                 )
 
-                with gr.Group(visible=False) as stereo_controls:
+                with gr.Group(visible=True) as stereo_controls:
                     gr.Markdown("""
                     **Stereological Counting Rules:**
                     - Cells touching LEFT or TOP exclusion zones are EXCLUDED
@@ -1416,7 +1418,7 @@ def build_tab(tab_index, masks_state, image_state, result_state):
                     left_excl = gr.Slider(
                         minimum=0,
                         maximum=50,
-                        value=10,
+                        value=1,
                         step=1,
                         label="Left Exclusion Width (%)",
                         info="Width of left exclusion zone"
@@ -1425,7 +1427,7 @@ def build_tab(tab_index, masks_state, image_state, result_state):
                     top_excl = gr.Slider(
                         minimum=0,
                         maximum=50,
-                        value=10,
+                        value=1,
                         step=1,
                         label="Top Exclusion Width (%)",
                         info="Width of top exclusion zone"
@@ -1471,6 +1473,21 @@ def build_tab(tab_index, masks_state, image_state, result_state):
 
         # ---- Event handlers ------------------------------------------------
 
+        def on_model_change(model_choice):
+            """Hemocytometer counting is only unbiased with the stereological
+            rules applied, so selecting that model turns them on. Left as a
+            normal checkbox rather than locked, so the setting can still be
+            switched off deliberately."""
+            if model_choice == "Hemocytometer Model":
+                return gr.update(value=True), gr.update(visible=True)
+            return gr.update(), gr.update()
+
+        model_dropdown.change(
+            fn=on_model_change,
+            inputs=[model_dropdown],
+            outputs=[use_stereo, stereo_controls]
+        )
+
         use_stereo.change(
             fn=toggle_stereological_mode,
             inputs=[use_stereo],