Update app.py

app.py

@@ -955,175 +955,7 @@ with gr.Blocks(
             inputs=[blue_threshold3, masks_state, image_state],
             outputs=[viability_overlay3, live_count_output3, dead_count_output3, viability_percent_output3, viability_info3]
         )
-    with gr.Tab("Tab 3"):
-        gr.Markdown("Run segmentation")
-
-        with gr.Row():
-            with gr.Column():
-                img_input3 = gr.Image(
-                    type="pil",
-                    label="Microscopy image",
-                    image_mode="RGB",
-                    height=512
-                )
-                    
-                model_dropdown3 = gr.Dropdown(
-                    choices=list(MODEL_OPTIONS.keys()),
-                    label="Select Model",
-                    value="Hemocytometer Model"
-                )
-                
-                min_size_slider3 = gr.Slider(
-                    minimum=0,
-                    maximum=500,
-                    value=0,
-                    step=10,
-                    label="Minimum Cell Size (pixels). Leave at zero for automated recommendation",
-                )
-                
-                max_size_slider3 = gr.Slider(
-                    minimum=0,
-                    maximum=10000,
-                    value=10000,
-                    step=10,
-                    label="Maximum Cell Size (pixels)",
-                )
-                
-                # Stereological counting option
-                gr.Markdown("### Stereological Counting")
-                use_stereology_checkbox3 = gr.Checkbox(
-                    label="Enable Stereological Counting",
-                    value=False,
-                    info="Use unbiased stereological rules for cell counting"
-                )
-                
-                # Stereological controls (initially hidden)
-                with gr.Group(visible=False) as stereology_controls3:
-                    gr.Markdown("""
-                    **Stereological Counting Rules:**
-                    - Cells touching LEFT or TOP exclusion zones are EXCLUDED
-                    - Cells touching RIGHT or BOTTOM edges are INCLUDED
-                    - This provides unbiased counting for quantification
-                    """)
-                    
-                    exclusion_preview3 = gr.Image(
-                        type="pil",
-                        label="Exclusion Zone Preview (Red = Excluded)",
-                        height=500
-                    )
-                    
-                    left_exclusion_slider3 = gr.Slider(
-                        minimum=0,
-                        maximum=50,
-                        value=10,
-                        step=1,
-                        label="Left Exclusion Width (%)",
-                        info="Width of left exclusion zone"
-                    )
-                    
-                    top_exclusion_slider3 = gr.Slider(
-                        minimum=0,
-                        maximum=50,
-                        value=10,
-                        step=1,
-                        label="Top Exclusion Width (%)",
-                        info="Width of top exclusion zone"
-                    )
-                
-                segment_btn3 = gr.Button("🔬 Run Segmentation", variant="primary", size="lg")
-
-            with gr.Column():
-                cell_count_output3 = gr.Number(label="Total Cells Detected", precision=0)
-                confluency_output3 = gr.Number(label="Confluency (%)", precision=1)
-                overlay_output3 = gr.Image(type="pil", label="Segmentation Result")
-                info_output3 = gr.Textbox(label="Processing Info", lines=4)
-
-        # Viability Assessment Section
-        with gr.Group(visible=False) as viability_section3:
-            gr.Markdown("### Viability Assessment (Trypan Blue)")
-            gr.Markdown("Adjust the threshold to classify cells as live (green) or dead (red).")
-
-            with gr.Row():
-                with gr.Column():
-                    blue_threshold3 = gr.Slider(
-                        minimum=0,
-                        maximum=100,
-                        value=25,
-                        step=1,
-                        label="Blue Threshold (%)",
-                        info="Higher values = more selective for blue cells"
-                    )
-
-                with gr.Column():
-                    live_count_output3 = gr.Number(label="Live Cells (Green)", precision=0)
-                    dead_count_output3 = gr.Number(label="Dead Cells (Red)", precision=0)
-
-            viability_overlay3 = gr.Image(type="pil", label="Viability Assessment (Green=Live, Red=Dead)")
-            viability_percent_output3 = gr.Number(label="Viability (%)", precision=1)
-            viability_info3 = gr.Textbox(label="Analysis Results", lines=5)
-
-        # Event handlers
-        
-        # Toggle stereological controls visibility
-        use_stereology_checkbox3.change(
-            fn=toggle_stereological_mode,
-            inputs=[use_stereology_checkbox3],
-            outputs=[stereology_controls3]
-        )
-        
-        # Update exclusion preview when image is uploaded or sliders change
-        img_input3.change(
-            fn=update_exclusion_preview,
-            inputs=[img_input3, left_exclusion_slider3, top_exclusion_slider3],
-            outputs=[exclusion_preview3]
-        )
-        
-        left_exclusion_slider3.change(
-            fn=update_exclusion_preview,
-            inputs=[img_input3, left_exclusion_slider3, top_exclusion_slider3],
-            outputs=[exclusion_preview3]
-        )
-        
-        top_exclusion_slider3.change(
-            fn=update_exclusion_preview,
-            inputs=[img_input3, left_exclusion_slider3, top_exclusion_slider3],
-            outputs=[exclusion_preview3]
-        )
-        
-        # Run segmentation
-        segment_btn3.click(
-            fn=run_segmentation,
-            inputs=[
-                img_input3, 
-                model_dropdown3, 
-                min_size_slider3, 
-                max_size_slider3,
-                use_stereology_checkbox3,
-                left_exclusion_slider3,
-                top_exclusion_slider3
-            ],
-            outputs=[
-                cell_count_output3, 
-                overlay_output3, 
-                info_output3, 
-                viability_section3, 
-                masks_state, 
-                image_state, 
-                confluency_output3, 
-                min_size_slider3
-            ]
-        ).then(  # Chain the initial viability assessment after segmentation
-            fn=update_viability_realtime,
-            inputs=[blue_threshold3, masks_state, image_state],
-            outputs=[viability_overlay3, live_count_output3, dead_count_output3, viability_percent_output3, viability_info3]
-        )
-
-        # Slider changes update viability in real-time
-        blue_threshold3.change(
-            fn=update_viability_realtime,
-            inputs=[blue_threshold3, masks_state, image_state],
-            outputs=[viability_overlay3, live_count_output3, dead_count_output3, viability_percent_output3, viability_info3]
-        )
+    
     with gr.Tab("Tab 4"):
         gr.Markdown("Run segmentation")