Update app.py

app.py

@@ -447,7 +447,7 @@ with gr.Blocks(
     masks_state = gr.State(value=None)
     image_state = gr.State(value=None)
 
-    with gr.Tab("Cell Quantification"):
+    with gr.Tab("Tab 1"):
         gr.Markdown("Run segmentation")
 
         with gr.Row():
@@ -616,6 +616,175 @@ with gr.Blocks(
             inputs=[blue_threshold1, masks_state, image_state],
             outputs=[viability_overlay1, live_count_output1, dead_count_output1, viability_percent_output1, viability_info1]
         )
+    with gr.Tab("Tab 2"):
+        gr.Markdown("Run segmentation")
+
+        with gr.Row():
+            with gr.Column():
+                img_input2 = gr.Image(
+                    type="pil",
+                    label="Microscopy image",
+                    image_mode="RGB",
+                    height=512
+                )
+                    
+                model_dropdown2 = gr.Dropdown(
+                    choices=list(MODEL_OPTIONS.keys()),
+                    label="Select Model",
+                    value="Hemocytometer Model"
+                )
+                
+                min_size_slider2 = gr.Slider(
+                    minimum=0,
+                    maximum=500,
+                    value=0,
+                    step=10,
+                    label="Minimum Cell Size (pixels). Leave at zero for automated recommendation",
+                )
+                
+                max_size_slider2 = gr.Slider(
+                    minimum=0,
+                    maximum=10000,
+                    value=10000,
+                    step=10,
+                    label="Maximum Cell Size (pixels)",
+                )
+                
+                # Stereological counting option
+                gr.Markdown("### Stereological Counting")
+                use_stereology_checkbox2 = 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_controls:
+                    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_preview2 = gr.Image(
+                        type="pil",
+                        label="Exclusion Zone Preview (Red = Excluded)",
+                        height=500
+                    )
+                    
+                    left_exclusion_slider2 = gr.Slider(
+                        minimum=0,
+                        maximum=50,
+                        value=10,
+                        step=1,
+                        label="Left Exclusion Width (%)",
+                        info="Width of left exclusion zone"
+                    )
+                    
+                    top_exclusion_slider2 = gr.Slider(
+                        minimum=0,
+                        maximum=50,
+                        value=10,
+                        step=1,
+                        label="Top Exclusion Width (%)",
+                        info="Width of top exclusion zone"
+                    )
+                
+                segment_btn2 = gr.Button("🔬 Run Segmentation", variant="primary", size="lg")
+
+            with gr.Column():
+                cell_count_output2 = gr.Number(label="Total Cells Detected", precision=0)
+                confluency_output2 = gr.Number(label="Confluency (%)", precision=1)
+                overlay_output2 = gr.Image(type="pil", label="Segmentation Result")
+                info_output2 = gr.Textbox(label="Processing Info", lines=4)
+
+        # Viability Assessment Section
+        with gr.Group(visible=False) as viability_section1:
+            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_threshold2 = 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_output2 = gr.Number(label="Live Cells (Green)", precision=0)
+                    dead_count_output2 = gr.Number(label="Dead Cells (Red)", precision=0)
+
+            viability_overlay2 = gr.Image(type="pil", label="Viability Assessment (Green=Live, Red=Dead)")
+            viability_percent_output2 = gr.Number(label="Viability (%)", precision=1)
+            viability_info2 = gr.Textbox(label="Analysis Results", lines=5)
+
+        # Event handlers
+        
+        # Toggle stereological controls visibility
+        use_stereology_checkbox2.change(
+            fn=toggle_stereological_mode,
+            inputs=[use_stereology_checkbox],
+            outputs=[stereology_controls]
+        )
+        
+        # Update exclusion preview when image is uploaded or sliders change
+        img_input2.change(
+            fn=update_exclusion_preview,
+            inputs=[img_input2, left_exclusion_slider2, top_exclusion_slider2],
+            outputs=[exclusion_preview]
+        )
+        
+        left_exclusion_slider2.change(
+            fn=update_exclusion_preview,
+            inputs=[img_input2, left_exclusion_slider2, top_exclusion_slider2],
+            outputs=[exclusion_preview]
+        )
+        
+        top_exclusion_slider2.change(
+            fn=update_exclusion_preview,
+            inputs=[img_input2, left_exclusion_slider2, top_exclusion_slider2],
+            outputs=[exclusion_preview]
+        )
+        
+        # Run segmentation
+        segment_btn2.click(
+            fn=run_segmentation,
+            inputs=[
+                img_input, 
+                model_dropdown2, 
+                min_size_slider2, 
+                max_size_slider2,
+                use_stereology_checkbox2,
+                left_exclusion_slider2,
+                top_exclusion_slider2
+            ],
+            outputs=[
+                cell_count_output2, 
+                overlay_output2, 
+                info_output2, 
+                viability_section2, 
+                masks_state, 
+                image_state, 
+                confluency_output2, 
+                min_size_slider2
+            ]
+        ).then(  # Chain the initial viability assessment after segmentation
+            fn=update_viability_realtime,
+            inputs=[blue_threshold2, masks_state, image_state],
+            outputs=[viability_overlay2, live_count_output2, dead_count_output2, viability_percent_output2, viability_info2]
+        )
+
+        # Slider changes update viability in real-time
+        blue_threshold2.change(
+            fn=update_viability_realtime,
+            inputs=[blue_threshold2, masks_state, image_state],
+            outputs=[viability_overlay2, live_count_output2, dead_count_output2, viability_percent_output2, viability_info2]
+        )
 
     # Instructions
     with gr.Accordion("Instructions", open=False):