Update app.py

app.py

@@ -755,7 +755,7 @@ with gr.Blocks(
         segment_btn2.click(
             fn=run_segmentation,
             inputs=[
-                img_input, 
+                img_input2, 
                 model_dropdown2, 
                 min_size_slider2, 
                 max_size_slider2,
@@ -786,6 +786,514 @@ with gr.Blocks(
             outputs=[viability_overlay2, live_count_output2, dead_count_output2, viability_percent_output2, viability_info2]
         )
 
+    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 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")
+
+        with gr.Row():
+            with gr.Column():
+                img_input4 = gr.Image(
+                    type="pil",
+                    label="Microscopy image",
+                    image_mode="RGB",
+                    height=512
+                )
+                    
+                model_dropdown4 = gr.Dropdown(
+                    choices=list(MODEL_OPTIONS.keys()),
+                    label="Select Model",
+                    value="Hemocytometer Model"
+                )
+                
+                min_size_slider4 = gr.Slider(
+                    minimum=0,
+                    maximum=500,
+                    value=0,
+                    step=10,
+                    label="Minimum Cell Size (pixels). Leave at zero for automated recommendation",
+                )
+                
+                max_size_slider4 = gr.Slider(
+                    minimum=0,
+                    maximum=10000,
+                    value=10000,
+                    step=10,
+                    label="Maximum Cell Size (pixels)",
+                )
+                
+                # Stereological counting option
+                gr.Markdown("### Stereological Counting")
+                use_stereology_checkbox4 = 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_controls4:
+                    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_preview4 = gr.Image(
+                        type="pil",
+                        label="Exclusion Zone Preview (Red = Excluded)",
+                        height=500
+                    )
+                    
+                    left_exclusion_slider4 = gr.Slider(
+                        minimum=0,
+                        maximum=50,
+                        value=10,
+                        step=1,
+                        label="Left Exclusion Width (%)",
+                        info="Width of left exclusion zone"
+                    )
+                    
+                    top_exclusion_slider4 = gr.Slider(
+                        minimum=0,
+                        maximum=50,
+                        value=10,
+                        step=1,
+                        label="Top Exclusion Width (%)",
+                        info="Width of top exclusion zone"
+                    )
+                
+                segment_btn4 = gr.Button("🔬 Run Segmentation", variant="primary", size="lg")
+
+            with gr.Column():
+                cell_count_output4 = gr.Number(label="Total Cells Detected", precision=0)
+                confluency_output4 = gr.Number(label="Confluency (%)", precision=1)
+                overlay_output4 = gr.Image(type="pil", label="Segmentation Result")
+                info_output4 = gr.Textbox(label="Processing Info", lines=4)
+
+        # Viability Assessment Section
+        with gr.Group(visible=False) as viability_section4:
+            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_threshold4 = 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_output4 = gr.Number(label="Live Cells (Green)", precision=0)
+                    dead_count_output4 = gr.Number(label="Dead Cells (Red)", precision=0)
+
+            viability_overlay4 = gr.Image(type="pil", label="Viability Assessment (Green=Live, Red=Dead)")
+            viability_percent_output4 = gr.Number(label="Viability (%)", precision=1)
+            viability_info4 = gr.Textbox(label="Analysis Results", lines=5)
+
+        # Event handlers
+        
+        # Toggle stereological controls visibility
+        use_stereology_checkbox4.change(
+            fn=toggle_stereological_mode,
+            inputs=[use_stereology_checkbox4],
+            outputs=[stereology_controls4]
+        )
+        
+        # Update exclusion preview when image is uploaded or sliders change
+        img_input4.change(
+            fn=update_exclusion_preview,
+            inputs=[img_input4, left_exclusion_slider4, top_exclusion_slider4],
+            outputs=[exclusion_preview4]
+        )
+        
+        left_exclusion_slider4.change(
+            fn=update_exclusion_preview,
+            inputs=[img_input4, left_exclusion_slider4, top_exclusion_slider4],
+            outputs=[exclusion_preview4]
+        )
+        
+        top_exclusion_slider4.change(
+            fn=update_exclusion_preview,
+            inputs=[img_input4, left_exclusion_slider4, top_exclusion_slider4],
+            outputs=[exclusion_preview4]
+        )
+        
+        # Run segmentation
+        segment_btn4.click(
+            fn=run_segmentation,
+            inputs=[
+                img_input4, 
+                model_dropdown4, 
+                min_size_slider4, 
+                max_size_slider4,
+                use_stereology_checkbox4,
+                left_exclusion_slider4,
+                top_exclusion_slider4
+            ],
+            outputs=[
+                cell_count_output4, 
+                overlay_output4, 
+                info_output4, 
+                viability_section4, 
+                masks_state, 
+                image_state, 
+                confluency_output4, 
+                min_size_slider4
+            ]
+        ).then(  # Chain the initial viability assessment after segmentation
+            fn=update_viability_realtime,
+            inputs=[blue_threshold4, masks_state, image_state],
+            outputs=[viability_overlay4, live_count_output4, dead_count_output4, viability_percent_output4, viability_info4]
+        )
+
+        # Slider changes update viability in real-time
+        blue_threshold3.change(
+            fn=update_viability_realtime,
+            inputs=[blue_threshold4, masks_state, image_state],
+            outputs=[viability_overlay4, live_count_output4, dead_count_output4, viability_percent_output4, viability_info4]
+        )
+
     # Instructions
     with gr.Accordion("Instructions", open=False):
         gr.Markdown("""