Update app.py

app.py

@@ -4,52 +4,52 @@ import numpy as np
 import cv2
 from PIL import Image
 
-# Load Cellpose pretrained model for cytoplasm
-model = models.CellposeModel(model_type='cyto')  # or 'nuclei' for nucleus
-
-def segment_and_count(image: Image.Image):
-    # Convert image to numpy RGB
-    img_np = np.array(image.convert("RGB"))
-
-    # Run Cellpose
-    masks, flows, styles, diams = model.eval(img_np, diameter=None, channels=[0, 0])  # grayscale or RGB
-
-    # Create overlay image
-    outlines = masks_to_overlay(img_np, masks)
-
-    # Count unique masks (excluding background=0)
-    unique_ids = np.unique(masks)
-    cell_count = len(unique_ids[unique_ids > 0])
-
-    return Image.fromarray(outlines), f"Detected cells: {cell_count}"
-
-# Draw outlines on image
+# Draw contours on original image
 def masks_to_overlay(image, masks):
     overlay = image.copy()
     contours, _ = cv2.findContours(masks.astype(np.uint8), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
     cv2.drawContours(overlay, contours, -1, (0, 255, 0), 1)
     return overlay
 
-# Gradio interface
+# Main processing function
+def segment_and_count(image: Image.Image, model_type: str, diameter: float):
+    img_np = np.array(image.convert("RGB"))
+    model = models.CellposeModel(model_type=model_type)
+    masks, _, _, _ = model.eval(img_np, diameter=None if diameter == 0 else diameter, channels=[0, 0])
+
+    overlay = masks_to_overlay(img_np, masks)
+    cell_count = len(np.unique(masks)) - 1  # exclude background 0
+
+    return Image.fromarray(overlay), f"Detected cells: {cell_count}"
+
+# Gradio UI
 with gr.Blocks() as demo:
-    gr.Markdown("## 🧬 Cell Counting with Cellpose")
+    gr.Markdown("Cell Counting with Cellpose (Interactive)")
+
     with gr.Row():
         with gr.Column():
             image_input = gr.Image(type="pil", label="Upload Microscopy Image")
-            run_btn = gr.Button("Count Cells")
-            count_output = gr.Textbox(label="Detected Cell Count")
+            model_selector = gr.Radio(["cyto", "nuclei"], label="Model Type", value="cyto")
+            diameter_slider = gr.Slider(0, 100, step=1, value=0, label="Cell Diameter (0 = Auto)")
+            run_btn = gr.Button("Run Cell Counting")
+            count_output = gr.Textbox(label="Cell Count")
+
             examples = gr.Examples(
                 examples=[
                     ["images/1.png"],
-                    ["images/2.jpg"],
-                    ["images/3.png"]
+                    ["images/1.png"],
+                    ["images/1.png"]
                 ],
                 inputs=[image_input],
                 label="Example Images"
             )
         with gr.Column():
-            image_output = gr.Image(type="pil", label="Cell Mask Overlay")
+            image_output = gr.Image(type="pil", label="Mask Overlay")
 
-    run_btn.click(fn=segment_and_count, inputs=image_input, outputs=[image_output, count_output])
+    run_btn.click(
+        fn=segment_and_count,
+        inputs=[image_input, model_selector, diameter_slider],
+        outputs=[image_output, count_output]
+    )
 
 demo.launch()