Upload app.py

app.py

@@ -8,13 +8,12 @@ def analyze_image(image, min_size, circularity, do_necrosis=True):
     return Image.fromarray(processed_img), picname, excelname
 
 # Z-stack analysis function (adapt with your own logic)
-def analyze_zstack(images, min_size, circularity, do_necrosis=True):
-    # images: list of PIL images
-    # Plug in your own z-stack segmentation logic here
-    # Example stub: pass images as a list to your analyzer
+def analyze_zstack(images, min_size, circularity, distance_cutoff=30, overlap_cutoff=0.4, do_necrosis=True):
     import Organoid_Analyzer_AI_zstack2_HF as analyzer
     images = [Image.open(f.name) for f in images]
-    processed_img, picname, excelname = analyzer.main([images, min_size, circularity,do_necrosis])
+    processed_img, picname, excelname = analyzer.main(
+        [images, min_size, circularity, distance_cutoff, overlap_cutoff, do_necrosis]
+    )
     return Image.fromarray(processed_img), picname, excelname
 
 with gr.Blocks() as demo:
@@ -26,6 +25,8 @@ with gr.Blocks() as demo:
     image_input_multi = gr.File(file_count="multiple", type="filepath", label="Upload Z-Stack Images", visible=False)
     min_size_input = gr.Number(label="Minimum Organoid Size (pixels)", value=1000)
     circularity_input = gr.Number(label="Minimum Circularity", value=0.25)
+    zstack_distance_cutoff_input = gr.Number(label="Z-Stack Centroid Distance Cutoff (pixels)", value=30, visible=False)
+    zstack_overlap_cutoff_input = gr.Number(label="Z-Stack Colony Overlap Cutoff", value=0.4, visible=False)
     output_image = gr.Image(type="pil", label="Analyzed Image")
     output_file_img = gr.File(label="Download Image")
     output_file_excel = gr.File(label="Download results (Excel)")
@@ -34,25 +35,38 @@ with gr.Blocks() as demo:
     def toggle_inputs(z_stack_enabled):
         return (
             gr.update(visible=not z_stack_enabled),  # single input
-            gr.update(visible=z_stack_enabled)        # multi input
+            gr.update(visible=z_stack_enabled),      # multi input
+            gr.update(visible=z_stack_enabled),      # zstack_distance_cutoff_input
+            gr.update(visible=z_stack_enabled)       # zstack_overlap_cutoff_input
         )
 
     z_stack_checkbox.change(
-        toggle_inputs,
-        inputs=z_stack_checkbox,
-        outputs=[image_input_single, image_input_multi]
-    )
+    toggle_inputs,
+    inputs=z_stack_checkbox,
+    outputs=[
+        image_input_single, 
+        image_input_multi, 
+        zstack_distance_cutoff_input, 
+        zstack_overlap_cutoff_input])
 
-    def conditional_analyze(z_stack, single_image, multi_images, min_size, circularity, do_necrosis=True):
+    def conditional_analyze(z_stack, single_image, multi_images, min_size, circularity, do_necrosis, distance_cutoff, overlap_cutoff):
         if z_stack:
-            return analyze_zstack(multi_images, min_size, circularity,do_necrosis)
+            return analyze_zstack(multi_images, min_size, circularity, distance_cutoff, overlap_cutoff, do_necrosis)
         else:
-            return analyze_image(single_image, min_size, circularity,do_necrosis)
+            return analyze_image(single_image, min_size, circularity, do_necrosis)
 
     process_btn.click(
-        conditional_analyze,
-        inputs=[z_stack_checkbox, image_input_single, image_input_multi, min_size_input, circularity_input, do_necrosis_checkbox],
-        outputs=[output_image, output_file_img, output_file_excel]
-    )
+    conditional_analyze,
+    inputs=[
+        z_stack_checkbox,
+        image_input_single,
+        image_input_multi,
+        min_size_input,
+        circularity_input,
+        do_necrosis_checkbox,
+        zstack_distance_cutoff_input,
+        zstack_overlap_cutoff_input
+    ],
+    outputs=[output_image, output_file_img, output_file_excel])
 
 demo.launch()