Update app.py

app.py

@@ -138,17 +138,19 @@ def cellpose_segment(img_input):
     flows = flows[0]
     # masks = np.zeros(img.shape[:2])
     # flows = np.zeros_like(img)
+
+    outpix = plot_outlines(img_input, masks)
+    overlay = plot_overlay(img_input, masks)
+    
     target_size = (img_input.shape[1], img_input.shape[0])
     if (target_size[0]!=img.shape[1] or target_size[1]!=img.shape[0]):
         # scale it back to keep the orignal size
         masks = cv2.resize(masks.astype('uint16'), target_size, interpolation=cv2.INTER_NEAREST).astype('uint16')
-        flows = cv2.resize(flows.astype('float32'), target_size).astype('uint8')
+        #flows = cv2.resize(flows.astype('float32'), target_size).astype('uint8')
     
-    outpix = plot_outlines(img_input, masks)
-    overlay = plot_overlay(img_input, masks)
-
-    crand = .2 + .8 * np.random.rand(np.max(masks.flatten()).astype('int')+1,).astype('float32')
-    crand[0] = 0
+    
+    #crand = .2 + .8 * np.random.rand(np.max(masks.flatten()).astype('int')+1,).astype('float32')
+    #crand[0] = 0
 
     #overlay = Image.fromarray(overlay)
     #flows = Image.fromarray(flows)    
@@ -183,17 +185,24 @@ with gr.Blocks(title = "Hello",
 
     with gr.Row():
         with gr.Column(scale=2):
+            gr.HTML("""<div style="font-family:'Times New Roman', 'Serif'; font-size:16pt; font-weight:bold; text-align:center; color:white;">Cellpose-SAM for cellular segmentation</div>""")
+            gr.HTML("""<h4 style="color:white;">You may need to refresh/login for 5 minutes of free GPU compute time/day. </h4>""")
+            gr.HTML("""<h4 style="color:white;">"pip install cellpose" for full functionality. </h4>""")
+
             input_image = gr.Image(label = "Input image", type = "numpy")
             send_btn = gr.Button("Run Cellpose-SAM")
-            with gr.Column(scale=1):
-                down_btn = gr.DownloadButton("Download masks (TIFF)", visible=False)
-            with gr.Column(scale=1):
+            with gr.Row():
+                down_btn = gr.DownloadButton("Download masks (TIFF)", visible=False)            
                 down_btn2 = gr.DownloadButton("Download outlines (PNG)", visible=False)
 
+            gr.HTML("""<li><a href="https://github.com/MouseLand/cellpose" target="_blank">github page for cellpose</a>""")
+            gr.HTML("""<li><a style="color:white;" href="https://github.com/MouseLand/cellpose" target="_blank">Cellpose-SAM paper</a>""")
+
+
         with gr.Column(scale=2):            
-            img_outlines = gr.Image(label = "Output image", type = "pil")            
-            img_overlay = gr.Image(label = "Output image", type = "numpy")            
-            flows = gr.Image(label = "Output image", type = "numpy")
+            img_outlines = gr.Image(label = "Outlines", type = "pil")            
+            img_overlay = gr.Image(label = "Overlay", type = "numpy")            
+            flows = gr.Image(label = "Cellpose flows", type = "numpy")
             #masks = gr.Image(label = "Output image", type = "numpy")