Improve explanations. Fix NMS default

app.py

@@ -44,7 +44,7 @@ main_app = ui.page_fluid(
                               accept=[".png", ".jpg", ".jpeg"]),
 
                 ui.input_slider("threshold", "Threshold for Discarding Overlapping Segmentations"
-                                             " (ADD a more descriptive label, and explain in text above).", 0, 1.0, 0.8),
+                                             " (ADD a more descriptive label, and explain in text above).", 0, 1.0, 0.7),
 
                 ui.tags.style(""" 
                     .irs.irs--shiny .irs-single { /* square with number */
@@ -119,15 +119,23 @@ app_ui = ui.page_fluid(
     ),
 
     ui.div(
+        ui.h4("Using this App"),
         ui.p(
-            "The protocol for taking images compatible with this model is available on ",
+            "This app is built to use a computer vision model to analyse images of orchid TZ tests and count the number of viable, non-viable and empty seeds."
+            " To use this app, upload images and click 'Analyse'."
+            " Segmented images will be displayed in the right-hand panel and results can be downloaded."),
+        ui.p(
+            "This app is built for use with specific types of images -- the protocol for taking images compatible with this model is available on ",
             ui.a("GitHub", href=protocol_url, target="_blank"),
-            ". The protocol is available in English, Indonesian, Thai, French, Spanish, Portuguese, Arabic, Mandarin, Malagasy and Japanese.",
-            " If you have any feedback on the app, please start a discussion on ",
-            ui.a("the HuggingFace space", href=discussion_url, target="_blank"),
-            ". Lorem ipsum dolor sit amet, consectetur adipiscing elit. Sed euismod, nunc ut laoreet placerat, urna purus rhoncus nisi, "
-            "vel facilisis magna sem sed tellus."
-        ),
+            ". The protocol is available in English, Indonesian, Thai, French, Spanish, Portuguese, Arabic, Mandarin, Malagasy and Japanese."),
+        ui.p(
+            "NMS set to 0.7 as this was found to be optimal for our data, but you can adjust this value in the slider and lower values may be useful for images"
+            "with more overlapping seeds."),
+        ui.p(" If you have any feedback on the app, please start a discussion on ",
+             ui.a("the HuggingFace space", href=discussion_url, target="_blank")
+             ),
+        ui.h4("Model Details and Accuracy"),
+        ui.p(),
         class_="body-bar"
     ),
     main_app,
@@ -138,6 +146,7 @@ app_ui = ui.page_fluid(
     #     id="page",
     # ),
     ui.div(
+        ui.h4("Acknowledgements"),
         ui.p(
             acknowledgement_text
         ),
@@ -264,14 +273,14 @@ def server(input, output, session: Session):
                     "viable": classes.count(0),
                     "non-viable": classes.count(1),
                     "empty": classes.count(2),
-                    "total": len(classes)
+                    "total": len(classes),
+                    'NMS threshold': input.threshold()
                 })
 
         # Update reactive value
         analysis_results.set(results)
         is_analyzing.set(False)  # Set analyzing flag to False when done
 
-    @output
     @render.ui
     def results_container():
         results = analysis_results.get()
@@ -321,7 +330,8 @@ def server(input, output, session: Session):
             "Viable": r.get("viable", ""),
             "Non-Viable": r.get("non-viable", ""),
             "Empty": r.get("empty", ""),
-            "Total": r.get("total", "")
+            "Total": r.get("total", ""),
+            'NMS Threshold': r.get('NMS threshold', ''),
         } for r in results])
 
         # Create in-memory CSV file

python_utils/get_model.py

@@ -68,7 +68,7 @@ def mask_nms(masks, scores, nms_threshold=0.5):
                 order.remove(j)
     return masks_kept
 
-def apply_nms(prediction, mask=False, cls_agnostic_nms=0.8):
+def apply_nms(prediction, mask=False, cls_agnostic_nms=0.7):
     from torchvision.ops import nms
     from detectron2.structures import Instances
     

styles.css

@@ -41,6 +41,7 @@ body {
   top: 0px;
   background: white;
     font-size: 1.1rem;
+    border-bottom: 2px solid #ddd;
 
   z-index: 10;
     margin-bottom: 10px;