Fixed skeleton size and image padding

pyproject.toml

@@ -34,6 +34,8 @@ dependencies = [
     "torch",
     "tensorflow==2.16.1",
     "skan"
+    "ultralytics"
+    "yolov5"
 ]
 
 # Required for documentation: tabs, sphinx_sphinx, myst_parser, sphinx_rtd_theme

src/microglia_analyzer/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "1.0.1"
+__version__ = "1.0.2"
 
 import re
 

src/microglia_analyzer/_widget.py

@@ -334,7 +334,7 @@ def run_batch(self):
         self.n_images = len(self.get_all_tiff_files(self.sources_folder))
         self.pbr = progress()
         self.pbr.set_description("Running on folder...")
-        self.run_batch_button.setText(f"▶ Run batch ({str(1).zfill(2)}/{self.n_images})")
+        self.run_batch_button.setText(f"▶ Run batch ({str(1).zfill(2)}/{str(self.n_images).zfill(2)})")
         self.set_active_ui(False)
         self.thread = QThread()
 
@@ -460,7 +460,7 @@ def update_pbr(self, text, current, total):
         #     self.pbr.reset(total=total)
         #     self.total = total
         if (self.n_images > 0):
-            self.run_batch_button.setText(f"▶ Run batch ({str(current+1).zfill(2)}/{self.n_images})")
+            self.run_batch_button.setText(f"▶ Run batch ({str(current+1).zfill(2)}/{str(self.n_images).zfill(2)})")
         # self.pbr.update(current)
 
     def clear_attributes(self):

src/microglia_analyzer/ma_worker.py

@@ -366,9 +366,11 @@ def analyze_as_graph(self):
             if label == 0:
                 continue
             mask = (self.mask == label).astype(np.uint8)
-            if np.sum(mask) < 3:
+            try:
+                r, s = self.analyze_skeleton(mask)
+            except:
                 continue
-            results[label], skeleton = self.analyze_skeleton(mask)
+            results[label], skeleton = r, s
             skeletons = np.maximum(skeletons, skeleton)
         self.graph_metrics = results
         self.skeleton = skeletons