neuro-sam 0.1.8__tar.gz → 0.1.9__tar.gz

{neuro_sam-0.1.8/src/neuro_sam.egg-info → neuro_sam-0.1.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: neuro-sam
-Version: 0.1.8
+Version: 0.1.9
 Summary: Neuro-SAM: Foundation Models for Dendrite and Dendritic Spine Segmentation
 Author-email: Nipun Arora <nipunarora8@yahoo.com>
 License: MIT License

{neuro_sam-0.1.8 → neuro_sam-0.1.9}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "neuro-sam"
-version = "0.1.8"
+version = "0.1.9"
 description = "Neuro-SAM: Foundation Models for Dendrite and Dendritic Spine Segmentation"
 readme = "README.md"
 authors = [

{neuro_sam-0.1.8 → neuro_sam-0.1.9}/src/neuro_sam/napari_utils/segmentation_module.py

@@ -172,18 +172,6 @@ class SegmentationWidget(QWidget):
         patch_size_layout.addWidget(self.patch_size_spin)
         params_layout.addLayout(patch_size_layout)
         
-        # Enable boundary cleanup for dendrites
-        self.enable_boundary_smoothing_cb = QCheckBox("Enable Light Boundary Cleanup")
-        self.enable_boundary_smoothing_cb.setChecked(False)  # Disabled by default for speed
-        self.enable_boundary_smoothing_cb.setToolTip("Apply light morphological cleanup (hole filling, small object removal)")
-        params_layout.addWidget(self.enable_boundary_smoothing_cb)
-        
-        # Dendrite structure enhancement
-        self.enhance_dendrite_cb = QCheckBox("Enhance Tubular Dendrite Structure")
-        self.enhance_dendrite_cb.setChecked(True)
-        self.enhance_dendrite_cb.setToolTip("Apply morphological operations to connect dendrite segments and make tubular structure")
-        params_layout.addWidget(self.enhance_dendrite_cb)
-        
         # # Minimum dendrite size for noise removal
         # min_size_layout = QHBoxLayout()
         # min_size_layout.addWidget(QLabel("Min Dendrite Size (pixels):"))
@@ -404,20 +392,9 @@ class SegmentationWidget(QWidget):
             
             # Get segmentation parameters
             patch_size = self.patch_size_spin.value()
-            enable_boundary_smoothing = self.enable_boundary_smoothing_cb.isChecked()
-            enhance_dendrite = self.enhance_dendrite_cb.isChecked()
             use_full_volume = False
             
-            # Update UI
-            enhancement_info = [f"{patch_size}x{patch_size} overlapping patches (50%)"]
-            if enable_boundary_smoothing:
-                enhancement_info.append("light cleanup")
-            if enhance_dendrite:
-                enhancement_info.append("tubular structure enhancement")
-            
-            enhancement_str = " + ".join(enhancement_info)
-            
-            self.status_label.setText(f"Status: Running dendrite segmentation on {path_name} with {enhancement_str}...")
+            self.status_label.setText(f"Status: Running dendrite segmentation on {path_name}...")
             self.segmentation_progress.setValue(0)
             self.run_segmentation_btn.setEnabled(False)
             
@@ -434,15 +411,11 @@ class SegmentationWidget(QWidget):
             print(f"Segmenting dendrite path '{path_name}' from frame {start_frame} to {end_frame}")
             print(f"Path has {len(brightest_path)} points")
             print(f"Parameters: patch_size={patch_size}x{patch_size}, overlap=50% (stride={patch_size//2})")
-            print(f"Light boundary cleanup: {enable_boundary_smoothing}")
             # print(f"Dendrite enhancement: {enhance_dendrite}, Min dendrite size: {min_dendrite_size} pixels")
             
             # Progress callback function
             def update_progress(current, total):
-                if enable_boundary_smoothing:
-                    progress = int((current / total) * 80)  # 0-80%
-                else:
-                    progress = int((current / total) * 90)  # 0-90%
+                progress = int((current / total) * 90)  # 0-90%
                 self.segmentation_progress.setValue(progress)
             
             # Try to run the segmentation with overlapping patches
@@ -542,11 +515,6 @@ class SegmentationWidget(QWidget):
                 total_pixels = np.sum(binary_masks)
                 
                 result_text = f"Results: Dendrite segmentation completed - {total_pixels} pixels segmented"
-                result_text += f"\nMethod: {enhancement_str}"
-                result_text += f"\nOverlap: 50% (stride={patch_size//2})"
-                # result_text += f"\nMin dendrite size: {min_dendrite_size} pixels"
-                if enable_boundary_smoothing:
-                    result_text += f"\nLight boundary cleanup applied"
                 
                 self.status_label.setText(result_text)
                 

{neuro_sam-0.1.8 → neuro_sam-0.1.9/src/neuro_sam.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: neuro-sam
-Version: 0.1.8
+Version: 0.1.9
 Summary: Neuro-SAM: Foundation Models for Dendrite and Dendritic Spine Segmentation
 Author-email: Nipun Arora <nipunarora8@yahoo.com>
 License: MIT License