neuro-sam 0.1.9__py3-none-any.whl → 0.1.11__py3-none-any.whl

neuro_sam/napari_utils/segmentation_module.py

@@ -171,6 +171,12 @@ class SegmentationWidget(QWidget):
         self.patch_size_spin.setToolTip("Size of overlapping patches (128x128 recommended)")
         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)
         
         # # Minimum dendrite size for noise removal
         # min_size_layout = QHBoxLayout()
@@ -389,6 +395,8 @@ class SegmentationWidget(QWidget):
             path_data = self.state['paths'][path_id]
             path_name = path_data['name']
             brightest_path = path_data['data']
+
+            enable_boundary_smoothing = self.enable_boundary_smoothing_cb.isChecked()
             
             # Get segmentation parameters
             patch_size = self.patch_size_spin.value()
@@ -415,7 +423,10 @@ class SegmentationWidget(QWidget):
             
             # Progress callback function
             def update_progress(current, total):
-                progress = int((current / total) * 90)  # 0-90%
+                if enable_boundary_smoothing:
+                    progress = int((current / total) * 80)  # 0-80%
+                else:
+                    progress = int((current / total) * 90)  # 0-90%
                 self.segmentation_progress.setValue(progress)
             
             # Try to run the segmentation with overlapping patches

{neuro_sam-0.1.9.dist-info → neuro_sam-0.1.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: neuro-sam
-Version: 0.1.9
+Version: 0.1.11
 Summary: Neuro-SAM: Foundation Models for Dendrite and Dendritic Spine Segmentation
 Author-email: Nipun Arora <nipunarora8@yahoo.com>
 License: MIT License

{neuro_sam-0.1.9.dist-info → neuro_sam-0.1.11.dist-info}/RECORD

@@ -33,7 +33,7 @@ neuro_sam/napari_utils/main_widget.py,sha256=yahfPLwmhBt_hImpRykIObzfMwbVZvVJTEK
 neuro_sam/napari_utils/path_tracing_module.py,sha256=bDhSawWNMfY-Vs-Zdt8XTb90pLkD9jUBRqpbC2_6li0,44070
 neuro_sam/napari_utils/punet_widget.py,sha256=WCAND8YLn4CA_20YW4quwcuJ_xEqPAc7GHrSBk4Anw0,16928
 neuro_sam/napari_utils/segmentation_model.py,sha256=mHXVjksqEcxHRH5KWp5-hXLEnRHgGhwPUxyUkV8eJGM,34141
-neuro_sam/napari_utils/segmentation_module.py,sha256=pp2WoWO6mfYQ4CLduiEC-_o3oQhqs7Vcz4i2B6ATnIc,26796
+neuro_sam/napari_utils/segmentation_module.py,sha256=g3Fs9Jqe4Vtdz96-S-I_ajs1mjv4Nev0HdEGlmH8-18,27446
 neuro_sam/napari_utils/visualization_module.py,sha256=JtZlBoKlfIwVLa2Sqg7b2KTr07fNlAcwR0M7fHsn2oM,24723
 neuro_sam/punet/deepd3_model.py,sha256=nGVEqzCPz_E4cFA6QmknW2CffDcjxH7VsdYAyTdAtY0,7509
 neuro_sam/punet/prob_unet_deepd3.py,sha256=syXNleUVrfYtmVveN9G461oAhumxsijsavps8in4VRw,14698
@@ -47,7 +47,7 @@ neuro_sam/training/train_dendrites.py,sha256=TMG4YrrQV0Q784omMziXsB71tNICEmGLYSH
 neuro_sam/training/utils/__init__.py,sha256=4hbcx57NtRu8nryvXQYqmXK4hyUgUYNDz97kCw3Efs8,31
 neuro_sam/training/utils/prompt_generation_dendrites.py,sha256=_ntzXNV1lXPrpInRKaZ5CPpq3akF2IuD1naOXbTC8TU,3201
 neuro_sam/training/utils/stream_dendrites.py,sha256=qS_ZWrhJdW1Sg3RBjoRUJFlCV0u5X1Ns_tjYgJUjWJw,11024
-neuro_sam-0.1.9.dist-info/licenses/LICENSE,sha256=akmTIN8IuZn3Y7UK_8qVQnyKDWSDcVUwB8RPGNXCojw,1068
+neuro_sam-0.1.11.dist-info/licenses/LICENSE,sha256=akmTIN8IuZn3Y7UK_8qVQnyKDWSDcVUwB8RPGNXCojw,1068
 sam2/__init__.py,sha256=uHyh6VzVS4F2box0rPDpN5UmOVKeQNK0CIaTKG9JQZ4,395
 sam2/automatic_mask_generator.py,sha256=Zt8mbb4UQSMFrjOY8OwbshswOpMhaxAtdn5sTuXUw9c,18461
 sam2/benchmark.py,sha256=m3o1BriIQuwJAx-3zQ_B0_7YLhN84G28oQSV5sGA3ak,2811
@@ -91,8 +91,8 @@ sam2/utils/__init__.py,sha256=NL2AacVHZOe41zp4kF2-ZGcUCi9zFwh1Eo9spNjN0Ko,197
 sam2/utils/amg.py,sha256=t7MwkOKvcuBNu4FcjzKv9BpO0av5Zo9itZ8b3WQMpdg,12842
 sam2/utils/misc.py,sha256=AWAMAcFhzQedcQb7HU2oRc-RqjGrK87K-MsVG21tIKI,13090
 sam2/utils/transforms.py,sha256=ujpk9GAMYvIJIGpt87QOP88TPtrjL61liDG7DCptEUY,4885
-neuro_sam-0.1.9.dist-info/METADATA,sha256=1VvaiDVMJtv5IMVoLsR61nJcprIkLEjvagdpOB5V8DY,9746
-neuro_sam-0.1.9.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-neuro_sam-0.1.9.dist-info/entry_points.txt,sha256=EQg0SmFbnbGGcchHq5ROmhO9pkgby72Y5G5w90WyLZI,220
-neuro_sam-0.1.9.dist-info/top_level.txt,sha256=yPbWxFcw79sErTk8zohihUHMK9LL31i3bXir2MrS4OQ,15
-neuro_sam-0.1.9.dist-info/RECORD,,
+neuro_sam-0.1.11.dist-info/METADATA,sha256=IClHWfaA9ApPwCyM4lK6smvFP8B9UGtiG0y_y2l0Ejk,9747
+neuro_sam-0.1.11.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+neuro_sam-0.1.11.dist-info/entry_points.txt,sha256=EQg0SmFbnbGGcchHq5ROmhO9pkgby72Y5G5w90WyLZI,220
+neuro_sam-0.1.11.dist-info/top_level.txt,sha256=yPbWxFcw79sErTk8zohihUHMK9LL31i3bXir2MrS4OQ,15
+neuro_sam-0.1.11.dist-info/RECORD,,