nettracer3d 1.2.3__py3-none-any.whl → 1.2.5__py3-none-any.whl

nettracer3d/filaments.py

@@ -93,16 +93,24 @@ class VesselDenoiser:
         # A voxel contributes to surface area if any neighbor is different
         for axis in range(3):
             for direction in [-1, 1]:
-                # Shift array to compare with neighbors
-                shifted = np.roll(labeled, direction, axis=axis)
+                # Pad with zeros only on the axis we're checking
+                pad_width = [(1, 1) if i == axis else (0, 0) for i in range(3)]
+                padded = np.pad(labeled, pad_width, mode='constant', constant_values=0)
                 
-                # Find faces exposed to different label (including background)
-                exposed_faces = (labeled != shifted) & (labeled > 0)
+                # Roll the padded array
+                shifted = np.roll(padded, direction, axis=axis)
+                
+                # Extract the center region (original size) from shifted
+                slices = [slice(1, -1) if i == axis else slice(None) for i in range(3)]
+                shifted_cropped = shifted[tuple(slices)]
+                
+                # Find exposed faces
+                exposed_faces = (labeled != shifted_cropped) & (labeled > 0)
                 
-                # Count exposed faces per label
                 face_counts = np.bincount(labeled[exposed_faces], 
                                          minlength=num_features + 1)
                 surface_areas += face_counts
+        del padded
         
         # Calculate sphericity for each component
         # Sphericity = (surface area of sphere with same volume) / (actual surface area)

nettracer3d/nettracer.py

@@ -750,35 +750,37 @@ def estimate_object_radii(labeled_array, gpu=False, n_jobs=None, xy_scale = 1, z
 
 def get_surface_areas(labeled, xy_scale=1, z_scale=1):
     labels = np.unique(labeled)
-    labels = labels[labels > 0]  # Remove background label
+    labels = labels[labels > 0]
     max_label = int(np.max(labeled))
     
-    # Size array to accommodate highest label value
     surface_areas = np.zeros(max_label + 1, dtype=np.float64)
     
-    # Check each of 6 face directions (±x, ±y, ±z)
     for axis in range(3):
-        # Determine face area based on axis (anisotropic scaling)
-        if axis == 2:  # z-axis: face is in xy plane
+        if axis == 2:
             face_area = xy_scale * xy_scale
-        else:  # x or y axis: face is perpendicular to xy plane
+        else:
             face_area = xy_scale * z_scale
         
         for direction in [-1, 1]:
-            # Shift array to compare with neighbors
-            shifted = np.roll(labeled, direction, axis=axis)
+            # Pad with zeros only on the axis we're checking
+            pad_width = [(1, 1) if i == axis else (0, 0) for i in range(3)]
+            padded = np.pad(labeled, pad_width, mode='constant', constant_values=0)
+            
+            # Roll the padded array
+            shifted = np.roll(padded, direction, axis=axis)
             
-            # Find faces exposed to different label (including background)
-            exposed_faces = (labeled != shifted) & (labeled > 0)
+            # Extract the center region (original size) from shifted
+            slices = [slice(1, -1) if i == axis else slice(None) for i in range(3)]
+            shifted_cropped = shifted[tuple(slices)]
+            
+            # Find exposed faces
+            exposed_faces = (labeled != shifted_cropped) & (labeled > 0)
             
-            # Count exposed faces per label
             face_counts = np.bincount(labeled[exposed_faces], 
                                      minlength=max_label + 1)
             surface_areas += face_counts * face_area
     
-    # Create dictionary mapping label to surface area
     result = {int(label): float(surface_areas[label]) for label in labels}
-        
     return result
 
 def break_and_label_skeleton(skeleton, peaks = 1, branch_removal = 0, comp_dil = 0, max_vol = 0, directory = None, return_skele = False, nodes = None, compute = True, unify = False, xy_scale = 1, z_scale = 1):
@@ -5560,14 +5562,14 @@ class Network_3D:
                 except:
                     pass
 
-            title1 = f'Neighborhood Distribution of Nodes in Network from Nodes: {root}'
-            title2 = f'Neighborhood Distribution of Nodes in Network from Nodes {root} as a proportion of total nodes of that ID'
+            title1 = f'Neighborhood Distribution of Nodes in Network from Node Type: {root}'
+            title2 = f'Neighborhood Distribution of Nodes in Network from Node Type {root} as a Proportion (# neighbors with ID x / Total # ID x)'
 
 
         elif mode == 1: #Search neighborhoods morphologically, obtain densities
             neighborhood_dict, total_dict, densities = morphology.search_neighbor_ids(self._nodes, targets, node_identities, neighborhood_dict, total_dict, search, self._xy_scale, self._z_scale, root, fastdil = fastdil)
-            title1 = f'Volumetric Neighborhood Distribution of Nodes in image that are {search} from nodes: {root}'
-            title2 = f'Density Distribution of Nodes in image that are {search} from Nodes {root} as a proportion of total node volume of that ID'
+            title1 = f'Volumetric Neighborhood Distribution of Nodes in image that are {search} from Node Type: {root}'
+            title2 = f'Density Distribution of Nodes in image that are {search} from Node Type {root} as a proportion (Vol neighors with ID x / Total vol ID x)'
 
 
         for identity in neighborhood_dict:
@@ -5578,7 +5580,7 @@ class Network_3D:
         network_analysis.create_bar_graph(proportion_dict, title2, "Node Identity", "Proportion", directory=directory)
 
         try:
-            network_analysis.create_bar_graph(densities, f'Relative Density of Node Identities with {search} from nodes {root}', "Node Identity", "Density Search/Density Total", directory=directory)
+            network_analysis.create_bar_graph(densities, f'Relative Density of Node Identities with {search} from Node Type {root}', "Node Identity", "Density within search region/Density within entire image", directory=directory)
         except:
             densities = None
 
@@ -6233,14 +6235,14 @@ class Network_3D:
         if proportional:
 
             identities2, id_set2 = self.community_id_info_per_com(proportional = True)
-            output = neighborhoods.plot_dict_heatmap(identities2, id_set2, title = "Neighborhood Heatmap by Proportional Composition of Nodes in Neighborhood vs All Nodes")
+            output = neighborhoods.plot_dict_heatmap(identities2, id_set2, title = "Neighborhood Heatmap by Proportional Composition of Nodes in Neighborhood vs All Nodes in Image")
             matrixes.append(output)
 
             identities3 = {}
             for iden in identities2:
                 identities3[iden] = identities2[iden]/len_dict[iden][1]
 
-            output = neighborhoods.plot_dict_heatmap(identities3, id_set2, title = "Neighborhood Heatmap by Proportional Composition of Nodes in Neighborhood vs All Nodes Divided by Neighborhood Total Proportion of All Nodes (val < 1 = underrepresented, val > 1 = overrepresented)", center_at_one = True)
+            output = neighborhoods.plot_dict_heatmap(identities3, id_set2, title = "Over/Underrepresentation of Node Identities per Neighborhood (val < 1 = underrepresented, val > 1 = overrepresented)", center_at_one = True)
             matrixes.append(output)
 
         return len_dict, matrixes, id_set

nettracer3d/nettracer_gui.py

@@ -10090,7 +10090,7 @@ class NeighborIdentityDialog(QDialog):
             self.root = None
 
         self.mode = QComboBox()
-        self.mode.addItems(["From Network - Based on Absolute Connectivity", "Use Labeled Nodes - Based on Morphological Neighborhood Densities"])
+        self.mode.addItems(["From Network - Quantifies Neighbors Based on Adjacent Network Connections", "Use Labeled Nodes - Quantifies Neighbors Volume of Neighbor Within Search Region"])
         self.mode.setCurrentIndex(0)
         layout.addRow("Mode", self.mode)
 

{nettracer3d-1.2.3.dist-info → nettracer3d-1.2.5.dist-info}/METADATA

@@ -1,10 +1,9 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 1.2.3
+Version: 1.2.5
 Summary: Scripts for intializing and analyzing networks from segmentations of three dimensional images.
 Author-email: Liam McLaughlin <liamm@wustl.edu>
 Project-URL: Documentation, https://nettracer3d.readthedocs.io/en/latest/
-Project-URL: Video_Tutorial, https://www.youtube.com/watch?v=cRatn5VTWDY
 Project-URL: Reference_Citation_For_Use, https://doi.org/10.1101/2024.07.29.605633
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: Other/Proprietary License
@@ -51,7 +50,7 @@ Please see: https://nettracer3d.readthedocs.io/en/latest/
 
 --- Installation ---
 
-To install nettracer3d, simply install Python and use this command in your command terminal:
+To install nettracer3d, simply install Python. Make sure the Python installation installs pip, and that both Python and pip are available on your PATH. Next, use this command in your command terminal:
 
 pip install nettracer3d
 
@@ -60,6 +59,10 @@ I recommend installing the program as an Anaconda package to ensure its modules
 
 https://www.anaconda.com/download?utm_source=anacondadocs&utm_medium=documentation&utm_campaign=download&utm_content=installwindows
 
+Alternatively, you can download a compiled .exe of version 1.2.4 here: https://doi.org/10.5281/zenodo.17873800 
+
+Unzip the folder, then double click the NetTracer3D executable to run the program. Note that this version will be missing a few features compared to the Python package, namely the 3D display and the ability to print updates to the command window. It will also not be updated as often.
+
 Optional Packages
 ~~~~~~~~~~~~~~~~~~
 I recommend including Napari (Chi-Li Chiu, Nathan Clack, the napari community, napari: a Python Multi-Dimensional Image Viewer Platform for the Research Community, Microscopy and Microanalysis, Volume 28, Issue S1, 1 August 2022, Pages 1576–1577, https://doi.org/10.1017/S1431927622006328) in the download as well, which allows NetTracer3D to use 3D displays. The standard package only comes with its native 2D slice display window. 
@@ -101,17 +104,14 @@ While not related to NetTracer3D, if you want to use Cellpose3 (for which GPU-us
 This gui is built from the PyQt6 package and therefore may not function on dockers or virtual envs that are unable to support PyQt6 displays.
 
 
-For a (slightly outdated) video tutorial on using the GUI: https://www.youtube.com/watch?v=cRatn5VTWDY
-
-NetTracer3D is free to use/fork for academic/nonprofit use so long as citation is provided, and is available for commercial use at a fee (see license file for information).
-The current citation is here: 
+NetTracer3D is freely available for academic and nonprofit use and can obtained from pip (pip install nettracer3d), provided that citation is included in any abstract, paper, or presentation utilizing NetTracer3D.
 
-McLaughlin, L., Zhang, B., Sharma, S. et al. Three dimensional multiscalar neurovascular nephron connectivity map of the human kidney across the lifespan. Nat Commun 16, 5161 (2025). https://doi.org/10.1038/s41467-025-60435-8
+(The official paper to cite is coming soon)
 
 NetTracer3D was developed by Liam McLaughlin while working under Dr. Sanjay Jain at Washington University School of Medicine.
 
--- Version 1.2.3 Updates --
+-- Version 1.2.5 Updates --
 
-	* Tweaked the 'branch unification params' - now hard rejects any sharp forks in the branches so branches will mostly be straight.
+	* Updated readme, license
 	
 	

{nettracer3d-1.2.3.dist-info → nettracer3d-1.2.5.dist-info}/RECORD

@@ -3,12 +3,12 @@ nettracer3d/branch_stitcher.py,sha256=gyDVPUnApS2jmlIglJoRVEVY8WXLqwpr0_8rNdvy9u
 nettracer3d/cellpose_manager.py,sha256=NfRqW6Zl7yRU4qHCS_KjmR0R6QANSSgCO0_dr-eivxg,6694
 nettracer3d/community_extractor.py,sha256=rPXXWwMX05mfD_ogULEouLy8CST-aOaoSw45NhloKVg,31754
 nettracer3d/excelotron.py,sha256=aNof6k-DgMxVyFgsl3ltSCxG4vZW49cuvCBzfzhYhUY,75072
-nettracer3d/filaments.py,sha256=-gUoiXg4n5qTHhGvzh1gkLeDjStECRGbaGpau_NGVRM,43280
+nettracer3d/filaments.py,sha256=ks3-ThdHRKu5hPk04R_YHAmVpwCqXraR0LWW0VRlAts,43693
 nettracer3d/modularity.py,sha256=pborVcDBvICB2-g8lNoSVZbIReIBlfeBmjFbPYmtq7Y,22443
 nettracer3d/morphology.py,sha256=QlBPsJAswBoinjZuouNwEfGEGwclvenlZ1Vmo288QLo,23287
 nettracer3d/neighborhoods.py,sha256=Bje77gWzXRIYyXkDlnFQnbUALnIt8dheLXHVFQsAKuc,53156
-nettracer3d/nettracer.py,sha256=JaoNXP67vLzaw6HUQ6mtB7qye1U92wZDJYI3vEpsDS4,294237
-nettracer3d/nettracer_gui.py,sha256=AKXT_4M-wuuijPzj6XfMV6fYKQ0WJYW0A_YdcO7kfYc,741978
+nettracer3d/nettracer.py,sha256=9iQ51fvYUNsHA90lZd4cEVz_4AZZToTy22SjJoZNPHY,294254
+nettracer3d/nettracer_gui.py,sha256=oStQZCqzi_nDFq8NKjMA1n0cuMv77gKekOd6XQFO5H4,742021
 nettracer3d/network_analysis.py,sha256=kBzsVaq4dZkMe0k-VGvQIUvM-tK0ZZ8bvb-wtsugZRQ,46150
 nettracer3d/network_draw.py,sha256=Uw0w1MoFiYMirkdM_XDAfy_m5_MoVaZkkGpoYzN9_-c,14259
 nettracer3d/node_draw.py,sha256=LeSftKJiNGkC7cpBJuf8Y9JeTUaUjcD6I2byclmZCb4,10484
@@ -21,9 +21,9 @@ nettracer3d/simple_network.py,sha256=dkG4jpc4zzdeuoaQobgGfL3PNo6N8dGKQ5hEEubFIvA
 nettracer3d/smart_dilate.py,sha256=gtL7hxzae93PJQsGLnUrwQ6Wb0evnHHREh0rHyUh_48,28644
 nettracer3d/stats.py,sha256=0YwrVLeEvll3PlbL5-0_9dstldr48PvxJrQm-PiC8jY,36607
 nettracer3d/tutorial.py,sha256=cUxiBf5RaBTtr9uJ2qoxZjRkcAY8mrvS9_LEqiwoxLc,153564
-nettracer3d-1.2.3.dist-info/licenses/LICENSE,sha256=jnNT-yBeIAKAHpYthPvLeqCzJ6nSurgnKmloVnfsjCI,764
-nettracer3d-1.2.3.dist-info/METADATA,sha256=rVv3ho6njj9VWX6XrKz0ri1mHYBwo_zO8Mb7d7XHBaM,7110
-nettracer3d-1.2.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-nettracer3d-1.2.3.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
-nettracer3d-1.2.3.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
-nettracer3d-1.2.3.dist-info/RECORD,,
+nettracer3d-1.2.5.dist-info/licenses/LICENSE,sha256=_Wg4zyCtT18lXBCXRov17IEop_-7z1OFo6o3JTzQj3g,568
+nettracer3d-1.2.5.dist-info/METADATA,sha256=KGky4Y1X3pHgoykGd-SaJkp6x4faTeH6K-uh2r7wvL0,7164
+nettracer3d-1.2.5.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+nettracer3d-1.2.5.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
+nettracer3d-1.2.5.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
+nettracer3d-1.2.5.dist-info/RECORD,,

{nettracer3d-1.2.3.dist-info → nettracer3d-1.2.5.dist-info}/licenses/LICENSE

@@ -1,5 +1,5 @@
-NetTracer3D is freely available for academic and nonprofit use and can be obtained from Liam McLaughlin (boom2449@gmail.com) OR at pip (pip install nettracer3d), provided that the following citation is included in any abstract, paper, or presentation utilizing NetTracer3D:
+NetTracer3D is freely available for academic and nonprofit use and can be obtained from Liam McLaughlin (boom2449@gmail.com) OR at pip (pip install nettracer3d), provided that citation is included in any abstract, paper, or presentation utilizing NetTracer3D.
 
-McLaughlin, L., Zhang, B., Sharma, S. et al. Three dimensional multiscalar neurovascular nephron connectivity map of the human kidney across the lifespan. Nat Commun 16, 5161 (2025). https://doi.org/10.1038/s41467-025-60435-8
+(The official paper to cite is coming soon)
 
 Commercial use is available for a fee. Copyright © is held by Washington University. Please direct all commercial requests for licensing, information, and limited evaluation copies to Washington University's Office of Technology Management at OTM@wustl.edu.