nettracer3d 1.2.3__tar.gz → 1.2.9__tar.gz

{nettracer3d-1.2.3 → nettracer3d-1.2.9}/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.

{nettracer3d-1.2.3/src/nettracer3d.egg-info → nettracer3d-1.2.9}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 1.2.3
+Version: 1.2.9
 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
+Project-URL: Youtube_Tutorial, https://www.youtube.com/watch?v=_4uDy0mzG94&list=PLsrhxiimzKJMZ3_gTWkfrcAdJQQobUhj7
+Project-URL: Downloadable_Version, https://doi.org/10.5281/zenodo.17873800
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: Other/Proprietary License
 Classifier: Operating System :: OS Independent
@@ -25,7 +25,6 @@ Requires-Dist: tifffile
 Requires-Dist: qtrangeslider
 Requires-Dist: PyQt6
 Requires-Dist: scikit-learn
-Requires-Dist: nibabel
 Requires-Dist: setuptools
 Requires-Dist: umap-learn
 Provides-Extra: cuda11
@@ -38,30 +37,78 @@ Provides-Extra: cellpose
 Requires-Dist: cellpose[GUI]; extra == "cellpose"
 Provides-Extra: viz
 Requires-Dist: napari; extra == "viz"
+Provides-Extra: rec
+Requires-Dist: napari; extra == "rec"
+Requires-Dist: edt; extra == "rec"
+Provides-Extra: edt
+Requires-Dist: edt; extra == "edt"
 Provides-Extra: all
 Requires-Dist: cellpose[GUI]; extra == "all"
 Requires-Dist: napari; extra == "all"
+Requires-Dist: edt; extra == "all"
 Dynamic: license-file
 
 NetTracer3D is a python package developed for both 2D and 3D analysis of microscopic images in the .tif file format. It supports generation of 3D networks showing the relationships between objects (or nodes) in three dimensional space, either based on their own proximity or connectivity via connecting objects such as nerves or blood vessels. In addition to these functionalities are several advanced 3D data processing algorithms, such as labeling of branched structures or abstraction of branched structures into networks. Note that nettracer3d uses segmented data, which can be segmented from other softwares such as ImageJ and imported into NetTracer3D, although it does offer its own segmentation via intensity and volumetric thresholding, or random forest machine learning segmentation. NetTracer3D currently has a fully functional GUI. To use the GUI, after installing the nettracer3d package via pip, enter the command 'nettracer3d' in your command prompt:
 
+
 --- Documentation ---
 
 Please see: https://nettracer3d.readthedocs.io/en/latest/
 
---- Installation ---
 
-To install nettracer3d, simply install Python and use this command in your command terminal:
+--- Video Tutorial ---
+
+Please see: https://www.youtube.com/watch?v=_4uDy0mzG94&list=PLsrhxiimzKJMZ3_gTWkfrcAdJQQobUhj7
+
+
+--- Installing as a Python package ---
+
+1. **Get Python and Pip on your path**: To install nettracer3d, first install Python version 3.12. Make sure the Python installation installs pip, and that both Python and pip are available on your PATH. I recommend installing Python using the installer which is available here. Make sure to check the option to 'add Python to PATH' when it appears: https://www.python.org/downloads/
+
+
+2. **Base Package**: Next, use this command in your command terminal
+
+	* pip install nettracer3d
 
-pip install nettracer3d
+
+3. **For 3D Displays**: Or if you also want Napari for 3D displays:
+
+	* pip install nettracer3d[viz]
+
+
+4. **Optional Performance Boost**: If you are trying to process large images, you may also want to include the 'edt' module in your package. This will allow parallelized CPU calculations for several of the search functions which can increase their speed by an order of magnitude or more depending on how many cores your CPU has. This can be a major benefit if you have a strong CPU and sufficient RAM. It requires an extra pre-installation step, thus is not included by default. You will also have to install the C++ build tools from windows. Please head to this link, then download and run the installer: https://visualstudio.microsoft.com/visual-cpp-build-tools/. In the menu of the installer, select the 'Desktop Development with C++' option, then proceed to download/install it using the installation menu. You will likely want to be using the Python distributed from the actual Python website and not the windows store (or elsewhere) or the edt module may not work properly. To bundle with edt use:
+
+	* pip install nettracer3d[edt]
+
+
+5. **Recommended full package**: Or if you want to just get both edt and napari at once:
+	
+	* pip install nettracer3d[rec]
+
+
+6. Likewise, if you already installed the default version, you can add napari and/or edt with just:
+
+	* pip install edt
+	* pip install napari
+
+   
+--- Installing as a Python package in Anaconda---
 
 I recommend installing the program as an Anaconda package to ensure its modules are work together on your specific system:
 (Install anaconda at the link below, set up a new python env for nettracer3d, then use the same pip command).
 
 https://www.anaconda.com/download?utm_source=anacondadocs&utm_medium=documentation&utm_campaign=download&utm_content=installwindows
 
-Optional Packages
-~~~~~~~~~~~~~~~~~~
+
+--- Using the downloadable version ---
+
+Alternatively, you can download a compiled .exe of version 1.2.7 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 GPU segmentation support 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. 
 If Napari is present, all 3D images and overlays from NetTracer3D can be easily displayed in 3D with a click of a button. To package with Napari, use this install command instead: 
 
@@ -74,13 +121,13 @@ To include Cellpose3 in the install, use this command:
 
     pip install nettracer3d[cellpose]
 
-Alternatively, both Napari and Cellpose can be included in the package with this command: (Or they can be independently installed with pip from the base package env)
+Alternatively, Napari, Cellpose, and edt can be included in the package with this command: (Or they can be independently installed with pip from the base package env)
 
 
     pip install nettracer3d[all]
 
-GPU
-~~~~~~~~~~~~~~~~~~
+
+--- GPU ---
 NetTracer3D is mostly CPU-bound, but a few functions can optionally use the GPU. To install optional GPU functionalities, first set up a CUDA toolkit that runs with the GPU on your machine. This requires an NVIDIA GPU. Then, find your GPUs compatible CUDA toolkit and install it with the auto-installer from the NVIDIA website: https://developer.nvidia.com/cuda-toolkit
 
 With a CUDA toolkit installed, use:
@@ -101,17 +148,13 @@ 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 1.2.9 Updates --
 
-	* Tweaked the 'branch unification params' - now hard rejects any sharp forks in the branches so branches will mostly be straight.
-	
+	* Some minor adjustments.
 	

{nettracer3d-1.2.3 → nettracer3d-1.2.9}/README.md

@@ -1,22 +1,64 @@
 NetTracer3D is a python package developed for both 2D and 3D analysis of microscopic images in the .tif file format. It supports generation of 3D networks showing the relationships between objects (or nodes) in three dimensional space, either based on their own proximity or connectivity via connecting objects such as nerves or blood vessels. In addition to these functionalities are several advanced 3D data processing algorithms, such as labeling of branched structures or abstraction of branched structures into networks. Note that nettracer3d uses segmented data, which can be segmented from other softwares such as ImageJ and imported into NetTracer3D, although it does offer its own segmentation via intensity and volumetric thresholding, or random forest machine learning segmentation. NetTracer3D currently has a fully functional GUI. To use the GUI, after installing the nettracer3d package via pip, enter the command 'nettracer3d' in your command prompt:
 
+
 --- Documentation ---
 
 Please see: https://nettracer3d.readthedocs.io/en/latest/
 
---- Installation ---
 
-To install nettracer3d, simply install Python and use this command in your command terminal:
+--- Video Tutorial ---
+
+Please see: https://www.youtube.com/watch?v=_4uDy0mzG94&list=PLsrhxiimzKJMZ3_gTWkfrcAdJQQobUhj7
+
+
+--- Installing as a Python package ---
+
+1. **Get Python and Pip on your path**: To install nettracer3d, first install Python version 3.12. Make sure the Python installation installs pip, and that both Python and pip are available on your PATH. I recommend installing Python using the installer which is available here. Make sure to check the option to 'add Python to PATH' when it appears: https://www.python.org/downloads/
+
+
+2. **Base Package**: Next, use this command in your command terminal
+
+	* pip install nettracer3d
 
-pip install nettracer3d
+
+3. **For 3D Displays**: Or if you also want Napari for 3D displays:
+
+	* pip install nettracer3d[viz]
+
+
+4. **Optional Performance Boost**: If you are trying to process large images, you may also want to include the 'edt' module in your package. This will allow parallelized CPU calculations for several of the search functions which can increase their speed by an order of magnitude or more depending on how many cores your CPU has. This can be a major benefit if you have a strong CPU and sufficient RAM. It requires an extra pre-installation step, thus is not included by default. You will also have to install the C++ build tools from windows. Please head to this link, then download and run the installer: https://visualstudio.microsoft.com/visual-cpp-build-tools/. In the menu of the installer, select the 'Desktop Development with C++' option, then proceed to download/install it using the installation menu. You will likely want to be using the Python distributed from the actual Python website and not the windows store (or elsewhere) or the edt module may not work properly. To bundle with edt use:
+
+	* pip install nettracer3d[edt]
+
+
+5. **Recommended full package**: Or if you want to just get both edt and napari at once:
+	
+	* pip install nettracer3d[rec]
+
+
+6. Likewise, if you already installed the default version, you can add napari and/or edt with just:
+
+	* pip install edt
+	* pip install napari
+
+   
+--- Installing as a Python package in Anaconda---
 
 I recommend installing the program as an Anaconda package to ensure its modules are work together on your specific system:
 (Install anaconda at the link below, set up a new python env for nettracer3d, then use the same pip command).
 
 https://www.anaconda.com/download?utm_source=anacondadocs&utm_medium=documentation&utm_campaign=download&utm_content=installwindows
 
-Optional Packages
-~~~~~~~~~~~~~~~~~~
+
+--- Using the downloadable version ---
+
+Alternatively, you can download a compiled .exe of version 1.2.7 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 GPU segmentation support 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. 
 If Napari is present, all 3D images and overlays from NetTracer3D can be easily displayed in 3D with a click of a button. To package with Napari, use this install command instead: 
 
@@ -29,13 +71,13 @@ To include Cellpose3 in the install, use this command:
 
     pip install nettracer3d[cellpose]
 
-Alternatively, both Napari and Cellpose can be included in the package with this command: (Or they can be independently installed with pip from the base package env)
+Alternatively, Napari, Cellpose, and edt can be included in the package with this command: (Or they can be independently installed with pip from the base package env)
 
 
     pip install nettracer3d[all]
 
-GPU
-~~~~~~~~~~~~~~~~~~
+
+--- GPU ---
 NetTracer3D is mostly CPU-bound, but a few functions can optionally use the GPU. To install optional GPU functionalities, first set up a CUDA toolkit that runs with the GPU on your machine. This requires an NVIDIA GPU. Then, find your GPUs compatible CUDA toolkit and install it with the auto-installer from the NVIDIA website: https://developer.nvidia.com/cuda-toolkit
 
 With a CUDA toolkit installed, use:
@@ -56,17 +98,13 @@ 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 1.2.9 Updates --
 
-	* Tweaked the 'branch unification params' - now hard rejects any sharp forks in the branches so branches will mostly be straight.
-	
+	* Some minor adjustments.
 	

{nettracer3d-1.2.3 → nettracer3d-1.2.9}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "nettracer3d"
-version = "1.2.3"
+version = "1.2.9"
 authors = [
   { name="Liam McLaughlin", email="liamm@wustl.edu" },
 ]
@@ -20,10 +20,8 @@ dependencies = [
     "qtrangeslider",
     "PyQt6",
     "scikit-learn",
-    "nibabel",
     "setuptools",
-    "umap-learn"
-]
+    "umap-learn"]
 
 readme = "README.md"
 requires-python = ">=3.7"
@@ -42,14 +40,16 @@ cupy = ["cupy"]
 # Features
 cellpose = ["cellpose[GUI]"]
 viz = ["napari"]
+rec = ["napari", "edt"]
+edt = ["edt"]
 
 # All non-GPU features
-all = ["cellpose[GUI]", "napari"]
+all = ["cellpose[GUI]", "napari", "edt"]
 
 [project.scripts]
 nettracer3d = "nettracer3d.run:main"
 
 [project.urls]
 Documentation = "https://nettracer3d.readthedocs.io/en/latest/"
-Video_Tutorial = "https://www.youtube.com/watch?v=cRatn5VTWDY"
-Reference_Citation_For_Use = "https://doi.org/10.1101/2024.07.29.605633"
+Youtube_Tutorial = "https://www.youtube.com/watch?v=_4uDy0mzG94&list=PLsrhxiimzKJMZ3_gTWkfrcAdJQQobUhj7"
+Downloadable_Version = "https://doi.org/10.5281/zenodo.17873800"

{nettracer3d-1.2.3 → nettracer3d-1.2.9}/src/nettracer3d/branch_stitcher.py

@@ -3,6 +3,7 @@ import networkx as nx
 from . import nettracer as n3d
 from scipy.ndimage import distance_transform_edt, gaussian_filter, binary_fill_holes
 from scipy.spatial import cKDTree
+from . import smart_dilate as sdl
 from skimage.morphology import remove_small_objects, skeletonize
 import warnings
 warnings.filterwarnings('ignore')
@@ -14,9 +15,13 @@ class VesselDenoiser:
     """
     
     def __init__(self, 
-                 score_thresh = 2):
+                 score_thresh = 2,
+                 xy_scale = 1,
+                 z_scale = 1):
 
         self.score_thresh = score_thresh
+        self.xy_scale = xy_scale
+        self.z_scale = z_scale
 
 
     def select_kernel_points_topology(self, data, skeleton):
@@ -336,7 +341,7 @@ class VesselDenoiser:
         # Compute distance transform
         if verbose:
             print("Computing distance transform...")
-        distance_map = distance_transform_edt(data)
+        distance_map = sdl.compute_distance_transform_distance(data, fast_dil = True)
         
         # Extract endpoints
         if verbose:
@@ -390,14 +395,14 @@ class VesselDenoiser:
         return label_dict
 
 
-def trace(data, labeled_skeleton, verts, score_thresh=10, verbose=False):
+def trace(data, labeled_skeleton, verts, score_thresh=10, xy_scale = 1, z_scale = 1, verbose=False):
     """
     Trace and unify skeleton labels using vertex-based endpoint grouping
     """
     skeleton = n3d.binarize(labeled_skeleton)
     
     # Create denoiser
-    denoiser = VesselDenoiser(score_thresh=score_thresh)
+    denoiser = VesselDenoiser(score_thresh=score_thresh, xy_scale = xy_scale, z_scale = z_scale)
     
     # Run label unification
     label_dict = denoiser.denoise(data, skeleton, labeled_skeleton, verts, verbose=verbose)

{nettracer3d-1.2.3 → nettracer3d-1.2.9}/src/nettracer3d/filaments.py

@@ -1,10 +1,11 @@
 import numpy as np
 import networkx as nx
 from . import nettracer as n3d
-from scipy.ndimage import distance_transform_edt, gaussian_filter, binary_fill_holes
+from scipy.ndimage import gaussian_filter, binary_fill_holes
 from scipy.spatial import cKDTree
 from skimage.morphology import remove_small_objects, skeletonize
 import warnings
+from . import smart_dilate as sdl
 warnings.filterwarnings('ignore')
 
 
@@ -22,6 +23,8 @@ class VesselDenoiser:
                  blob_volume = 200,
                  spine_removal=0,
                  score_thresh = 2,
+                 xy_scale = 1,
+                 z_scale = 1,
                  radius_aware_distance=True):
         """
         Parameters:
@@ -46,6 +49,8 @@ class VesselDenoiser:
         self.spine_removal = spine_removal
         self.radius_aware_distance = radius_aware_distance
         self.score_thresh = score_thresh
+        self.xy_scale = xy_scale
+        self.z_scale = z_scale
 
         self._sphere_cache = {}  # Cache sphere masks for different radii
 
@@ -93,16 +98,24 @@ 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)
@@ -931,7 +944,7 @@ class VesselDenoiser:
         
         if verbose:
             print("Step 3: Computing distance transform...")
-        distance_map = distance_transform_edt(cleaned)
+        distance_map = sdl.compute_distance_transform_distance(cleaned, fast_dil = True)
         
         # Step 3: Sample kernels along skeleton
         if verbose:
@@ -1028,7 +1041,7 @@ class VesselDenoiser:
         return result
 
 
-def trace(data, kernel_spacing = 1, max_distance = 20, min_component = 20, gap_tolerance = 5, blob_sphericity = 1.0, blob_volume = 200, spine_removal = 0, score_thresh = 2):
+def trace(data, kernel_spacing = 1, max_distance = 20, min_component = 20, gap_tolerance = 5, blob_sphericity = 1.0, blob_volume = 200, spine_removal = 0, score_thresh = 2, xy_scale = 1, z_scale = 1):
 
     """Main function with user prompts"""
     
@@ -1046,7 +1059,9 @@ def trace(data, kernel_spacing = 1, max_distance = 20, min_component = 20, gap_t
         blob_sphericity = blob_sphericity,
         blob_volume = blob_volume,
         spine_removal = spine_removal,
-        score_thresh = score_thresh
+        score_thresh = score_thresh,
+        xy_scale = xy_scale,
+        z_scale = z_scale
     )
     
     # Run denoising

{nettracer3d-1.2.3 → nettracer3d-1.2.9}/src/nettracer3d/modularity.py

@@ -103,7 +103,7 @@ def read_excel_to_lists(file_path, sheet_name=0):
 
 
 
-def show_communities_flex(G, master_list, normalized_weights, geo_info=None, geometric=False, directory=None, weighted=True, partition=None, style=0):
+def show_communities_flex(G, master_list, normalized_weights, geo_info=None, geometric=False, directory=None, weighted=True, partition=None, style=0, show_labels = True):
 
     if normalized_weights is None:
         G, edge_weights = network_analysis.weighted_network(master_list)
@@ -179,7 +179,8 @@ def show_communities_flex(G, master_list, normalized_weights, geo_info=None, geo
                 normalized_weight = G[edge[0]][edge[1]]['weight']
                 nx.draw_networkx_edges(G, pos, edgelist=[edge], width=5 * normalized_weight, edge_color='black')
 
-            nx.draw_networkx_labels(G, pos)
+            if show_labels:
+                nx.draw_networkx_labels(G, pos)
 
         else:
             pos = nx.spring_layout(G)
@@ -195,20 +196,28 @@ def show_communities_flex(G, master_list, normalized_weights, geo_info=None, geo
                 normalized_weight = G[edge[0]][edge[1]]['weight']
                 nx.draw_networkx_edges(G, pos, edgelist=[edge], width=5 * normalized_weight, edge_color='black')
 
-            nx.draw_networkx_labels(G, pos)
+            if show_labels:
+                nx.draw_networkx_labels(G, pos)
 
     else:
         # Create node color list based on partition and the same color mapping
-        node_colors = [colors_matplotlib[partition[node]] for node in G.nodes()]
+        node_colors = []
+        for node in G.nodes():
+            try:
+                node_colors.append(colors_matplotlib[partition[node]])
+            except:
+                node_colors.append((1, 1, 1))
+
+        #node_colors = [colors_matplotlib[partition[node]] for node in G.nodes()]
 
         if geometric:
             pos, z_pos = simple_network.geometric_positions(geo_info[0], geo_info[1])
             node_sizes_list = [z_pos[node] for node in G.nodes()]
-            nx.draw(G, pos, with_labels=True, font_color='black', font_weight='bold', 
+            nx.draw(G, pos, with_labels=show_labels, font_color='black', font_weight='bold', 
                    node_size=node_sizes_list, node_color=node_colors, alpha=0.8, font_size=12)
         else:
             pos = nx.spring_layout(G)
-            nx.draw(G, pos, with_labels=True, font_color='black', font_weight='bold', 
+            nx.draw(G, pos, with_labels=show_labels, font_color='black', font_weight='bold', 
                    node_size=100, node_color=node_colors, alpha=0.8)
 
     plt.axis('off')

{nettracer3d-1.2.3 → nettracer3d-1.2.9}/src/nettracer3d/morphology.py

@@ -337,7 +337,7 @@ def search_neighbor_ids(nodes, targets, id_dict, neighborhood_dict, totals, sear
     targets = np.isin(nodes, targets)
     targets = nettracer.binarize(targets)
         
-    dilated = nettracer.dilate(targets, search, xy_scale = xy_scale, z_scale = z_scale, fast_dil = fastdil)
+    dilated = nettracer.dilate_3D_dt(targets, search, xy_scaling = xy_scale, z_scaling = z_scale, fast_dil = fastdil)
     dilated = dilated - targets #technically we dont need the cores
     search_vol = np.count_nonzero(dilated) * xy_scale * xy_scale * z_scale #need this for density
     targets = dilated != 0