nettracer3d 1.1.9__tar.gz → 1.2.8__tar.gz

{nettracer3d-1.1.9 → nettracer3d-1.2.8}/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-1.1.9/src/nettracer3d.egg-info → nettracer3d-1.2.8}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 1.1.9
+Version: 1.2.8
 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 +37,86 @@ 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
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+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]
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
 
-pip install nettracer3d
+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 +129,13 @@ 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:
@@ -101,21 +156,14 @@ 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 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.
 
-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: 
-
-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 1.1.9 Updates --
+-- Version 1.2.8 Updates --
 
-	* Fixed saving of Boolean True/False arrays.
-	* Fixed branch functions not working correctly when a temporary downsample was being applied
-	* Added the 'filaments tracer' which can be used to improve vessel based segmentations
-	* Removed options for 'cubic' downsampling during processing as this option actually made outputs worse.
-	* Rearranged the 'Analyze -> Stats' menu
-	
+	* Made edt an optional dependency.
+	* Updated readme
 	

{nettracer3d-1.1.9 → nettracer3d-1.2.8}/README.md

@@ -1,22 +1,72 @@
 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
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+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]
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
 
-pip install nettracer3d
+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 +79,13 @@ 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:
@@ -56,21 +106,14 @@ 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 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.
 
-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: 
-
-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 1.1.9 Updates --
+-- Version 1.2.8 Updates --
 
-	* Fixed saving of Boolean True/False arrays.
-	* Fixed branch functions not working correctly when a temporary downsample was being applied
-	* Added the 'filaments tracer' which can be used to improve vessel based segmentations
-	* Removed options for 'cubic' downsampling during processing as this option actually made outputs worse.
-	* Rearranged the 'Analyze -> Stats' menu
-	
+	* Made edt an optional dependency.
+	* Updated readme
 	

{nettracer3d-1.1.9 → nettracer3d-1.2.8}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "nettracer3d"
-version = "1.1.9"
+version = "1.2.8"
 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"