nettracer3d 1.2.7__py3-none-any.whl → 1.3.1__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- nettracer3d/branch_stitcher.py +245 -142
- nettracer3d/nettracer.py +205 -32
- nettracer3d/nettracer_gui.py +1975 -2026
- nettracer3d/network_analysis.py +16 -4
- nettracer3d/network_graph_widget.py +2066 -0
- nettracer3d/painting.py +158 -298
- nettracer3d/simple_network.py +4 -4
- nettracer3d/smart_dilate.py +19 -7
- nettracer3d/tutorial.py +38 -3
- {nettracer3d-1.2.7.dist-info → nettracer3d-1.3.1.dist-info}/METADATA +51 -17
- {nettracer3d-1.2.7.dist-info → nettracer3d-1.3.1.dist-info}/RECORD +15 -14
- {nettracer3d-1.2.7.dist-info → nettracer3d-1.3.1.dist-info}/WHEEL +0 -0
- {nettracer3d-1.2.7.dist-info → nettracer3d-1.3.1.dist-info}/entry_points.txt +0 -0
- {nettracer3d-1.2.7.dist-info → nettracer3d-1.3.1.dist-info}/licenses/LICENSE +0 -0
- {nettracer3d-1.2.7.dist-info → nettracer3d-1.3.1.dist-info}/top_level.txt +0 -0
nettracer3d/smart_dilate.py
CHANGED
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@@ -7,7 +7,11 @@ from concurrent.futures import ThreadPoolExecutor, as_completed, ProcessPoolExec
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from skimage.segmentation import watershed
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import cv2
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import os
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try:
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import edt
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print("Parallel search functions enabled")
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except:
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print("Some parallel search functions disabled (requires edt package), will fall back to single-threaded")
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import math
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import re
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from . import nettracer
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@@ -293,9 +297,13 @@ def process_chunk(start_idx, end_idx, nodes, ring_mask, nearest_label_indices):
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def smart_dilate(nodes, dilate_xy = 0, dilate_z = 0, directory = None, GPU = True, fast_dil = True, predownsample = None, use_dt_dil_amount = None, xy_scale = 1, z_scale = 1):
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if fast_dil:
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try:
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import edt
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dilated = nettracer.dilate_3D_dt(nodes, use_dt_dil_amount, xy_scale, z_scale, fast_dil = True)
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return smart_label_watershed(dilated, nodes, directory = None, remove_template = False)
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except:
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print("edt package not found. Please use 'pip install edt' if you would like to enable parallel searching.")
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return smart_dilate_short(nodes, use_dt_dil_amount, directory, xy_scale, z_scale)
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else:
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return smart_dilate_short(nodes, use_dt_dil_amount, directory, xy_scale, z_scale)
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@@ -699,7 +707,7 @@ def compute_distance_transform_distance(nodes, sampling=[1, 1, 1], fast_dil=Fals
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str(nodes.dtype),
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tuple(sampling)
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)
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result_shape, result_dtype = future.result(
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result_shape, result_dtype = future.result()
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distance = np.ndarray(result_shape, dtype=result_dtype, buffer=output_shm.buf).copy()
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@@ -711,8 +719,12 @@ def compute_distance_transform_distance(nodes, sampling=[1, 1, 1], fast_dil=Fals
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except Exception as e:
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print(f"Parallel distance transform failed ({e}), falling back to scipy")
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try:
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import edt
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import traceback
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traceback.print_exc() # See the full error
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except:
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print("edt package not found. Please use 'pip install edt' if you would like to enable parallel searching.")
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distance = distance_transform_edt(nodes, sampling=sampling)
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else:
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distance = distance_transform_edt(nodes, sampling=sampling)
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nettracer3d/tutorial.py
CHANGED
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@@ -1627,12 +1627,44 @@ def setup_connectivity_tutorial(window):
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action=MenuHelper.create_widget_interaction(tutorial, 'con_dialog', 'remove_trunk', 'setText("")')
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)
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tutorial.add_step(
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MenuHelper.create_widget_getter(tutorial, 'con_dialog', 'voronoi_safe'),
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"The next few options present alternate ways to handle the trunk/edges if desired. Selecting this 'Auto-Trunk' method will make edge elements that exist as plexuses between nodes simplify themselves to make local connections but avoid more distant connections that have more local connectivity available. This is done by first computing the normal network, then computing a second network where the search regions are fully maxed out (and therefore naturally split trunks up; note, this step will not use parallel dilation), then pruning the second network to drop connections that don't exist in the first region. As such, it will be somewhat slower if enabled.",
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highlight_type=None,
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message_position="beside",
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pre_action=MenuHelper.create_widget_interaction(tutorial, 'con_dialog', 'voronoi_safe', 'click()'),
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action = MenuHelper.create_widget_interaction(tutorial, 'con_dialog', 'voronoi_safe', 'toggle()')
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)
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tutorial.add_step(
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MenuHelper.create_widget_getter(tutorial, 'con_dialog', 'labeled_branches'),
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"The 'Convert Edges to Nodes' option will make your edges become nodes. This can be a good way to visualize direct connectivity paths, and is a robust way to mitigate bias in what is or isn't a trunk. However, the network dynamics will be altered by edge inclusion, resulting in much less node clusters in favor of edge-derived hubs.",
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highlight_type=None,
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message_position="beside",
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pre_action=MenuHelper.create_widget_interaction(tutorial, 'con_dialog', 'labeled_branches', 'click()'),
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action = MenuHelper.create_widget_interaction(tutorial, 'con_dialog', 'labeled_branches', 'toggle()')
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)
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tutorial.add_step(
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MenuHelper.create_widget_getter(tutorial, 'con_dialog', 'edge_node'),
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"The 'Pre-labeled edges' option will allow you to use pre-made edge labels, such as if you had previously labeled the branches of your edges. Instead of just joining nodes together, all edge labels will participate as nodes as well. This can be a way to visualize how branch-like structures in your edges interact with your main node objects. You can also do this from the modify network after the calculation has been done.",
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highlight_type=None,
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message_position="beside",
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pre_action=MenuHelper.create_widget_interaction(tutorial, 'con_dialog', 'edge_node', 'click()'),
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action = MenuHelper.create_widget_interaction(tutorial, 'con_dialog', 'edge_node', 'toggle()')
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"""
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tutorial.add_step(
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"Deselecting this button will have the system not consider 'inner edges'. Inner edges are portions of your edge image that exist solely within nodes (as well as their expanded search regions). You can deselect this to ignore inner connections between within node clusters, for example if you only wanted to consider more distal connections to get a simpler network. However, I would recommend keeping this enabled unless you had a good reason to not.",
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pre_action=MenuHelper.create_widget_interaction(tutorial, 'con_dialog', 'inners', 'click()'))
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"""
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tutorial.add_step(
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tutorial.add_step(
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"The first auto-correction option will automatically merge any internal labels that arise with their outer-neighbors. This is something that can occasionally happen with fat, trunk-like branches that are tricky to algorithmically decipher. I have found that this merge handles these issues quite well, so this option is enabled by default. An alternate option will make the internal labels only merge with external structures that are not 'branch-like'. This is a good thing to enable if you are also enabling the 'reunify main branches' correction, as it will stop long branches from merging with core-like elements.",
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"The second auto-correction step will automatically correct any branches that aren't contiguous in space. Rarely (Depending on the segmentation, really) a branch can initially be labeled non-contiguously, which is usually not correct. This is because the 'meat' of any branch is at first labeled based on which internal filament it's closest to. So if you have a very wide branch it may rarely aquire labels of nearby smaller branches across gaps. Enabling this will split those labels into seperate regions as to not confound the connectivity graph. The largest component is considered the 'correct one' and keeps its label, while smaller components inherit the label of the largest shared border of a 'real' branch they are bordering. It is enabled here by default to mitigate any potential errors, although note this does not apply to the branchpoint networks since they don't actually utilize the branches themselves.",
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"This 'attempt to auto correct skeleton looping' option should generally be enabled for 3D data. In short it applies an extra algorithmic step to improve the branch detection algorithm. However, this does not really apply to 2D data. It will be enabled by default for 3D data and disabled by default for 2D data.",
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Metadata-Version: 2.4
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Name: nettracer3d
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Version: 1.
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Version: 1.3.1
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Summary: Scripts for intializing and analyzing networks from segmentations of three dimensional images.
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Author-email: Liam McLaughlin <liamm@wustl.edu>
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Project-URL: Documentation, https://nettracer3d.readthedocs.io/en/latest/
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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:
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Please see: https://www.youtube.com/watch?v=_4uDy0mzG94&list=PLsrhxiimzKJMZ3_gTWkfrcAdJQQobUhj7
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---
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--- Installing as a Python package ---
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To install nettracer3d,
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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/
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2. **Base Package**: Next, use this command in your command terminal
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* pip install nettracer3d
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3. **For 3D Displays**: Or if you also want Napari for 3D displays:
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* pip install nettracer3d[viz]
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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:
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5. **Recommended full package**: Or if you want to just get both edt and napari at once:
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--- Installing as a Python package in Anaconda---
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I recommend installing the program as an Anaconda package to ensure its modules are work together on your specific system:
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(Install anaconda at the link below, set up a new python env for nettracer3d, then use the same pip command).
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https://www.anaconda.com/download?utm_source=anacondadocs&utm_medium=documentation&utm_campaign=download&utm_content=installwindows
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--- Using the downloadable version ---
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Alternatively, you can download a compiled .exe of version 1.2.7 here: https://doi.org/10.5281/zenodo.17873800
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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.
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--- Optional Packages ---
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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.
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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:
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pip install nettracer3d[cellpose]
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Alternatively,
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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)
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pip install nettracer3d[all]
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--- GPU ---
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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
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With a CUDA toolkit installed, use:
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@@ -118,12 +155,9 @@ NetTracer3D is freely available for academic and nonprofit use and can obtained
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NetTracer3D was developed by Liam McLaughlin while working under Dr. Sanjay Jain at Washington University School of Medicine.
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-- Version 1.
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-- Version 1.3.1 Updates --
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*
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*
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*
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* Removed dependency on nibabel (which was just being used to open .nii files). .nii files can still be opened if nibabel is installed manually.
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* Added option to not show numerical labels when displaying network graph.
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* Updated GUI to use pyqtgraph for image display rather than matplotlib
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* Upgraded the network graph visualization to also use pyqtgraph rather than matplotlib - now renders much faster, is embedded in the main window, and interacts with the main image view display.
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* Other minor tweaks and bug fixes
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@@ -1,5 +1,5 @@
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1
1
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nettracer3d/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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2
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-
nettracer3d/branch_stitcher.py,sha256=
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nettracer3d/branch_stitcher.py,sha256=rCTeh-28o7yN6ghYwxVSfrn2oc-TiPOm1xB3xJ5RWbw,21216
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3
3
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nettracer3d/cellpose_manager.py,sha256=NfRqW6Zl7yRU4qHCS_KjmR0R6QANSSgCO0_dr-eivxg,6694
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4
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nettracer3d/community_extractor.py,sha256=rPXXWwMX05mfD_ogULEouLy8CST-aOaoSw45NhloKVg,31754
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5
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nettracer3d/excelotron.py,sha256=aNof6k-DgMxVyFgsl3ltSCxG4vZW49cuvCBzfzhYhUY,75072
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@@ -7,23 +7,24 @@ nettracer3d/filaments.py,sha256=liuhikdRoANUmYA_hiPUPtDV-lYtR8wKbgnUVk55Hgs,4395
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nettracer3d/modularity.py,sha256=HgaVQSVjgAX3LAfJeUL1ZZ3P3xGuALJpQHqtYrhgw5c,22762
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nettracer3d/morphology.py,sha256=eusirbmDFQD__tlhkwZbctd8N4AARXVU0IGowr7M8cA,23297
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nettracer3d/neighborhoods.py,sha256=Bje77gWzXRIYyXkDlnFQnbUALnIt8dheLXHVFQsAKuc,53156
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nettracer3d/nettracer.py,sha256=
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nettracer3d/nettracer_gui.py,sha256=
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nettracer3d/network_analysis.py,sha256=
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nettracer3d/nettracer.py,sha256=kvatS_orNSLUQXuDZ5zBluP-Yau8nyoIYYWEcZyMzrs,298024
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11
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+
nettracer3d/nettracer_gui.py,sha256=SIGGetHwyRv8xJShVjwvabhEIgPWtHAOvcKZMleyPVM,732175
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12
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+
nettracer3d/network_analysis.py,sha256=QYZrzZ0T6Ubifw4hctvpw-V2lATN5jV5QtIF_UpcSpU,46363
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nettracer3d/network_draw.py,sha256=1Dj6VSMtMZbMxmrA7bWGxaLChqvM17xnZo85EUgG2PM,14291
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+
nettracer3d/network_graph_widget.py,sha256=dVuTRGEdjVOOJ4-DBCtOwQe-QpO3FwXvVYhC-oT3Xpo,80989
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nettracer3d/node_draw.py,sha256=Md12OiBtEyQmF2W_enO4qrSPFTRfoV4sOCMeEEdTNz4,10488
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-
nettracer3d/painting.py,sha256=
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nettracer3d/painting.py,sha256=10XBjDqfOb1nTbGgIicOpoeIKRZZ4al2uFtrv-8MIBE,16760
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nettracer3d/proximity.py,sha256=xvJLt61nTsKMdpJ0aiwJsB5vPriO34KG0LQwDjyfhC8,41410
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nettracer3d/run.py,sha256=xYeaAc8FCx8MuzTGyL3NR3mK7WZzffAYAH23bNRZYO4,127
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nettracer3d/segmenter.py,sha256=20ch_uLqedV9srwT1eL5eFs88ojkb2gELWJKgtYk2qk,72791
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nettracer3d/segmenter_GPU.py,sha256=FwzevixleTUoRmwVa8jPPzW82RZoC6nL2eEeZ4-2ZR8,80015
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nettracer3d/simple_network.py,sha256=
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nettracer3d/smart_dilate.py,sha256=
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nettracer3d/simple_network.py,sha256=1InpqSXfae_L-6lmf8lXgV7n_rk7Porg1hc_in9vkHg,10499
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22
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+
nettracer3d/smart_dilate.py,sha256=1UzLnX5LCj6OuFIy7_gHcZe9OIHkVJdIkZJDuJNqyYc,32009
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nettracer3d/stats.py,sha256=0YwrVLeEvll3PlbL5-0_9dstldr48PvxJrQm-PiC8jY,36607
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nettracer3d/tutorial.py,sha256=
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nettracer3d-1.
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nettracer3d-1.
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nettracer3d-1.
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nettracer3d-1.
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nettracer3d-1.
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nettracer3d-1.
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+
nettracer3d/tutorial.py,sha256=48__h2pWuERJLxC08_khFRW4XVf5vSXZtWnNUAFyWDY,154591
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25
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+
nettracer3d-1.3.1.dist-info/licenses/LICENSE,sha256=_Wg4zyCtT18lXBCXRov17IEop_-7z1OFo6o3JTzQj3g,568
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26
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+
nettracer3d-1.3.1.dist-info/METADATA,sha256=SVbWu_ycx1tghOiGVAA8w3EwlvVsnCKTGae6R9Io-RM,9676
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27
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+
nettracer3d-1.3.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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28
|
+
nettracer3d-1.3.1.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
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29
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+
nettracer3d-1.3.1.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
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+
nettracer3d-1.3.1.dist-info/RECORD,,
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File without changes
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File without changes
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File without changes
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File without changes
|