NetTracer3D documentation

Welcome to NetTracer3D

NetTracer3D is a powerful tool for 2D and 3D analysis of microscopic/medical images. It supports generation of 3D networks showing relationships between objects in three dimensional space, either by proximity, grouped by interactivity with another object such as nerves, or between branches of objects like vessels or nerves.

Key Features

• Algorithms to group objects into three-dimensional networks, abstracting big data into a manageable form for analysis.

• Segmentation using machine learning

• Fully functional, user friendly GUI supporting interactive 2D and 3D displays.

• A plethora of tools for 3D image analysis and modification, such as branch labeling and 3D watershedding.

• A suite of tools for analyzing and exporting network data.

Getting Started

To get started with NetTracer3D, check out the Installation guide and then proceed to the Quickstart - Segmenting Data and Generating Connectivity Networks tutorial.

A youtube tutorial on installing and using the program can be found here: https://www.youtube.com/watch?v=_4uDy0mzG94&list=PLsrhxiimzKJMZ3_gTWkfrcAdJQQobUhj7

User Guide:

• Installation
  • System Requirements
  • Installing NetTracer3D
  • Verifying Installation
  • Troubleshooting
  • Next Steps
• Quickstart - Segmenting Data and Generating Connectivity Networks
  • Launch NetTracer3D
  • Interface Overview
  • The Control Panel
  • Loading an Image
  • Basic Navigation of the Image Viewer Window
  • Segmenting Data
  • Introduction to Types of Networks
  • The Connectivity Network - Generating a Network Using An Edge Image
  • Analysis
  • Exporting Data
  • Next Steps
• Proximity Networks - Ideal for Cellular Data
  • Generating a Network Based on Proximity
  • Cellular Data - Modality of Analysis
  • Using Proximity Networks for Advanced Cellular Neighborhood Analysis - Walthrough Analysis of CODEX sample
  • Next Steps
• Labeling Branches and Branch Networks
  • Labeling Branches
  • Examples of Tweaking Branch Labels (Optional)
  • Branch Adjacency Network
  • Using Branch Labels as Nodes
  • Branchpoint Networks
  • Next Steps
• Properties of a Network3D Object
  • Main Properties
  • Necessary Structures to Properties stored in CSVs
  • Temp Properties
  • Next Steps
• Using the Spreadsheet Loader
  • Opening the Excel Helper
  • Next Steps
• Available Keyboard Shortcuts
  • In the default viewer mode:
  • If in the upper right or lower right network/tabulated data widgets:
  • If in paint mode:
  • If using the machine-learning segmenter:
  • Next Steps

Detailed Function Guide:

• Right Clicking - All Options Available by Right Clicking in the GUI
  • Right Clicking in the Image Viewer Window
  • Right Clicking in the Network Table Widget
  • Right Clicking in the Tabbed Data Widget
  • Next Steps
• All File Menu Options
  • Save
  • Save As
  • Load
  • Images -> Node Identities
  • Next Steps
• All Analyze Menu Options
  • ‘Analyze -> Network -> Show Network’
  • ‘Analyze -> Network -> Generic Network Report’
  • ‘Analyze -> Network -> Create Communities based on Network’
  • ‘Analyze -> Network -> Create Communities based on Nodes Immediate Neighbors’
  • ‘Analyze -> Network -> Create Communities Based on Hexagonal/Rhomboid Proximity Cells?’
  • ‘Analyze -> Network -> Calculate Composition of Network Communities (And UMAP)’
  • ‘Analyze -> Network -> Convert Network Communities Into Supercommunities (Also Returns Compositional Heatmaps)’
  • ‘Analyze -> Stats -> Network Related -> Calculate Generic Network Stats’
  • ‘Analyze -> Stats -> Network Related -> Network Statistics Histograms’
  • ‘Analyze -> Stats -> Network Related -> Radial Distribution Analysis’
  • ‘Analyze -> Stats -> Network Related -> Network Nearest Neighbors’
  • ‘Analyze -> Stats -> Network Related -> Community Cluster Heatmap’
  • ‘Analyze -> Stats -> Spatial -> Identity Distribution of Neighbors’
  • ‘Analyze -> Stats -> Spatial -> Ripley Clustering Analysis’
  • ‘Analyze -> Stats -> Spatial -> Average Nearest Neighbors (With Clustering Heatmaps)’
  • ‘Analyze -> Stats -> Spatial -> Calculate Node < > Edge Interactions’
  • ‘Analyze -> Stats -> Morphological -> Calculate Volumes’
  • ‘Analyze -> Stats -> Morphological -> Calculate Radii’
  • ‘Analyze -> Stats -> Morphological -> Calculate Surface Area’
  • ‘Analyze -> Stats -> Morphological -> Calculate Sphericities’
  • ‘Analyze -> Stats -> Morphological -> Calculate Branch Stats’
  • ‘Analyze -> Stats -> Significance Testing’
  • ‘Analyze -> Stats -> Cellular-Esque Analysis’
  • ‘Analyze -> Data/Overlays -> Get Degree Information’
  • ‘Analyze -> Data/Overlays -> Get Hub Information’
  • ‘Analyze -> Data/Overlays -> Get Transcommunity Nodes’
  • ‘Analyze -> Data/Overlays -> Code Communities’
  • ‘Analyze -> Data/Overlays -> Code Identities’
  • ‘Analyze -> Data/Overlays -> Centroid UMAP’
  • ‘Analyze -> Randomize -> Generate Equivalent Random Network’
  • ‘Analyze -> Randomize -> Scramble Nodes (Centroids)’
  • Next Steps
• All Process Menu Options
  • ‘Process -> Calculate Network -> Calculate Connectivity Network…’
  • ‘Process -> Calculate Network -> Calculate Proximity Network…’
  • ‘Process -> Calculate Network -> Calculate Branchpoint Network…’
  • ‘Process -> Calculate Network -> Calculate Branch Adjacency Network’
  • ‘Process -> Calculate Network -> Calculate Centroids…’
  • ‘Process -> Image -> Resize’
  • ‘Process -> Image -> Clean Segmentation’
  • ‘Process -> Image -> Dilate’
  • ‘Process -> Image -> Erode’
  • ‘Process -> Image -> Fill Holes’
  • ‘Process -> Image -> Binarize’
  • ‘Process -> Image -> Label Objects’
  • ‘Process -> Image -> Neighborhood Labels’
  • ‘Process -> Image -> Threshold/Segment’
  • ‘Process -> Image -> Mask Channel’
  • ‘Process -> Image -> Crop Channels’
  • ‘Process -> Image -> Channel dtype’
  • ‘Process -> Image -> Skeletonize’
  • ‘Process -> Image -> Binary Watershed’
  • ‘Process -> Image -> Gray Watershed’
  • ‘Process -> Image -> Invert’
  • ‘Process -> Image -> Z-Project’
  • ‘Process -> Image -> Normalize Brigthness’
  • ‘Process -> Generate -> Generate Nodes (From Node Centroids)’
  • ‘Process -> Generate -> Generate Nodes (From ‘Edge’ Vertices)’
  • ‘Process -> Generate -> Label Branches’
  • ‘Process -> Generate -> Trace Filaments’
  • ‘Process -> Generate -> Generate Voronoi Diagram’
  • ‘Process -> Generate -> Generate Convex Hull’
  • ‘Process -> Generate -> Generate Artificial Hexagonal Nodes’
  • ‘Process -> Modify Network/Properties’
  • Next Steps
• All Image Menu Options
  • ‘Image -> Properties’
  • ‘Image -> Adjust Brightness/Contrast’
  • ‘Image -> Channel Colors’
  • ‘Image -> Overlays -> Create Network Overlay’
  • ‘Image -> Overlays -> Create ID Overlay’
  • ‘Image -> Overlays -> Color Nodes (or edges)’
  • ‘Image -> Overlays -> Shuffle’
  • ‘Image -> Select Objects’
  • ‘Image -> Show 3D (Napari)’
  • ‘Image -> Cellpose’

Development:

• Contact
• Changelog
• About
• Usage