• Versatile tracing methods
• Obtain branch length and diameter statistics
• Manually draw segments with automatic centering
• Utilize multiple branch selection methods
• Visualize filaments along with non-filamentous structures

ImageJ is highly extensible, with thousands of plugins and scripts for performing a wide variety of tasks, and a large user community.

• Open source: ImageJ is a tool for the scientific community. To maintain transparency, the ImageJ application and its source code will always be freely available.
• Reproducible: Powerful tools such as the Script Editor and personal update sites help you develop and share reproducible analysis workflows.
• Interoperable: ImageJ is not an island. Use the best tool for the job, including KNIME, ITK, MATLAB, and a multitude of scripting languages.

• the number of dendrites, axons, nodes, synapses, and spines
• the length, width, and volume of dendrites and axons
• the area and volume of the soma
• the complexity and extension of neurons

Namely Nilearn leverages the scikit-learn Python toolbox for multivariate statistics with applications such as predictive modelling,
classification, decoding, or connectivity analysis.

The PLIViewer is visualization software for 3D-Polarized Light Imaging (3D-PLI), to interactively explore the scalar and vector datasets; it provides additional methods to transform data, thus revealing new insights that are not available in the raw representations. The high resolution provided by 3D-PLI produces massive, terabyte-scale datasets, which makes visualization challenging.

The PLIViewer tackles this problem by providing functionality to select areas of interests from the dataset, and options for downscaling. It makes it possible to interactively compute and visualize Orientation Distribution Functions (ODFs) and polar plots from the vector field, which reveal mesoscopic and macroscopic scale information from the microscopic dataset without significant loss of detail. The PLIViewer equips the neuroscientist with specialized visualization tools needed to explore 3D-PLI datasets through direct and interactive visualization of the data.

This plugin is designed to allow easy semi-automatic tracing of neurons or other tube-like structures (e.g., blood vessels) through 3D image stacks. The plugin has built-in tools for analysis and hardware accelerated 3D visualization of the results. Data can be imported and exported in SWC files for interaction with other software, or details of the traces can be exported as CSV files for analysis in spreadsheets or statistical software. The native file format is open and XML-based. This plugin is Free Software (also known as Open Source software).

A usage example demonstrates the visualization of spike data resulting from a NEST simulation of a spatially structured point-neuron network with excitatory and inhibitory neuron populations and an external stimulus.

VTK is part of Kitware’s collection of supported platforms for software development.
The platform is used worldwide in commercial applications, as well as in research and development.