Visualization Catalogue

Visualization Tools.

The visualization of data is key element in data analysis workflows in neuroscience, computing, and brain-related medicine.
This catalogue of visualization tools provides information and navigation techniques to find the right tool for a designated analysis task.
It covers tools developed in and outside of HBP.

For questions and comments, please contact Benjamin Weyers (weyers@uni-trier.de).


The filters presented on the right enable interactive selection of visualization tools by means of the following fields:

Usage: Indicates the designated type of usage the tool is developed for, such as interactive analysis or presentation.
Data Type: Indicates the type of data, which can be visualized by the tools, such as abstract, 2D or 3D spatial data.
Data Format: Indicates the data format the tool supports, such as DICOM or NifTi.
Deployment: Indicates, on which type of device the software tool can be deployed, such as HPC or mobile systems.
Display Device: Indicates, on which type of device the resulting visualization can be displayed, such as desktop or VR.
HBP: Indicates whether the software tool has been developed in HPB or is an external software.

Active Filter:

 

Filtered Software:


    3DSlicer


    3D Slicer is an open source software platform for medical image informatics,
    image processing, and three-dimensional visualization.
    Built over two decades through support from the National Institutes of Health and a worldwide developer community,
    Slicer brings free, powerful cross-platform processing tools to physicians, researchers, and the general public.

    Date of Release January 2019
    Availability External
    License BSD
    Framework
    Version of software 4.10.1
    Version of documentation
    Software available https://www.slicer.org
    Documentation https://github.com/Slicer/Slicer
    Responsible The Slicer Community
    Requirements & dependencies CMake >= 3.13.4, Git >= 1.7.10, NSIS (optional), Qt5, SVN, Visual Studio
    Platforms Linux
    MacOS
    Windows
    Deployment Standalone
    Displaytype Desktop
    Input Formats Analyze, BMP, BioRad, Brains2, DICOM, GIPL, LSM, MGH-NMR, MRC, MetalImage, NRRD, NifTi, PNG, Stimulate, TIFF, VTK
    Output Formats Analyze, BMP, BioRad, Brains2, GH-NMR, GIPL, JPEG, LSM, MRC, MetalImage, NRRD, NifTi, PNG, Stimulate, TIFF, VTK



    FilamentTracer


    FilamentTracer is the most advanced software product for the automatic detection
    of neurons (dendritic trees, axons and spines), microtubules, and other filament-like structures in 2D, 3D and 4D. When combined with ImarisTrack,
    detection of temporal changes in length and volume of developing spines and dendrites will help researchers understand alterations caused by
    developmental and environmental changes.

    • 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

    Date of Release
    Availability External
    License Proprietary commercial software license
    Framework
    Version of software
    Version of documentation
    Software available http://www.bitplane.com/imaris/filamenttracer
    Documentation
    Responsible Bitplane AG

    (
    eusupport@bitplane.com
    )

    Requirements & dependencies Imaris
    Platforms MacOS
    Windows
    Deployment Standalone
    Displaytype Desktop
    Input Formats CSV
    Output Formats CSV



    ImageJ



    ImageJ is an open source image processing program designed for scientific multidimensional images.

    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.

    Date of Release Dezember 2018
    Availability External
    License Public Domain
    Framework
    Version of software imagej-2.0.0-rc-71
    Version of documentation
    Software available http://imagej.net/
    Documentation https://github.com/imagej/imagej
    Responsible Curtis Rueden

    (ctrueden@wisc.edu)
    Wayne Rasband
    (rasbandw@mail.nih.gov)

    Requirements & dependencies Java >= 1.8
    Platforms Linux
    MacOS
    Windows
    Deployment Standalone
    Displaytype Desktop
    Input Formats BMP, DICOM, FITS, GIF, JPEG, PGM, PNG, TIFF
    Output Formats AVI, BMP, FITS, GIF, JPEG, LUT, PNG, Raw Data, TIFF



    MRIcron



    MRIcron is a cross-platform NIfTI format image viewer.
    It can load multiple layers of images, generate volume renderings and draw volumes of interest.
    It also provides dcm2nii for converting DICOM images to NIfTI format and NPM for statistics.
    MRIcron is a mature and useful tool, however you may want to consider the more recent MRIcroGL as an alternative.

    Date of Release August 2008
    Availability External
    License BSD License
    Framework
    Version of software
    Version of documentation
    Software available https://people.cas.sc.edu/rorden/mricron/index.html
    Documentation
    Responsible Chris Rorden

    (rorden@sc.edu)

    Requirements & dependencies
    Platforms Linux
    MacOS
    Windows
    Deployment Standalone
    Displaytype Desktop
    Input Formats DICOM, HDR, HEAD, MGH, MGZ, MHA, NHDR, NII, NII.GZ, NRRD, VOI
    Output Formats BMP, NlfTI



    Neurolucida



    Neurolucida is the gold standard for creating and analyzing realistic, meaningful, and quantifiable neuron reconstructions from microscope images. Perform detailed morphometric analyses of neurons, such as quantifying:

    • 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

    Date of Release 2019
    Availability External
    License Proprietary commercial software license
    Framework
    Version of software Neurolucida Version 2019
    Version of documentation
    Software available http://www.mbfbioscience.com/neurolucida
    Documentation
    Responsible MBF Bioscience (support@mbfbioscience.com)
    Requirements & dependencies
    Platforms Windows
    Deployment Standalone
    Displaytype Desktop
    Input Formats
    Output Formats MP4



    Nilearn



    Nilearn: Machine learning for Neuro-Imaging in Python,
    is a software package to facilitate the use of statistical learning on NeuroImaging data.

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

    Date of Release April 2019
    Availability External
    License BSD license (3 clause)
    Framework
    Version of software 0.5.2
    Version of documentation
    Software available http://nilearn.github.io/
    Documentation https://github.com/nilearn/nilearn
    Responsible INRIA
    Requirements & dependencies Python
    Platforms Linux
    MacOS
    Windows
    Deployment Standalone
    Displaytype Desktop
    Input Formats NII
    Output Formats



    PLIViewer


    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.

    The original dataset: Fibre Orientation Maps rendered on top of Retardation map
    A full slice from the Fibre Orientation Map of a Vervet Monkey
    Orientation Distribution Functions (ODFs) rendered with Streamline Tractography
    Close-up view of the ODFs

    Date of Release February 2018
    Availability Internal
    License Public Domain
    Framework
    Version of software
    Version of documentation 1.1.0
    Software available https://devhub.vr.rwth-aachen.de/VR-Group/pli_vis
    Documentation https://devhub.vr.rwth-aachen.de/VR-Group/pli_vis
    Responsible Ali Demiralp
    (demiralp@gmx.com)
    Requirements & dependencies
    Platforms Linux
    Deployment Standalone
    Displaytype Desktop
    Input Formats HDF5
    Output Formats



    Simple Neurite Tracer



    Fiji’s framework for semi-automated tracing of neurons and other tube-like structures.

    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).

    Date of Release March 2018
    Availability External
    License GPLv3
    Framework ImageJ
    Version of software 3.1.5
    Version of documentation 3.1.3
    Software available http://imagej.net/Simple_Neurite_Tracer
    Documentation https://github.com/fiji/Simple_Neurite_Tracer
    Responsible Curtis Rueden
    Tiago Ferreira
    Requirements & dependencies ImageJ, Java >= 1.8
    Platforms Linux
    MacOS
    Windows
    Deployment Standalone
    Displaytype Desktop
    Input Formats SWC, TRACES
    Output Formats CSV, SWC, TRACES



    Vaa3D


    Vaa3D is an open source 3D/4D/5D image visualization and analysis software
    for bioimage analysis. It is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) image volumes and surface objects.
    It is also a container of powerful modules/plugins for high dimensional image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc).
    This makes Vaa3D suitable for various bioimage informatics applications, and a nice platform to develop new 3D image analysis algorithms for high-throughput processing.
    In short, Vaa3D streamlines the workflow of visualization-assisted analysis.

    Date of Release March 2019
    Availability External
    License MIT license
    Framework
    Version of software v3.597
    Version of documentation
    Software available http://vaa3d.org
    Documentation https://github.com/Vaa3D
    Responsible Konrad Rokicki
    Requirements & dependencies
    Platforms Linux
    MacOS
    Windows
    Deployment Standalone
    Displaytype Desktop
    VR
    Input Formats TIFF, Vaa3D raw
    Output Formats APO, SWC, TIFF, Vaa3D raw



    VIOLA


    VIOLA (Visualization Of Layer Activity) is an interactive, web-based tool to visualize activity data in multiple 2D layers such as the simulation output of neuronal networks with 2D geometry.

    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.

    Date of Release November 2018
    Availability External
    License GPLv2
    Framework
    Version of software
    Version of documentation
    Software available http://hbpvis.github.io/VIOLA/
    Documentation https://github.com/HBPVIS/VIOLA
    Responsible Benjamin Weyers
    Espen Hagen
    Johanna Senk
    Requirements & dependencies
    Platforms Linux
    MacOS
    Windows
    Deployment Web
    Displaytype Desktop
    Input Formats DAT, GDF, JSON, LFP
    Output Formats



    Visualization Toolkit



    The Visualization Toolkit (VTK) is open source software for manipulating and displaying scientific data.
    It comes with state-of-the-art tools for 3D rendering, a suite of widgets for 3D interaction, and extensive 2D plotting capability.

    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.

    Date of Release January 2019
    Availability External
    License 3-Clause BSD
    Framework
    Version of software 8.2.0
    Version of documentation
    Software available https://www.vtk.org
    Documentation https://gitlab.kitware.com/vtk/vtk
    Responsible Kitware Inc.

    (kitware@kitware.com)

    Requirements & dependencies
    Platforms Android
    Linux
    MacOS
    Windows
    Deployment HPC
    Mobile
    Standalone
    Web
    Displaytype Desktop
    Input Formats 3D Studio, AVS “UCD” format, CAD STL, DICOM, Ensight, Facet, Facet, Fluent GAMIT ASCII, Gaussian, Marching Cubes, Movie BYU, OBJ, Open Inventor 2.0, PDB, PLOT3D, PLY, Particle, VTK Poly Data, VTK Structured Grid, XYZ
    Output Formats CAD STL, CGM, Facet, Marching Cubes, Movie BYU, OBJ, Open Inventor 2.0, PLY, Renderman, VRML 2.0, VTK Poly Data, VTK Structured Grid