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VisBio
Designed for easy visualization and analysis of multidimensional image data. VisBio software is an end-user application built from the ground up to handle visualization and analysis of multidimensional image data, regardless of size or dimensionality. By creating low-resolution thumbnail images during data import, the program conserves memory while providing fluid image browsing and animation capabilities. Other tools include flexible color mapping, semitransparent volume rendering, 3D slicing at arbitrary orientations, 3D measurements, movie capturing, and powerful data export tools.
Dipy / Diffusion Imaging in Python
Allows to study diffusion Magnetic Resonance Imaging (MRI) data. Dipy is a program allowing users to share their code and experiments. One of its objectives is to provide transparent implementations for all the different steps of the dMRI analysis with a uniform programming interface. It implements two interfaces for probabilistic Markov fiber tracking: (1) it allows the user to provide the distribution evaluated on a discrete set of possible tracking directions, and (2) it accommodates tracking methods where the fiber orientation distribution function (fODF) cannot be easily computed.
ANTs / Advanced Normalization Tools
Computes high-dimensional mappings to capture the statistics of brain structure and function. ANTs allows users to organize, visualize and statistically explore large biomedical image sets. It integrates imaging modalities and related information in space and time, and works across species or organ systems with minimal customization. ANTs depends on the Insight ToolKit (ITK), a widely used medical image processing library to which ANTs developers contribute. ANTs can be used paired with ANTsR, an emerging tool supporting standardized multimodality image analysis. ANTs is popularly considered a state-of-the-art medical image registration and segmentation toolkit.
VPV / Volume Phenotype Viewer
Enables rapid identification of phenotypically abnormal structures. Data are easily loaded by drag and drop, with support for most commonly used file formats. On loading the registration results, embryos may be overlaid with the t-statistic heatmaps to reveal regions of dysmorphology. We have adopted a hot red/blue colour scheme to be consistent with previously reported results. The heatmap data can be filtered by t statistic value to emphasize regions of different statistical significances. Vector field data can also be loaded into VPV and filtered by magnitude to identify where the most significant deformations have taken place during registration.
BoneJ
A plugin for bone image analysis in ImageJ. BoneJ provides free, open source tools for trabecular geometry and whole bone shape analysis. It calculates several trabecular, cross-sectional and particulate parameters in a convenient format. Java technology allows BoneJ to run on commodity computers, independent of scanner devices, fully utilising hardware resources. ImageJ’s plugin infrastructure provides a flexible working environment that can be tailored to diverse experimental setups. BoneJ is a working program and a starting point for further development, which will be directed by users’ requests and the emergence of new techniques.
Mango / Multi-image Analysis GUI
Automates regional behavioral analysis of human brain images. Mango provides analysis tools and a user interface to navigate image volumes. The tool is ease to use, multi-platform Java application and extensive region of interest tools. It has the ability to add and update software as a plugin module and offers full access to a suite of image viewing and processing features. The software is able to rapidly determine regionally specific behaviors for researchers’ brain studies.
BrainBrowser
Exposes a set of web-based 3D visualization tools primarily targeting neuroimaging. Using open web technologies, such as WebGL and HTML5, BrainBrowser allows for real-time manipulation and analysis of 3D imaging data through any modern web browser. BrainBrowser includes two major components. The BrainBrowser Surface Viewer is a WebGL-based 3D viewer capable of displaying 3D surfaces in real time and mapping various sorts of data to them. The BrainBrowser Volume Viewer is an HTML5 Canvas-based viewer allowing slice-by-slice traversal of 3D or 4D MINC volumetric data. All source code for BrainBrowser is freely available for download. Furthermore, a BrainBrowser Surface Viewer widget can be load into a web page to view data through an HTTP request.
iELVis / Intracranial ELectrode VISualization
Assists users in neuroimaging co-registration and overlay creation. iELVis has several features: it (i) implements a set of standard tools for electrode localization/visualization using MATLAB code, (ii) establishes a pipeline and toolset to standardize localization across multiple laboratories, (iii) implements quality control metrics to help identify erroneous localizations and (iv) produces interactive, multi-view representations of the brain that can simultaneously represent multiple data modalities.
AMIDE / Amide's a Medical Imaging Data Examiner
Displays and analyzes multimodality volumetric medical images. AMIDE provides the research community with a relatively full-featured, freely available, and open source solution for single and multimodality volumetric medical image analysis. It provides a variety of additional features useful to the molecular imaging researcher, including fully three dimensional ROI drawing and analysis for static and dynamic images, two and three way linked viewing (dual cursor mode), rigid body registration using fiducial markers, filtering and cropping of data sets, movie generation, series viewing, and volume rendering.
NMT / National Institute of Mental Health Macaque Template
Provides a high-resolution in vivo magnetic resonance imaging template of the average macaque brain generated from 31 subjects, as well as a neuroimaging tool for improved data analysis and visualization. From the NMT volume, maps of tissue segmentation and cortical thickness were generated. Surface reconstructions and transformations to previously published digital brain atlases are also provided. An analysis pipeline using the NMT automates and standardizes the time-consuming processes of brain extraction, tissue segmentation, and morphometric feature estimation for anatomical scans of individual subjects. The NMT and associated tools thus provide a common platform for precise single-subject data analysis and for characterizations of neuroimaging results across subjects and studies.
Display
Allows users to display and manipulate three dimensional objects, mainly human cortical surfaces and sulcal curves. Display includes visualization and segmentation of 3D and 4D medical images. It supports a number of visualization features such as: visualization of 3D surfaces; the intersection of the 3D surface with the volumetric data; viewing an arbitrary, oblique plane through the volumetric data. It also permits researchers to annotate structural features on either a surface or a volumetric dataset.
ScAnVP / Scan Analysis and Visualization Processor
Processes and analyzes multimodality neuroimaging data. ScAnVP provides applications for retrieving, visualizing, and group processing of single-volume brain images acquired via nuclear medicine and other radiological techniques. The software also includes computing routines for brain mapping analyses of volumes of interest (VOI’s). It includes several functions, for instance to calculate neurobiological parameters from both functional and anatomical brain images, or to extract and convert brain images from various scanners.
Simpleware ScanIP
Provides a software environment for comprehensively processing 3D image data (MRI, CT, micro-CT, FIB-SEM…). Simpleware ScanIP offers powerful image visualisation, analysis, segmentation, and quantification tools. It includes video recording features and options to export surface models/meshes from segmented data for CAD and 3D printing. Additional modules are available for exporting CAE meshes, integrating image data and CAD, exporting NURBS and calculating effective material properties from scans.
Visible patient
Provides a list of tools to aid researchers in reading, interpreting, reporting, and treatment planning. Visible patient includes detection and labeling tools of organ segments. It contains basic imaging tools for: (1) general images; (2) including 2D viewing, (3) volume rendering and 3D volume viewing, (4) orthogonal Multi-Planar Reconstructions (MPR), (5) image fusion, (6) surface rendering, (7) measurements, (8) reporting, (9) storing, (10) general image management; and (11) administration.
Amira 3D Software for Life Sciences
Allows users to visualize, manipulate, and understand data from imaging modalities such as computed tomography, microscopy or Magnetic resonance imaging (MRI). Amira 3D Software for Life Sciences provides features to import and process 2D and 3D images data, visualization techniques and tools for visual analysis. Users can also create and share presentations. The base product can be customized by adding functional extensions to fit special needs in different application areas.
Scalable Brain Atlas
Obsolete
Allows users to browse brain atlases. Scalable Brain Atlas centralizes multiple repositories among seven species (macaque, mouse, rat, human, marmoset, opossum and ferret). The application includes a plurality of features including: (i) the ability to convert scalable vector graphics (SVG)-based renderings to bitmap images; (ii) the computation of several metrics; (iii) the creation of a hierarchical list of regions for each imported atlas and; (iv) the exporting of atlas delineations to label volumes.
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