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FreeSurfer
Allows the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. FreeSurfer proposes a suite of tools that provide extensive and automated analysis of key features in the human brain. This includes skull stripping, image registration, subcortical segmentation, cortical surface reconstruction, cortical segmentation, cortical thickness estimation, longitudinal processing, fMRI analysis, tractography, FreeView Visualization GUI, etc... FreeSurfer is freely available, runs on a wide variety of hardware and software platforms, and is open source.
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.
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.
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.
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.
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.
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