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Lead-DBS / Lead Deep Brain Stimulation
Aims to assists users in spotting and displaying electrodes in patients treated with deep brain stimulation (DBS). Lead-DBS is a program that gathers tools facilitating DBS electrode reconstructions and related processing. This toolkit works by using 3D visualization mode and electrode reconstruction algorithms. It includes the following features: (1) reconstruction of the electrode trajectories; (2) manual correction of the electrode localization; or (3) visualization of a 3D model showing DBS electrodes and their target areas.
Enables largely automated processing of magnetic resonance images (MRI) of the human brain. BrainSuite provides a sequence of low-level operations that can produce accurate brain segmentations in clinical time. It produces classified brain volumes that can be useful for quantitative studies of different regions of the brain. The tool consists of several modules that performs skull and scalp removal, nonuniformity correction, tissue classification, and object topology correction.
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.
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.
CBS Tools
Allows ultra-high-resolution brain segmentation at 7 Tesla (T). CBS Tools is an automated computational framework for brain segmentation and cortical reconstruction at the ultra-high resolution of 0.4 mm, based on quantitative T1 images acquired at 7 T with the MP2RAGE sequence. The software is implemented as a plug-in for the MIPAV and JIST medical image processing platforms. It supports many image formats, and includes a user-friendly interface for image visualization and editing as well as a graphical pipeline engine for large-scale processing.
MANTiS / Morphologically Adaptive Neonatal Tissue Segmentation
Extends the unified segmentation approach to tissue classification implemented in Statistical Parametric Mapping (SPM) software to neonates. MANTiS utilizes a combination of unified segmentation, template adaptation via morphological segmentation tools and topological filtering, to segment the neonatal brain into eight tissue classes: cortical gray matter, white matter, deep nuclear gray matter, cerebellum, brainstem, cerebrospinal fluid (CSF), hippocampus and amygdala. It is able to segment neonatal brain tissues well, even in images that have brain abnormalities common in preterm infants.
ITK / Insight Segmentation and Registration Toolkit
Allows to perform registration and segmentation for image analysis. Segmentation is the process of identifying and classifying data found in a digitally sampled representation. ITK uses a model of software development known as Extreme Programming. The sampled representation is an image acquired from such medical instrumentation as Computed Tomography (CT), Magnetic Resonance Imaging (MRI) or ultrasound scanners. Registration is the task of aligning or developing correspondences between data. For example, in the medical environment, a CT scan may be aligned with a MRI scan in order to combine the information contained in both.
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.
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.
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.
Provides a free volume (3D image) viewer and segmentation tool. BrainSeg3D is a graphic application that make segmentation of volumes more accurate by providing tools for semi-automated segmentation combined with a user friendly graphic interface. This application is based on Seg3D, a free volume segmentation and processing tool. It was developed for medical professionals who need to perform image analysis as part of their research or for researchers working in the field of image analysis.
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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