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.
Allows researchers to visualize and explore data. AFQ-Browser is a visualization tool for the quantitative analysis of diffusion magnetic resonance imaging (MRI) data in the web browser. It assists user in removing barriers to public data release. It also makes possible creation of an interactive website of companion data for a manuscript with a single command.
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 users to segment structures in 3D medical images. ITK-SNAP provides semi-automatic segmentation using active contour methods, as well as manual delineation and image navigation. It is an application providing a method to extract structures in 3D image data of different modalities and from different anatomical regions. Moreover, it permits users to link cursor for 3D navigation or to post-process the segmentation results.
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.
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.
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.
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.
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.
Provides a platform for diffusion-weighted magnetic resonance imaging (dMRI) and tractography data visualization. FiberWeb allows users to display virtual dissection, streamlines and volumes in real time, in a wide range of imaging formats. The tool also permits to interact with data by performing real-time deterministic and probabilistic tractography (RTT). It is suited to support large datasets.
Allows users to develop algorithms and to process large-scale images. JIST is a program that generates graphical user interfaces and provides advanced batch processing tools to the scientific community. This software can integrate MIPAV to supply user visualization and exploration of the multi-dimensional imaging data as well as three-dimensional structures. It can be used to encapsulate difficult and time-consuming steps in the analysis and visualization of data from a single subject, or to process data from many subjects.
Creates 3D PDF documents for biomedical publications. MeVisLab aims to facilitate the generation of U3D files by reducing the number of necessary tools to only one application in the field of biomedical image processing. It allows users to build sophisticated applications with graphical user interfaces that hide the underlying platform and do not require substantial programming knowledge. This tool permits simple assembling of image processing networks.
Provides solutions to users for viewing, modeling, and analyzing 3-D image data for structural biology. IMOD is designed for observing data from tomographic, serial section, and optical section reconstructions. Moreover, this program is also able to measure areas, volumes, and contour lengths, and to count objects of any model class.
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.
Provides a method for high-resolution MR angiographic (MRA) images rebuilding low-resolution k-space data. CODE allows users to speed reconstruction for dataset whose whole samples are equals to 3 pixels or larger. It offers a way for visualizing boundaries of large vessels by generating high definition images and intends to be easy to implement.
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.
Allows detailed investigation and evaluation of multidimensional biomedical images. AnalyzePro can serve for magnetic resonance imaging, radionuclide emission tomography, ultrasound tomography, and 3-D imaging modalities based on x-ray computed tomography. It contains features for interactive display, manipulation and measurement of multidimensional image data.
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.
Manipulates medical images NetCDF (MINC) files. JIV2 is a program which can be run as both a standalone application or through a web browser. It provides features allowing the synchronized views of several volumes, the sharing of views which can be accessed through the web platform, the conversion of MINC files towards raw format as well as the displaying of multiple anatomical labels.
Provides domain specific visualization capabilities. ImageVis3D is a volume renderer for rendering large scale data on commodity workstations. It offers a flexible interface and allows users to explore terabyte-sized data sets on hardware ranging from mobile devices to high-end graphics workstations. The tool can be reuse and modified by users.
Allows users to visualize and compare multiple 3D image datasets. JIV provides a method to display 3D medical imaging datasets by three orthogonal 2D slices through the same location in the volume. It assists users to observe slices side-by-side, all at the same position in the volume. This software can be used in remote data processing - when data goes to a central, well-equipped, site for image processing and storage.
Enables quantitative analysis and visualization of medical images of numerous modalities such as PET (positron emission tomography), MRI (magnetic resonance imaging), CT (computerized tomography), or microscopy. Using MIPAV's standard user-interface and analysis tools, researchers at remote sites (via the internet) can easily share research data and analyses, thereby enhancing their ability to research, diagnose, monitor, and treat medical disorders.
Offers functions to display images and surfaces. AMILab contains two-dimensional function plot and histogram scripts. It employs the automatic wrapping of the VTK and wxWidgets to proceed. The tool scripting language features can be extended with manual and automatic wrapping. It can be useful for: sub-images, resizing, arithmetic operations, Gaussian convolutions, mathematical morphology, distance transforms and skeletonization.
Allows to realize analysis and visualisation of 3D biological image data, and more particularly traced neurons. NAT accepts 3D images in NRRD and 'Amira' AmiraMesh formats. The data can be manipulated and visualized in 3D. The manipulation includes applying calculated registrations, e.g. using the 'CMTK' registration suite. This tool permits morphological comparison between neurons including clustering and searching.
Allows users to research and visualize medical images. medInria is a platform for the diffusion of research software in medical imaging created by Inria teams. This platform offers several types of functions such as: (1) management of the database and file importation; (2) 2D or 4D visualization; (3) distribution of images processing; (4) segmentation of images or (5) registration of images; (6) filtering of images.
Aims to develop prototype and create new applications for image-guided surgery. IGSTK is an open-source repository which is mainly composed of three components: (i) a visualization window to supply a graphical user interface, (ii) The SpatialObjects section to represent geometrical shapes in the scene of the surgical room, (iii) and a device for providing position and orientation information about objects in the scene.
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.
Assists users in segmenting and visualizing 3D digital image. SkullyDoo provides the following features: (1) loading of various 3D images in multiple formats, (2) visualization and interaction with 3D images and surfaces, (3) application to filters to images and surfaces, and (4) application of different segmentation algorithms. The software is customizable, and it is possible to define new image/surface processing filters.
Hosts heterogeneous tools dedicated to neuroimaging research. BrainVISA aims to help researchers in developing new neuroimaging tools, sharing data and distributing software. It offers a way to define viewers which may use any visualization software. Thanks to its data management functions, the tool can define the data types handled by the software, associate key attributes for indexation, and filename patterns to make the link between the filesystem and the database schema.
Provides an image viewer for neuroimaging data. MRIcron is a platform able to support multiple layers, draw an identified region of brain injury, view data’s volume rendering and computes statistical results. The software also includes a functionality which allows users to convert DICOM images to NIfTI format and NPM for statistics.
Assists in updating image calibration after the first reslicing. Dynamic Reslice is a plugin for ImageJ and enables orthogonal slice through the volume represented by the stack. This software is compatible with the Fiji script. Users can use this plugin to drawn resliced window and change the region of interest (ROI) shape with some options like a 90° rotation or a vertical flip.
Offers a digital imaging and communications in medicine (DICOM) solution. OsiriX is an image processing software that provides displaying, reviewing, interpreting and post-processing image files. It supports DICOM standard for a complete integration in a workflow environment and in a picture archiving and communication system (PACS).
Allows users to display multiplanar, orthogonal views, volume and surface renderings with thresholding-based tissue segmentation. 3DimViewer is a lightweight 3D viewer of medical digital imaging and communications in medicine (DICOM) datasets. It contains several features such as: distance and density measuring, high quality volume rendering for direct 3D visualization, surface reconstruction of any segmented tissue, or 3D surface rendering.
Furnishes an open source data model for neuroscientific data visualization and investigation. Ogles employs slice derived volume data combined with surface meshes and can be applied in the context of stereotactic neurosurgery. It enables to convert 3D brain atlas data into individual brain configurations. This tool can determine the effects of electrical fields of deep brain stimulation (DBS) electrodes.
Permits three-dimensional (3D) measurement and volume visualization. VoxBlast consists of a general-purpose rendering application for research. It furnishes functions for pseudo- coloring, transparency, lighting, 2D and 3D measurements, 2D slice viewing, cropping, seed fill, movie loop generation, filters, palette editing, surface extraction and polygon rendering. This tool is designed for computed tomography (CT) scans, magnetic resonance (MR) scans, or microscope data.
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.
Provides users a medical imaging file format and Toolbox for use in medical imaging. The original MINC file format and tools were based upon the NetCDF data format. The actual version was changed to HDF in order to support large files and other new features.
Serves for three-dimensional design and modelling. Materialise Mimics is an image processing software that can be used for creating 3D surface models from stacks of 2D image data. It can calculate surface 3D models from stacked image data. This tool is useful to represent the patient’s anatomy in a virtual 3D model and to increase the quality patient care.
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.
Allows users to view clinical images. WEASIS is a software consisting of a multipurpose web-based viewer and dealing with digital imaging and communications in medicine (DICOM) dataset. It supplies different types of image in an application that can be run as a Java platform independent stand-alone application and stored on a DVD along with a data set.
Assists users to display different medical images such as magnetic resonance imaging (MRI), computerized tomography (CT), X-ray and ultrasound. ezDICOM can detect the format of any medical image and visualize it on the screen. For any operation, users must drag and drop an image onto the program to display it.
Consists of a library designed for volume rendering. VolPack supports user-specified transfer functions for both opacity and color. It furnishes a shading model with directional light sources, multiple material types with several reflective properties, depth cueing, and shadows. This tool can be employed to arbitrary affine view transformations. It constructs color or grayscale renderings.
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.
Offers a platform dedicated to the visualization of medical images. MRIcro is a program which primarily aims to complement the statistical parametric mapping (SPM) software but which can also be run as a standalone application. It provides features allowing users to localize regions of interest (ROIs), normalize scans, segmentation, produce multiple slices images as well as utilities to facilitate the export of brain images.
Provides a common visualization and storage platform, which can be used for visualization of data from any source, provided that an import filter exists for this format. This platform can be extended by various software packages, individually designed for analysis of specific data sets. Visualization is based on multi-planar reconstruction allowing extraction of arbitrary slices from a 3D-volume.
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.
Enables objects visualization and handling for medical imaging. Anatomist is one of the BrainVisa suite’s softwares. Features are based on management of several types of objects, management of coordinate systems and transformations, possibility of building complex 3D scenes with several objects of any type and tools such as color palettes, region of interest module, or mathematic morphology.
Allows users to display medical research image viewer. Papaya is a program that assists researchers to explore and study different parts of human brain. It supports overlays, atlases, or diffusion tensor imaging (DTI) data. Its users interface is configurable with many display, menu and control options and can be run on a web server or as a local, shareable file.
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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