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 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.
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.
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.
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 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.
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.
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.
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.
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.
Allows users to display medical images in digital imaging and communications in medicine (DICOM) format. Jivex DICOM Viewer offers an interactive interface to manipulate different types of medical 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.
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