Allows users to perform a broad range of morphometric analyses for two- or three-dimensional landmark data. MorphoJ provide a single, integrated environment for geometric morphometrics by implementing the standard range of multivariate techniques that are widely used in geometric morphometrics, as well as several more specialized methods. The software fully takes into account the symmetry of landmark configurations throughout the analyses.
Calculates the fractal dimensionality of a 3D structure. calcFD is designed to work with intermediate files from FreeSurfer analysis pipeline, but can also use other volumes. The toolbox includes options to use different masking files and is implemented to use either the box-counting or dilation algorithms and to use either the filled volume or just the surface of the structure. The toolbox can easily be run on all of the participants in a FreeSurfer subject folder, or just on specified subject folders. The Matlab toolbox also includes several functions designed to improve functionality, such as the automatic ‘cropping’ of the volume space to the smallest bounding box necessary to contain the volume, improving computation time drastically. Example files are also provided to aid in using the toolbox for the user‘s needs.
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.
A computer-aided diagnosis MATLAB toolbox. TBXpredict has been developed for automated prediction of tuberculosis (TB) from chest X-ray (CXRs) of patients. This software was developed by incorporating diversified global features extraction methods such as Gist and PHOG. It contains two modules: Training and Prediction Modules. Prediction Module predicts input digital CXR(s) image as TB or non-TB. Training module enables user to develop a model trained on his/her own TB and non-TB chest radiographs. The user developed automated model could be used for detection of TB from CXR(s). User has also option to choose between Gist and PHOG features to be used in both Training and Prediction Module. This TBXpredict software is extremely efficient and has a maximum prediction accuracy of 94.2% with sensitivity of 0.961 for Gist features.
Provides a superpixel segmentation algorithm focused on the lung CT images. HMSLIC uses a hexagonal method to obtain more regular segmented superpixels and improve edge information preservation. Besides, it uses morphology to combine bright superpixels to eliminate the influence of bright blob-like blood vessels with the aim of reducing the complexity of the subsequent calculation of distance.
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.
Generates mandibular asymmetry measurements from dental panoramic radiographs. Lemos Asymmetry Analysis is a plugin of ImageJ that can simplifies and automates measurements. The software can perform a full set of imaging manipulations. It offers an analysis method for differential diagnosis between functional and morphological asymmetry. The software can be useful for planning of early orthodontic intervention, and for avoiding the progression of asymmetries and their consequences.
Assists in phenotyping the germination and seedling growth of Arabidopsis (Arabidopsis thaliana). Arabidopsis Seedlings Tool is a program enabling users to screen large numbers of lines under various conditions. It is profitable to high-throughput phenotyping using robotics. This tool is a phenotyping method for Arabidopsis including a noninvasive quantification of seedlings by image analysis.
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.
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.
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.
Offers several functions for geometric morphometrics analyses. Arothron contains tools of virtual anthropology to align two unarticulated parts from the same specimen. The main goal is to construct virtual cavities as endocast and users can import and export coordinates of landmarks and 3D paths into ‘landmarkAscii’ and ‘am’ format files. It can also extract from a point of view visible vertices belonging to the point cloud of a mesh.
Offers a platform for fractal analysis and morphology functions. FracLac is a module that can be used as an ImageJ or FIJI plugin. The application includes features such as: (i) analyzing complexity and heterogeneity, (ii) measuring difficult to describe geometrical forms; (iii) extracting of pattern from several types of images for analysis. The software is suitable for images of biological cells as well as for other structures such as branching structures or known fractals.
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.
Supplies routines for all stages of a geometric morphometric analysis in 2D and 3D. geomorph performs, in the R statistical computing environment, all stages of geometric morphometric shape analysis of landmark points and curves in 2D and 3D, as well as 3D surfaces. The software mains features are statistical analyses, visualization, and data collection.
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