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calcFD
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.
VPV / Volume Phenotype Viewer
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.
BoneJ
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.
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.
TBXpredict
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.
HMSLIC / Hexagonal clustering and Morphological optimize Sequential Linear Iterative Clustering algorithm
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.
Lemos Asymmetry Analysis
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.
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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