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.
Constructs deformable brain images. HAMMER can reveal geometric characteristics of the underlying anatomical structures. It employs a hierarchical deformation mechanism and an attribute vector to work. This tool can reflect the geometric properties of the underlying structure from a local scale, to a global scale that reflected spatial relationships with more distant surface points.
Offers a framework dedicated to image segmentation. SegAN proposes an approach derived from Generative Adversarial Networks (GANs) framework, trained on whole images with the aim of optimizing segmentation tasks in medical images. The application is based on multi-scale loss function for both the segmentor and critic networks. The application was tested on the segmentation of brain tumor images.
Rebuilds 3D models of lesioned arteries and enabled quantitative assessment of stenoses. 3D reconstruction algorithm builds a 3D computational patient-specific model of lesioned vessel, directly from 2D projections acquired while computing invasive coronary X-ray angiography, and is relevant for immediate geometric and quantitative analysis. The 3D model result is appropriate for isogeometric analysis (IGA) of blood flow in the coronary arteries.
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.
Identifies and classifies the pulmonary nodules in CT-Scan images. DFCNet is a generic classifier built on deep fully convolutional neural network. The classification is separated into two classes of nodule (diseased-malignant of benign) and non-nodule (normal). Images classified as nodules are then categorized into four lung cancer stages, but this computer assisted detection (CAD) system can be used for the detection of other types of cancer because this software is a generic method for detection.
Allows users to segment the prostate on computerized tomography (CT) images. This approach combines the population learning and patient-specific learning together for segmenting the prostate on 3D CT images. It overcomes the inter-patient variations by taking advantage of the patient-specific learning. It can be applied to prostate imaging applications, including: (1) targeted biopsy, (2) diagnosis, and (3) treatment planning.
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.
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.
Captures the mass spectrometry (MS) lesion spatial distribution and identifies lesions regardless of their orientation, shape or size. RMNMS detects MS lesions using a training library containing T2-weighted (T2W) and FLAIR images along with manual T2W lesion masks. Moreover, it assists users in the detection of presence of lesions as lesion-wise measures.
Segments nearly elliptic objects via parametric active contour. E-Snake applies an active contour (named snake) segmentation method by using exponential splines as basis functions to represent the outline of the shape. This ImageJ plugin emulates elliptical and circular shapes and can produce an approximation of any closed curve in the plane. These proprieties can be useful to delineate cross sections of cylindrical-like conduits and to outline blob-like objects.
Assists users in cancer diagnosis system. DeepLung is a fully automated lung computed tomography (CT) that combines nodule detection network and nodule classification network. It works in several steps: (i) for a CT image, the detection subnetwork detects candidate nodules, (ii) the classification subnetwork classifies detected nodules into either malignant or benign and (iii) the patient-level diagnosis result is achieved for the whole CT by fusing the diagnosis result of each nodule.
Segments organs-at-risks (OARs). AnatomyNet consists of a deep learning approach employing a single network, trained end-to-end to work. It uses functionalities from all slices to segment anatomical regions with the advantage of 3D ConvNets. This tool utilizes a hybrid loss consisting of contributions from both dice loss and focal loss. It is a variant of U-Net, designed for anatomy segmentation.
Permits users to mine the big data source. DeepEM is a deep 3D convolutional nets with Expectation-Maximization optimization. It was developed for pulmonary nodule detection by taking advantage of abundantly available weakly labeled data extracted from electronic medical records (EMR). This method is general and can be also readily applied to other medical image deep learning applications.
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.
Serves as an automated delineation tool based on spatial analysis for non-small cell lung cancer (NSCLC). This algorithm intends to delineate lung nodules and larger NSCLC masses. It extracts regions of interest (ROI) regardless of the affected lobe side and can obtain low sensitivity values for endo-bronchial masses which are difficult to extract. In this case, the method only segments the nodule while ignoring the bronchus and unrelated pathological objects attached to the same branch.
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.
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.
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.
Takes an average of 15 seconds to produce a result for one case, which a professional human analyst would expect to spend between 30 minutes to an hour working on. Arterys introduce a SaaS (software as a service) analytics platform founded on cloud computation to revolutionize medical imaging. It visualizes medical images of unlimited file size in a web browser at frame rates of up to 100fps when connected to the Arterys™ Cloud.
Serves for radiotherapy image processing. Plastimatch focuses on volumetric registration medical images like: positron emission tomography (PET), magnetic resonance imaging (MRI), and X-ray computed tomography (CT). It is also a useful tool to treat of image computing.
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.
Performs image segmentation and registration. CMP-BIA is dedicated to ImageJ/Fiji and contains a plugin named jSLIC. This plugin is a segmentation method for clustering, in a given image, similar regions (as known as superpixels) which are usually used for other segmentation techniques, classification and registration. It gives reliable superpixels shapes, with no need of decreasing their size.
Assists in visualization of tumoral masses in computerized tomography (CT) images. Yawi 3D is an ImageJ plugin that enables and simplifies the selection of a tumoral region on each slice of a CT analysis, and computes the volume of the selected region. With this tool, volume measurements can be used to understand the course of the illness, providing a forecast on its alterations.
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.
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.
Focuses on combinatorial optimization via graph cuts for digital image analysis. GC is a library aiming to finds solution to energy minimization based discrete labeling problems such as image segmentation. The software provides access to several algorithms, such as maximum flow algorithms, Metric approximation, Multi-label discrete energy optimization, and Image segmentation.
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