In the past, biomedical imaging was heavily reliant on analog, low-throughput methods, which would produce two-dimensional images. However, newer, digital, and high-throughput three-dimensional (3D) imaging methods, which rely on computer vision and computer graphics, are transforming the way biomedical professionals practice. 3D imaging has been useful in diagnostic, prognostic, and therapeutic decision-making for the medical and biomedical professions.
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.
Aims to quantify local resolution. ResMap is an algorithm that can be used for calculating the local resolution of 3D density maps studied in structural biology, primarily cryo electron-microscopy (cryoEM). This tool processes by applying a hypothesis test at every voxel. Moreover, it utilizes the likelihood ratio statistic to decide between the hypotheses at a given p-value.
Allows image processing of electron micrographs, interpretation of reconstructions, molecular modeling, and general image processing. The Bsoft code is modularized to allow for rapid testing and deployment of new processing algorithms, while also providing sufficient infrastructure to deal with many file formats and parametric data. The design is deliberately open to allow interchange of information with other image and molecular processing software through a standard parameter file and its support of multiple image and molecular formats. The graphical user interface is the program bshow, which is used for many interactive purposes such as fitting the contrast transfer function or picking particles. Bsoft also offers various tools to manipulate atomic structures and to refine the fit of a known molecular structure to a density in a reconstruction.
Analyzes, processes and visualizes multi-dimensional microscopy images. BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes.
Assists in molecular 3D structures visualization. BobScript offers an extended version of the MolScript software that focuses on complex graphic representations. The application adds features relative to map drawing, sticks and spheres, or color ramping. It is also able to represent electron density (EM) maps. The program is delivered on demand by users owning an effective MolScript licence.
Permits users to get 3D models of macromolecular complexes using electron microscopy (3DEM). Scipion offers four methods direct detection devices (DDD) movie alignment: motioncorr, correlation, unblur and optical flow. This open-source tool can also align movie frames by using any one of these approaches or any combination. It is able to save all tasks performed by the user during the processing workflow, including all parameters selected and logs.