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.
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.
Serves for effective segmentation of multidimensional datasets. MIB can recognize several number of imaging formats and offers a variety of image processing tools. It also simplifies utilization and quantification of acquired data. It permits users to segment large datasets, to realize 3D visualization, and to quantify images and models. Its parameters enable users to insert plugin s to customize the program for specific needs.
Supplies an environment for handling data from electron cryo-microscopy (cryoEM) and low-resolution X-ray crystallography. Gorgon aims to provide a modeling environment for subnanometer to near-atomic resolution density maps. The platform includes features such as a visualization framework for volumetric data, geometric operations as well as methods for refining molecular models.
A web-based tool for real-time comparison and analysis of electron microscopy (EM) density maps. EM-SURFER compares the shape of EM map isosurfaces, generated using author-recommended contour values. Users can either upload an EM map or choose an existing map in the EMDataBank and compare it against maps stored in the EMDataBank.
Offers a platform dedicated to image processing. VolumeRover is a toolkit able to handle 3D imaging data and to visualize datasets of arbitrary size. It provides multiple features to treat, improve, and analyze volumetric data as well as generating computational models. For instance, it can perform anisotropic diffusion, generalized digitized total variation (GDTV) filtering, secondary structure elucidation or boundary-free image skeletonization.
Exploits volumetric data and eases research in volume rendering. Drishti implements mesh generation and coloring options. It can resample, filter, enhance contrast and trim the volumes inputted. It serves to visualize volume rendered images. This tool permits researchers to make certain regions transparent based on the surface normal. It can be applied to tomography data or electron-microscopy data.
A version of the public domain image analysis software NIH Image that has been extended to handle the loading, display and analysis of scanning microscope images. Image SXM supports SAM, SCM, SEM, SFM, SLM, SNOM, SPM and STM images.
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.
Assists in focusing microscopic images of 3D objects and organisms. Extended Depth of Field is based on different wavelet algorithms. This ImageJ plugin offers users two interfaces: a simplified mode and an expert mode with a complete set of parameters. It benefits from a RGB to grayscale conversion method that assures contrast and intensity in order to process color data.
Supplies a library dedicated to handling and visualization of large macromolecule structures. SAIL furnishes a wide range of features for reading, writing, annotating, studying and segmenting. In addition, the application can build MPEG/MPEG2 animations.
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